From 3d208e20fd2cd2333c96b6bbda39f8d6296b29f3 Mon Sep 17 00:00:00 2001
From: Srimeenakshi Sankaranarayanan <sankaran@hhu.de>
Date: Thu, 18 Jan 2024 16:40:21 +0100
Subject: [PATCH] Uploaded the microscopic data for Study 1

---
 .gitattributes                                |   1 +
 .../S10_A1_microscopy_FM4-64/isa.assay.xlsx   | Bin 6907 -> 6908 bytes
 assays/S10_A2_microscopy_CMAG/isa.assay.xlsx  | Bin 6905 -> 6906 bytes
 assays/S1_A1_microscopy_yeast/isa.assay.xlsx  | Bin 6957 -> 6958 bytes
 assays/S1_A2_microscopy_hyphae/isa.assay.xlsx | Bin 6959 -> 6960 bytes
 assays/S2_A1_microscopy_DIC/isa.assay.xlsx    | Bin 6904 -> 6905 bytes
 .../S2_A2_microscopy_Rrm4-Gfp/isa.assay.xlsx  | Bin 6907 -> 6908 bytes
 .../S2_A3_protein_expression/isa.assay.xlsx   | Bin 6904 -> 6905 bytes
 .../S2_A4_microscopy_Rfp_Gfp/isa.assay.xlsx   | Bin 6906 -> 6907 bytes
 .../isa.assay.xlsx                            | Bin 6914 -> 6915 bytes
 .../isa.assay.xlsx                            | Bin 6914 -> 6915 bytes
 .../dataset/01_hyperTRIBE_v5_verfied_rrm4.Rmd | 996 ++++++++++++++++++
 .../01_hyperTRIBE_v5_verfied_rrm4.html        |   3 +
 .../isa.assay.xlsx                            | Bin 6912 -> 6968 bytes
 .../S4_A1_microscopy_DIC_Gfp/isa.assay.xlsx   | Bin 6908 -> 6909 bytes
 .../S4_A2_protein_expression/isa.assay.xlsx   | Bin 6904 -> 6905 bytes
 .../isa.assay.xlsx                            | Bin 6915 -> 6916 bytes
 .../isa.assay.xlsx                            | Bin 6912 -> 6913 bytes
 assays/S5_A3_GO-term/isa.assay.xlsx           | Bin 6899 -> 6900 bytes
 assays/S6_A1_RNAseq_data/isa.assay.xlsx       | Bin 6901 -> 6902 bytes
 .../isa.assay.xlsx                            | Bin 6915 -> 6916 bytes
 .../isa.assay.xlsx                            | Bin 6910 -> 6911 bytes
 .../isa.assay.xlsx                            | Bin 6920 -> 6921 bytes
 assays/S7_A1_microscopy/isa.assay.xlsx        | Bin 6901 -> 6901 bytes
 assays/S7_A2_Kat_protein_level/isa.assay.xlsx | Bin 6906 -> 6906 bytes
 assays/S7_A3_Kat_mRNA_level/isa.assay.xlsx    | Bin 6905 -> 6905 bytes
 assays/S8_A1_microscopy/isa.assay.xlsx        | Bin 6901 -> 6901 bytes
 .../isa.assay.xlsx                            | Bin 6913 -> 6913 bytes
 isa.investigation.xlsx                        | Bin 8488 -> 8489 bytes
 .../S10_membrane_trafficking/isa.study.xlsx   | Bin 7693 -> 7693 bytes
 .../S1_characterization_khd4D/isa.study.xlsx  | Bin 7757 -> 7757 bytes
 .../isa.study.xlsx                            | Bin 7743 -> 7743 bytes
 studies/S3_HyperTRIBE_Rrm4/isa.study.xlsx     | Bin 7672 -> 7725 bytes
 .../isa.study.xlsx                            | Bin 7650 -> 7650 bytes
 studies/S5_HyperTRIBE_Khd4/isa.study.xlsx     | Bin 7800 -> 7800 bytes
 studies/S6_RNAseq/isa.study.xlsx              | Bin 7810 -> 7810 bytes
 studies/S7_Kat_motif_strains/isa.study.xlsx   | Bin 7727 -> 7727 bytes
 studies/S8_Kat-target_strains/isa.study.xlsx  | Bin 7751 -> 7751 bytes
 studies/S9_modelling/isa.study.xlsx           | Bin 7502 -> 7502 bytes
 39 files changed, 1000 insertions(+)
 create mode 100644 assays/S3_A3_HyperTRIBE_Rrm4_iCLIP/dataset/01_hyperTRIBE_v5_verfied_rrm4.Rmd
 create mode 100644 assays/S3_A3_HyperTRIBE_Rrm4_iCLIP/dataset/01_hyperTRIBE_v5_verfied_rrm4.html

diff --git a/.gitattributes b/.gitattributes
index 81c4cba..f3b384d 100644
--- a/.gitattributes
+++ b/.gitattributes
@@ -4,3 +4,4 @@ publication/sankaranarayanan-et-al-2023-the-mrna-stability-factor-khd4-defines-a
 _publication/pnas.2301731120.sapp.pdf filter=lfs diff=lfs merge=lfs -text
 _publication/pnas.2301731120.sd05.xlsx filter=lfs diff=lfs merge=lfs -text
 _publication/sankaranarayanan-et-al-2023-the-mrna-stability-factor-khd4-defines-a-specific-mrna-regulon-for-membrane-trafficking-in.pdf filter=lfs diff=lfs merge=lfs -text
+assays/S3_A3_HyperTRIBE_Rrm4_iCLIP/dataset/01_hyperTRIBE_v5_verfied_rrm4.html filter=lfs diff=lfs merge=lfs -text
diff --git a/assays/S10_A1_microscopy_FM4-64/isa.assay.xlsx b/assays/S10_A1_microscopy_FM4-64/isa.assay.xlsx
index 9b1bc432d28318f3ae8857c967c27108607d9ba6..efbb3fa7fd7d5890b8c077f2c79af502ae9fe63e 100644
GIT binary patch
delta 683
zcmexu`p1+vz?+$ci-CcGgFz-mWg~ApBQubmJe^SyL~q{B$PW=X%OnSuc*mpymJnr@
zgGiXMXo3ZjShh2P88YlMAu>BSAWH9Z>|z7U%;BF0Rx;UE2qKdrw4RX@XidbUi_0?O
zC(DRv)=zej?{b=Ot1Eb-mgtpL=GWs6sBYA)&OCAddZmEF(<`^noqJOue=e<k6Gz<v
ztCd%$99i7KvS5c;Q0}snt#jJ>RSHf_NoWl-P&KtMI-PHn7qm`yPgL%KMJ(bK%1?vx
zmZfxO1bNBccRG3Jg!UBm>$j%y*lv-|lDNN-_kv2-yA00y6D-bd(uXhb^ex#gQnSIN
zI(iFRQ?SMYme#&wi)YN+!m+I+oIC27Po&ox-k7O!Cmm}GiUh(!O;;UTd*!?Q<^H3m
zqph<vLN{yishnr=-^to`>zVe};9WtIwx>;PymS=uFW0_M-v0j=TVHGygPque9aGu<
z&b9ia^zi(~=3SS<EE3PhEqE5hlejqdZlL-T$AdC@e|BCMI+9%b>Z|_Lue;x-F$n&c
zyW}og|C!%EURGMFR|=_4Ht0H>v8iWr$($wIzt8tQFaA~i@TU4F_xs$N>-Kfm&-~AX
z62+Sri*`WbM^D@i6fKkU#SOvqVsSGteMejmOb19xPu7r-1hZWvT)}jYge90hA>j<B
z`6TVZbbzD@m~NMZn0Z3d0xB*&SxyRKhLw~xQe@XjnaP8qK26uTE{2hTp@fNnfghL-
Q5n%e{%Th{g3gRFU01fT<*Z=?k

delta 682
zcmexk`rDK@z?+$ci-CcGgCRUbc_VK-BQubmJe^SyL~q{B$PW=X%OnSuc*mpymJnr@
zgGiXMXo3ZjShh2P88YlMAu>BSAWH9Z>|z7U%;BF0Rx;UE2qKdrw4RX@XibFcnVHw(
zCd-Iu)(bnV=$fRkRdl&hs8;Cedok6F(~oR>vsAG@{<))q*7AF0WogHM7woc`>iU8C
zn&(<0A%7*IhDT8zTTh?3ohEv3@&U!*CebKIx2%GcnfI68QHhDJ*m$eKl~eD7+bPvM
zDJlIKLSC}>olo95qCG`@`>km_wp*;TB<wfHUdR;D&ETv*!Q$*DefR=T-;(VjH5*La
zqqnd%1#2u|Y3(~Uc}Cn8j%_98+)>ZGBE8n|-kCD*q+@MSkw93e>B_XVSH8<%?*IBZ
z+d4}lbh8$pia)FW4%W6?&+=a_C|Md*H8s0pN`%9`Wxp@Dzx(l(S7!GYh8mp%h1$Ho
ztV^G0JUn06u<KHoMZ)>MfMU(I4VSmQTfzNlK?2|Pe|MreA1&PX<=1qt-*?N58#w;>
zP0DLde^&eL$Ck*6HB!FM6GhrD<_No=%$avae7^7b#lN}}Z`yy#Kfc+~{{D;jXZulN
zc=Hm`4oLLqi`#)>WpaVIA(&nwZU(0BitB;tKuPJzni7&=wyT6InC_LZ1k)!aoWV4|
zq&=7plr#a;9g+|;PfA)q#ib|9OF_)Ama;~Q>v}0Oc~H!!={ncNFfuTdFflOj1Ct>F
POq+Z~N{LNg93%n&Ir{#q

diff --git a/assays/S10_A2_microscopy_CMAG/isa.assay.xlsx b/assays/S10_A2_microscopy_CMAG/isa.assay.xlsx
index cc2273df208160251e40478d347899acc45010c6..97b479e89e74d720e0d52ff6fc80c562d606348e 100644
GIT binary patch
delta 683
zcmexq`pc9zz?+$ci-CcGgFz-mWg~ApBQubmJe^SyL~q{B$PW=X%OnSuc*mpymJnr@
zgGiXMXo3ZjShh2P88YnCAu`)IAWH9Y>|z7U%;KL1Rx;UI2qKdtw4RX@XidbUi_0?O
zCrgQF)=zej?{b=Ot1Eb-mgtpL=GWs6sBYA)&OCAddZmEF(<`^noqJOue=e<k6Gz<v
ztCd%$99i7KvS5c;Q0}snt#jJ>RSHf_NoWl-P&KtMI-PHn7qm`yPgL%KMJ(bK%1?vx
zmZfxO1bNBccRG3Jg!UBm>$j%y*lv-|lDNN-_kv2-yA00y6D-bd(uXhb^ex#gQnSIN
zI(iFRQ?SMYme#&wi)YN+!m+I+oIC27Po&ox-k7O!Cmm}GiUh(!O;;UTd*!?Q<^H3m
zqph<vLN{yishnr=-^to`>zVe};9WtIwx>;PymS=uFW0_M-v0j=TVHGygPque9aGu<
z&b9ia^zi(~=3SS<EE3PhEqE5hlejqdZlL-T$AdC@e|BCMI+9%b>Z|_Lue;x-F$n&c
zyW}og|C!%EURGMFR|=_4Ht0H>v8iWr$($wIzt8tQFaA~i@TU4F_xs$N>-Kfm&-~AX
z62+SrigrNaM@QTa6fKi;#SOvqLUA)NeM?*qOfyPJPgawV1hbtaT)}jgge90hCgBXG
zc_i(@G)QfxBt&hiB*fffk`_=o6EJNdWsMZsHBx5spr}vNb*_tHWMC*^VqoA0rb7gn
OI{BiM5}TYjNCW_mocII)

delta 682
zcmexm`qPv*z?+$ci-CcGgCRUbc_VK-BQubmJe^SyL~q{B$PW=X%OnSuc*mpymJnr@
zgGiXMXo3ZjShh2P88YnCAu`)IAWH9Y>|z7U%;KL1Rx;UI2qKdtw4RX@XibFcnVHw(
zCQFHE)(bnV=$fRkRdl&hs8;Cedok6F(~oR>vsAG@{<))q*7AF0WogHM7woc`>iU8C
zn&(<0A%7*IhDT8zTTh?3ohEv3@&U!*CebKIx2%GcnfI68QHhDJ*m$eKl~eD7+bPvM
zDJlIKLSC}>olo95qCG`@`>km_wp*;TB<wfHUdR;D&ETv*!Q$*DefR=T-;(VjH5*La
zqqnd%1#2u|Y3(~Uc}Cn8j%_98+)>ZGBE8n|-kCD*q+@MSkw93e>B_XVSH8<%?*IBZ
z+d4}lbh8$pia)FW4%W6?&+=a_C|Md*H8s0pN`%9`Wxp@Dzx(l(S7!GYh8mp%h1$Ho
ztV^G0JUn06u<KHoMZ)>MfMU(I4VSmQTfzNlK?2|Pe|MreA1&PX<=1qt-*?N58#w;>
zP0DLde^&eL$Ck*6HB!FM6GhrD<_No=%$avae7^7b#lN}}Z`yy#Kfc+~{{D;jXZulN
zc=ICB4oLLqirax=WpbXlA(&nyZU&}ri|c`De@W@d>JpM*wzGsQnC_Oa1k=YQoWV4&
zq&=ASmox#>ZITc(k4suW#ib|9N<qx9l(I&O>sl!@c~H!!={ncNFfuTdFflOj1Ct>F
POqqO1N{LNY93%n&|Hb}q

diff --git a/assays/S1_A1_microscopy_yeast/isa.assay.xlsx b/assays/S1_A1_microscopy_yeast/isa.assay.xlsx
index 58eb6f8885e004369b25c71d7c54cf063e64b2e1..75c6dbb93d55d913c09ea5998acb456cbb9bedea 100644
GIT binary patch
delta 661
zcmZ2$w$6+<z?+$ci-CcGgFz-mWg~ApBQubmJe^SyL~q{B$PW=X%OnSuc*mpymJnr@
zgGiXMXo3ZjSWYm38M^GdATqBwAW8)}cd>zG&hgI!E18@x1d*90w4RX@XidbUi_0?O
zC;N$L)=zej?{b=Ot1Eb-mgtpL=GWs6sBYA)&OCAddZmEF(<`^noqJOue=e<k6Gz<v
ztCd%$99i7KvS5c;Q0}snt#jJ>RSHf_NoWl-P&KtMI-PHn7qm`yPgL%KMJ(bK%1?vx
zmZfxO1bNBccRG3Jg!UBm>$j%y*lv-|lDNN-_kv2-yA00y6D-bd(uXhb^ex#gQnSIN
zI(iFRQ?SMYme#&wi)YN+!m+I+oIC27Po&ox-k7O!Cmm}GiUh(!O;;UTd*!?Q<^H3m
zqph<vLN{yishnr=-^to`>zVe};9WtIwx>;PymS=uFW0_M-v0j=TVHGygPque9aGu<
z&b9ia^zi(~=3SS<EE3PhEqE5hlejqdZlL-T$AdC@e|BCMI+9%b>Z|_Lue;x-F$n&c
zyW}og|C!%EURGMFR|=_4Ht0H>v8iWr$($wIzt8tQFaA~i@TU4F_xs$N>-Kfm&-~AX
z62+UZigrNaCqdi}6fKh%iW`FItKw#0nomLxOxsJCfax*`S1`R#!V*mXl5hso4wCj@
z+Fn9>@?1$tFngyY#LQok7I3)$DTrK-lr>UhZ;*o6_EJik@#JJyX(hHGabPlJ007Lo
B`APr)

delta 660
zcmZ2yw$_X{z?+$ci-CcGgCRUbc_VK-BQubmJe^SyL~q{B$PW=X%OnSuc*mpymJnr@
zgGiXMXo3ZjSWYm38M^GdATqBwAW8)}cd>zG&hgI!E18@x1d*90w4RX@XibFcnVHw(
zCi{tK)(bnV=$fRkRdl&hs8;Cedok6F(~oR>vsAG@{<))q*7AF0WogHM7woc`>iU8C
zn&(<0A%7*IhDT8zTTh?3ohEv3@&U!*CebKIx2%GcnfI68QHhDJ*m$eKl~eD7+bPvM
zDJlIKLSC}>olo95qCG`@`>km_wp*;TB<wfHUdR;D&ETv*!Q$*DefR=T-;(VjH5*La
zqqnd%1#2u|Y3(~Uc}Cn8j%_98+)>ZGBE8n|-kCD*q+@MSkw93e>B_XVSH8<%?*IBZ
z+d4}lbh8$pia)FW4%W6?&+=a_C|Md*H8s0pN`%9`Wxp@Dzx(l(S7!GYh8mp%h1$Ho
ztV^G0JUn06u<KHoMZ)>MfMU(I4VSmQTfzNlK?2|Pe|MreA1&PX<=1qt-*?N58#w;>
zP0DLde^&eL$Ck*6HB!FM6GhrD<_No=%$avae7^7b#lN}}Z`yy#Kfc+~{{D;jXZulN
zc=I*U4oLJQirax=W%43%Loj_!+zd?fOXz`V2MH4}T`u7YruR!&g6ZE9&S2V6(jH7Z
zNJvkfCn*VL?~;U=`CHNgE*B^Tk;|2`MvCi=QV`o-Nl7!Fn9L@v#1<$HOoa>pd;R|&

diff --git a/assays/S1_A2_microscopy_hyphae/isa.assay.xlsx b/assays/S1_A2_microscopy_hyphae/isa.assay.xlsx
index c6b6227f3a83d2daf957c4f1f0c8f641657b2453..3eabbf3e1e39527cd66e387d74632fafcdb02fd7 100644
GIT binary patch
delta 661
zcmZ2)w!w@yz?+$ci-CcGgFz-mWg~ApBQubmJe^SyL~q{B$PW=X%OnSuc*mpymJnr@
zgGiXMXo3ZjSWYm38M^FyATn<_AWDTfcd>zGF7VF-E16s<1d*8`w4RX@XidbUi_0?O
zCkKdV)=zej?{b=Ot1Eb-mgtpL=GWs6sBYA)&OCAddZmEF(<`^noqJOue=e<k6Gz<v
ztCd%$99i7KvS5c;Q0}snt#jJ>RSHf_NoWl-P&KtMI-PHn7qm`yPgL%KMJ(bK%1?vx
zmZfxO1bNBccRG3Jg!UBm>$j%y*lv-|lDNN-_kv2-yA00y6D-bd(uXhb^ex#gQnSIN
zI(iFRQ?SMYme#&wi)YN+!m+I+oIC27Po&ox-k7O!Cmm}GiUh(!O;;UTd*!?Q<^H3m
zqph<vLN{yishnr=-^to`>zVe};9WtIwx>;PymS=uFW0_M-v0j=TVHGygPque9aGu<
z&b9ia^zi(~=3SS<EE3PhEqE5hlejqdZlL-T$AdC@e|BCMI+9%b>Z|_Lue;x-F$n&c
zyW}og|C!%EURGMFR|=_4Ht0H>v8iWr$($wIzt8tQFaA~i@TU4F_xs$N>-Kfm&-~AX
z62+UZi*`WbCrR866fKh%iyMOJ>*8i$T0lY%Ogl=LfawYeS1^4*!V*mXk#GjnPLlRu
z+EGG!@_b22FnhNo#LPdE7I3*BDTrL2lr>UhZ<2!8_F77s@$_VNX(hH0abPlJ00072
B`G^1j

delta 652
zcmdmBw%&|4z?+$ci-CcGgCRUbc_VK-BQubmJe^SyL~q{B$PW=X%OnSuc*mpymJnr@
zgGiXMXo3ZjSWYm38M^FyATn<_AWDTfcd>zGF7VF-E16s<1d*8`w4RX@XibFcnVHw(
zCI^UU)(bnV=$fRkRdl&hs8;Cedok6F(~oR>vsAG@{<))q*7AF0WogHM7woc`>iU8C
zn&(<0A%7*IhDT8zTTh?3ohEv3@&U!*CebKIx2%GcnfI68QHhDJ*m$eKl~eD7+bPvM
zDJlIKLSC}>olo95qCG`@`>km_wp*;TB<wfHUdR;D&ETv*!Q$*DefR=T-;(VjH5*La
zqqnd%1#2u|Y3(~Uc}Cn8j%_98+)>ZGBE8n|-kCD*q+@MSkw93e>B_XVSH8<%?*IBZ
z+d4}lbh8$pia)FW4%W6?&+=a_C|Md*H8s0pN`%9`Wxp@Dzx(l(S7!GYh8mp%h1$Ho
ztV^G0JUn06u<KHoMZ)>MfMU(I4VSmQTfzNlK?2|Pe|MreA1&PX<=1qt-*?N58#w;>
zP0DLde^&eL$Ck*6HB!FM6GhrD<_No=%$avae7^7b#lN}}Z`yy#Kfc+~{{D;jXZulN
zc=HX>4oLJQi`#)>W%3enLoj_q+zd<$O6Y-UCkYcUT`A!TrVmP3g6Y2!&S2VE(jH8=
uN<!4_k%XA{SJDD3ZXpE`&zG`BisQ{v5L@0zNi&|B%ptAB7Ay`-eGCB01^r9_

diff --git a/assays/S2_A1_microscopy_DIC/isa.assay.xlsx b/assays/S2_A1_microscopy_DIC/isa.assay.xlsx
index dff85e8672f5921b5967395a2741d781a6f89fa9..6012fa5a3dcd217fd1268cc356e18989e15de41c 100644
GIT binary patch
delta 680
zcmexi`qPv*z?+$ci-CcGgFz-mWg~ApBQubmJe^SyL~q{B$PW=X%OnSuc*mpymJnr@
zgGiXMXo3ZjShh2P88YnCATnDyAWH9W>|z7U%;cX3Rx;U22qKdxw4RX@XidbUi_0?O
zCrgTG)=zej?{b=Ot1Eb-mgtpL=GWs6sBYA)&OCAddZmEF(<`^noqJOue=e<k6Gz<v
ztCd%$99i7KvS5c;Q0}snt#jJ>RSHf_NoWl-P&KtMI-PHn7qm`yPgL%KMJ(bK%1?vx
zmZfxO1bNBccRG3Jg!UBm>$j%y*lv-|lDNN-_kv2-yA00y6D-bd(uXhb^ex#gQnSIN
zI(iFRQ?SMYme#&wi)YN+!m+I+oIC27Po&ox-k7O!Cmm}GiUh(!O;;UTd*!?Q<^H3m
zqph<vLN{yishnr=-^to`>zVe};9WtIwx>;PymS=uFW0_M-v0j=TVHGygPque9aGu<
z&b9ia^zi(~=3SS<EE3PhEqE5hlejqdZlL-T$AdC@e|BCMI+9%b>Z|_Lue;x-F$n&c
zyW}og|C!%EURGMFR|=_4Ht0H>v8iWr$($wIzt8tQFaA~i@TU4F_xs$N>-Kfm&-~AX
z62+Srh;~5YM_b$u6fKi;#0|mp0&z1ieN$WyL{E~Eo~$Y%2^Mmca0Szy5|&{4sDv|^
z=9aVv(IBN6k`SdWk`PmmN?JgqOu#D5rL2)+x?0Li9u)6sy3Tbmj0_AVObiVCz(j}u
PQzl=KQeu-82Z;ax$fx(?

delta 682
zcmexq`ookrz?+$ci-CcGgCRUbc_VK-BQubmJe^SyL~q{B$PW=X%OnSuc*mpymJnr@
zgGiXMXo3ZjShh2P88YnCATnDyAWH9W>|z7U%;cX3Rx;U22qKdxw4RX@XibFcnVHw(
zCQFKF)(bnV=$fRkRdl&hs8;Cedok6F(~oR>vsAG@{<))q*7AF0WogHM7woc`>iU8C
zn&(<0A%7*IhDT8zTTh?3ohEv3@&U!*CebKIx2%GcnfI68QHhDJ*m$eKl~eD7+bPvM
zDJlIKLSC}>olo95qCG`@`>km_wp*;TB<wfHUdR;D&ETv*!Q$*DefR=T-;(VjH5*La
zqqnd%1#2u|Y3(~Uc}Cn8j%_98+)>ZGBE8n|-kCD*q+@MSkw93e>B_XVSH8<%?*IBZ
z+d4}lbh8$pia)FW4%W6?&+=a_C|Md*H8s0pN`%9`Wxp@Dzx(l(S7!GYh8mp%h1$Ho
ztV^G0JUn06u<KHoMZ)>MfMU(I4VSmQTfzNlK?2|Pe|MreA1&PX<=1qt-*?N58#w;>
zP0DLde^&eL$Ck*6HB!FM6GhrD<_No=%$avae7^7b#lN}}Z`yy#Kfc+~{{D;jXZulN
zc=JNh4oLLqh}(f;Wpb{#A(&n$ZU&}riR*!BMk(pZY7&xQwv&V_nC_CW1k=YPoWV4Y
zq&=7hsm+vxsBM*mn0rjp0xD+$rY)qbk>a{W%1j;<^J%)ybuo+#3?)nq4E(@khyar(
NUzAc}lMx4r005h?{kZ@D

diff --git a/assays/S2_A2_microscopy_Rrm4-Gfp/isa.assay.xlsx b/assays/S2_A2_microscopy_Rrm4-Gfp/isa.assay.xlsx
index b7546684d40992209835340c2280452c30c69ec4..4ef1e2cada95b9a0cd7b3c802f9659e2d861868c 100644
GIT binary patch
delta 683
zcmexu`p1+vz?+$ci-CcGgFz-mWg~ApBQubmJe^SyL~q{B$PW=X%OnSuc*mpymJnr@
zgGiXMXo3ZjShh2P88YlMAu>BSAWH9Z>|z7U%;BF0Rx;UE2qKdrw4RX@XidbUi_0?O
zC(DRv)=zej?{b=Ot1Eb-mgtpL=GWs6sBYA)&OCAddZmEF(<`^noqJOue=e<k6Gz<v
ztCd%$99i7KvS5c;Q0}snt#jJ>RSHf_NoWl-P&KtMI-PHn7qm`yPgL%KMJ(bK%1?vx
zmZfxO1bNBccRG3Jg!UBm>$j%y*lv-|lDNN-_kv2-yA00y6D-bd(uXhb^ex#gQnSIN
zI(iFRQ?SMYme#&wi)YN+!m+I+oIC27Po&ox-k7O!Cmm}GiUh(!O;;UTd*!?Q<^H3m
zqph<vLN{yishnr=-^to`>zVe};9WtIwx>;PymS=uFW0_M-v0j=TVHGygPque9aGu<
z&b9ia^zi(~=3SS<EE3PhEqE5hlejqdZlL-T$AdC@e|BCMI+9%b>Z|_Lue;x-F$n&c
zyW}og|C!%EURGMFR|=_4Ht0H>v8iWr$($wIzt8tQFaA~i@TU4F_xs$N>-Kfm&-~AX
z62+Sri*`WbM^D@i6fKkU#SOvqVsSGteMejmOb19xPu7r-1hZWvT)}jYge90hA>j<B
z`6TVZbbzD@m~NMZn0Z3d0xB*&SxyRKhLw~xQe@XjnaP8qK26uTE{2hTp@fNnfghL-
Q5n%e{%Th{g3gRFU01fT<*Z=?k

delta 682
zcmexk`rDK@z?+$ci-CcGgCRUbc_VK-BQubmJe^SyL~q{B$PW=X%OnSuc*mpymJnr@
zgGiXMXo3ZjShh2P88YlMAu>BSAWH9Z>|z7U%;BF0Rx;UE2qKdrw4RX@XibFcnVHw(
zCd-Iu)(bnV=$fRkRdl&hs8;Cedok6F(~oR>vsAG@{<))q*7AF0WogHM7woc`>iU8C
zn&(<0A%7*IhDT8zTTh?3ohEv3@&U!*CebKIx2%GcnfI68QHhDJ*m$eKl~eD7+bPvM
zDJlIKLSC}>olo95qCG`@`>km_wp*;TB<wfHUdR;D&ETv*!Q$*DefR=T-;(VjH5*La
zqqnd%1#2u|Y3(~Uc}Cn8j%_98+)>ZGBE8n|-kCD*q+@MSkw93e>B_XVSH8<%?*IBZ
z+d4}lbh8$pia)FW4%W6?&+=a_C|Md*H8s0pN`%9`Wxp@Dzx(l(S7!GYh8mp%h1$Ho
ztV^G0JUn06u<KHoMZ)>MfMU(I4VSmQTfzNlK?2|Pe|MreA1&PX<=1qt-*?N58#w;>
zP0DLde^&eL$Ck*6HB!FM6GhrD<_No=%$avae7^7b#lN}}Z`yy#Kfc+~{{D;jXZulN
zc=Hm`4oLLqi`#)>WpaVIA(&nwZU(0BitB;tKuPJzni7&=wyT6InC_LZ1k)!aoWV4|
zq&=7plr#a;9g+|;PfA)q#ib|9OF_)Ama;~Q>v}0Oc~H!!={ncNFfuTdFflOj1Ct>F
POq+Z~N{LNg93%n&Ir{#q

diff --git a/assays/S2_A3_protein_expression/isa.assay.xlsx b/assays/S2_A3_protein_expression/isa.assay.xlsx
index 8b9402c72452ef9552af0b3ca69d3cfbc143fb47..e143d22fbef5c0b6451383e0b4b538ebc40b49c5 100644
GIT binary patch
delta 680
zcmexi`qPv*z?+$ci-CcGgFz-mWg~ApBQubmJe^SyL~q{B$PW=X%OnSuc*mpymJnr@
zgGiXMXo3ZjShh2P88YnCATnDyAWH9W>|z7U%;cX3Rx;U22qKdxw4RX@XidbUi_0?O
zCrgTG)=zej?{b=Ot1Eb-mgtpL=GWs6sBYA)&OCAddZmEF(<`^noqJOue=e<k6Gz<v
ztCd%$99i7KvS5c;Q0}snt#jJ>RSHf_NoWl-P&KtMI-PHn7qm`yPgL%KMJ(bK%1?vx
zmZfxO1bNBccRG3Jg!UBm>$j%y*lv-|lDNN-_kv2-yA00y6D-bd(uXhb^ex#gQnSIN
zI(iFRQ?SMYme#&wi)YN+!m+I+oIC27Po&ox-k7O!Cmm}GiUh(!O;;UTd*!?Q<^H3m
zqph<vLN{yishnr=-^to`>zVe};9WtIwx>;PymS=uFW0_M-v0j=TVHGygPque9aGu<
z&b9ia^zi(~=3SS<EE3PhEqE5hlejqdZlL-T$AdC@e|BCMI+9%b>Z|_Lue;x-F$n&c
zyW}og|C!%EURGMFR|=_4Ht0H>v8iWr$($wIzt8tQFaA~i@TU4F_xs$N>-Kfm&-~AX
z62+Srh;~5YM_b$u6fKi;#0|mp0&z1ieN$WyL{E~Eo~$Y%2^Mmca0Szy5|&{4sDv|^
z=9aVv(IBN6k`SdWk`PmmN?JgqOu#D5rL2)+x?0Li9u)6sy3Tbmj0_AVObiVCz(j}u
PQzl=KQeu-82Z;ax$fx(?

delta 682
zcmexq`ookrz?+$ci-CcGgCRUbc_VK-BQubmJe^SyL~q{B$PW=X%OnSuc*mpymJnr@
zgGiXMXo3ZjShh2P88YnCATnDyAWH9W>|z7U%;cX3Rx;U22qKdxw4RX@XibFcnVHw(
zCQFKF)(bnV=$fRkRdl&hs8;Cedok6F(~oR>vsAG@{<))q*7AF0WogHM7woc`>iU8C
zn&(<0A%7*IhDT8zTTh?3ohEv3@&U!*CebKIx2%GcnfI68QHhDJ*m$eKl~eD7+bPvM
zDJlIKLSC}>olo95qCG`@`>km_wp*;TB<wfHUdR;D&ETv*!Q$*DefR=T-;(VjH5*La
zqqnd%1#2u|Y3(~Uc}Cn8j%_98+)>ZGBE8n|-kCD*q+@MSkw93e>B_XVSH8<%?*IBZ
z+d4}lbh8$pia)FW4%W6?&+=a_C|Md*H8s0pN`%9`Wxp@Dzx(l(S7!GYh8mp%h1$Ho
ztV^G0JUn06u<KHoMZ)>MfMU(I4VSmQTfzNlK?2|Pe|MreA1&PX<=1qt-*?N58#w;>
zP0DLde^&eL$Ck*6HB!FM6GhrD<_No=%$avae7^7b#lN}}Z`yy#Kfc+~{{D;jXZulN
zc=JNh4oLLqh}(f;Wpb{#A(&n$ZU&}riR*!BMk(pZY7&xQwv&V_nC_CW1k=YPoWV4Y
zq&=7hsm+vxsBM*mn0rjp0xD+$rY)qbk>a{W%1j;<^J%)ybuo+#3?)nq4E(@khyar(
NUzAc}lMx4r005h?{kZ@D

diff --git a/assays/S2_A4_microscopy_Rfp_Gfp/isa.assay.xlsx b/assays/S2_A4_microscopy_Rfp_Gfp/isa.assay.xlsx
index 4cea5094e5cea47978188b5deee2220eea31c4b5..063b56145d1671f67819718efacb53b7de27025c 100644
GIT binary patch
delta 713
zcmexm`rDK@z?+$ci-CcGgFz-mWg~ApBQubmJe^SyL~q{B$PW=X%OnSuc*mpymJnr@
zgGiXMXo3ZjShh2P88YlMATrxIAWH9X>|z7U%;uj5Rx;T}2qKd#w4RX@XidbUi_0?O
zCrgWH)=zej?{b=Ot1Eb-mgtpL=GWs6sBYA)&OCAddZmEF(<`^noqJOue=e<k6Gz<v
ztCd%$99i7KvS5c;Q0}snt#jJ>RSHf_NoWl-P&KtMI-PHn7qm`yPgL%KMJ(bK%1?vx
zmZfxO1bNBccRG3Jg!UBm>$j%y*lv-|lDNN-_kv2-yA00y6D-bd(uXhb^ex#gQnSIN
zI(iFRQ?SMYme#&wi)YN+!m+I+oIC27Po&ox-k7O!Cmm}GiUh(!O;;UTd*!?Q<^H3m
zqph<vLN{yishnr=-^to`>zVe};9WtIwx>;PymS=uFW0_M-v0j=TVHGygPque9aGu<
z&b9ia^zi(~=3SS<Eb7n4EqE5hlejqdZlL-T$AdC@e|BCMI+9%b>Z|_Lue;x-F$n&c
zyW}og|C!%EURGMFR|=_4Ht0H>v8iWr$($wIzt8tQFaA~i@TU4F_xs$N>-Kfm&-~AX
z62%c|y3Tbmj0_AVObiVCz=*HN(J#+0%1+A9&(^Ehd_Xh{5_`JhcA!X`oF{GwrWc8u
zf$7`gdSKdLQhKtwgd~{lEa3{KyCp2a^l=GiFwHAz52pPkO~7=UB*e_)k`_>L>B+KE
j5Hl>LtdWvJt(2KOC}E&G7U*6mm^S&6loFe~IEV`X9}WPV

delta 682
zcmexu`pc9zz?+$ci-CcGgCRUbc_VK-BQubmJe^SyL~q{B$PW=X%OnSuc*mpymJnr@
zgGiXMXo3ZjShh2P88YlMATrxIAWH9X>|z7U%;uj5Rx;T}2qKd#w4RX@XibFcnVHw(
zCQFNG)(bnV=$fRkRdl&hs8;Cedok6F(~oR>vsAG@{<))q*7AF0WogHM7woc`>iU8C
zn&(<0A%7*IhDT8zTTh?3ohEv3@&U!*CebKIx2%GcnfI68QHhDJ*m$eKl~eD7+bPvM
zDJlIKLSC}>olo95qCG`@`>km_wp*;TB<wfHUdR;D&ETv*!Q$*DefR=T-;(VjH5*La
zqqnd%1#2u|Y3(~Uc}Cn8j%_98+)>ZGBE8n|-kCD*q+@MSkw93e>B_XVSH8<%?*IBZ
z+d4}lbh8$pia)FW4%W6?&+=a_C|Md*H8s0pN`%9`Wxp@Dzx(l(S7!GYh8mp%h1$Ho
ztV^G0JUn06u<KHoMZ)>MfMU(I4VSmQTfzNlK?2|Pe|MreA1&PX<=1qt-*?N58#w;>
zP0DLde^&eL$Ck*6HB!FM6GhrD<_No=%$avae7^7b#lN}}Z`yy#Kfc+~{{D;jXZulN
zc=KY>4oLLqiQ9o<Wpci_A(&n)ZU(0Bi0gsr07>b|8WNIVwu^)-nC_9V1k)!ZoWV4o
zq&=7pkTe0)?UE2PPe@uo#ib|9NkPo8lCnmM>pCejc~H!!={ncNFfuTdFflOj1Ct>F
POr3mLN{LNQ93%n&9OwRx

diff --git a/assays/S3_A1_HyperTRIBE_Rrm4_workflow/isa.assay.xlsx b/assays/S3_A1_HyperTRIBE_Rrm4_workflow/isa.assay.xlsx
index 7878e85917b1d0cf2dc4935b1274bf5111743219..10a7d76426e9ffb0c959fa1efd9c0d49db511904 100644
GIT binary patch
delta 661
zcmZoNYc}Hz@MdP=Vqjq4V30{s*~r_@$PA<>PiIsF(VKTO@<Rm9GRc7@-Z80wB}AF!
zAQEOQnqYw>mhDVnh79`xh|GQth|*^qyV$@oi}~k)l}vUKg2-eGt!Lx}S`+c;;<C*6
z$;u*{^^+asyPPK6>I$ByC3<C*`SrL1svC8yGf&*VUMb-4^vdmX=iXGvpG#}s#8G#^
zYUR}_M;3RmEZ89yl)Eft>zsCem4Xvf5?aFyR81|6PUjot1+CNF6P0^l5sP?*^3$Na
zWhvbmL0+==olf34p*=<Y`mJd^wp*mLB<^qIy`a+dE`ziF1dFqq^x+FUeM`2B)NC-R
zj^4u76s)m;rM2(a;u-U{aBM3H=Z<>j6X~^vH)g8bNyplPB7v|_(^bdTUimJ6x&P?t
zXzMJE(9K$WD(6}Jce1wKdZxWKcvq05?P*gRFCB&a%e60*xBvge))!mFU?=uq$5ghz
zbFDrpJv_g$dDo>di^TJB3!Vk>BreXq8>s%o@t};}pPko*jwIK<`l>(m>+ZK{41z!A
zF1gFrf9Cg(mz9?4l|rhM4Z03zZ0ea@GH1#5@AG}ni+@!=ys7@l{XX~Rx_#aCGygN8
zMDgZTq8*U<F%`E1Ma$$eaYHb@O56-gKNi;m(_B*0ll3Je!EA2{S1>(U!V*lMmv9Et
zqLTJt8l<*J5~8+G5@POoNeif)37B@2vPO#RRw;;W`=q29=S{vPrNpK#4orp&0Lp9j
A@c;k-

delta 660
zcmZoRYck^v@MdP=Vqjq4U<eOU-pJd|$PA<>PiIsF(VKTO@<Rm9GRc7@-Z80wB}AF!
zAQEOQnqYw>mhDVnh79`xh|GQth|*^qyV$@oi}~k)l}vUKg2-eGt!Lx}S`*=VX6CiH
z$;u*{^}-G-x+W=X6<w|rsujBWUQ9LP^dsBeELE(Jf9|NDwftULS=#a61-opfx_)53
z=DF5L$X`jQ;Zc;w*3&0$r-|O1d_Xa{Ni@pQEvq19=KZC2RAQnlHr{G*<<$G&c1rb5
zN=ko*keBRz=aYAiXirh!erp<!?H21S3HuGQ7cxb3GdSx{usFL(AHKlTw`99W%?1<q
z=q+qb!5Rx#TKkSoo)Nc&V_S(ichoblNUt@#cc#oc=~!D-BoG#Ax-xC;mGAPG`@eq9
zw$9QB-K@o@;?L^8gSG9}v;0>JN|pvyP0g;D65()f+3ySP?|yvcmD&A;p+@IGp*HU?
z>(VD056>4i?79?Yk#N2*pjfkQ!{u%7R&ak>kid8S-<@dAM+^6T`8D0^_uVq%297^|
zlk%F=pVfZ*u_bb1jg;^6M3MH3Il}HIbLO29pYMBq@vrX0oA#gbk8gIgzyBis*?yE5
z-n?400~&GScA!|9TrO@1rdNxbf$1mWdSIGcN_w(^gd~{lBjF0Br$|_W=?fChU|LMl
y9!!JO7E40Z_De#{y&!1;l`{d;PEyuLaor{bv2DMUG~?XKx22TW)Wm_QkO2U7BmBhx

diff --git a/assays/S3_A2_HyperTRIBE_Rrm4_analysis/isa.assay.xlsx b/assays/S3_A2_HyperTRIBE_Rrm4_analysis/isa.assay.xlsx
index 14d907a4fcb6d47a9099c28f8004d88746037462..d7e734cc9b4b81456501d4c32a3d564e48ad534a 100644
GIT binary patch
delta 661
zcmZoNYc}Hz@MdP=Vqjq4V30{s*~r_@$PA<>PiIsF(VKTO@<Rm9GRc7@-Z80wB}AF!
zAQEOQnqYw>mhDVnh79`xh|GQth|*^qyV$@oi}~k)l}vUKg2-eGt!Lx}S`+c;;<C*6
z$;u*{^^+asyPPK6>I$ByC3<C*`SrL1svC8yGf&*VUMb-4^vdmX=iXGvpG#}s#8G#^
zYUR}_M;3RmEZ89yl)Eft>zsCem4Xvf5?aFyR81|6PUjot1+CNF6P0^l5sP?*^3$Na
zWhvbmL0+==olf34p*=<Y`mJd^wp*mLB<^qIy`a+dE`ziF1dFqq^x+FUeM`2B)NC-R
zj^4u76s)m;rM2(a;u-U{aBM3H=Z<>j6X~^vH)g8bNyplPB7v|_(^bdTUimJ6x&P?t
zXzMJE(9K$WD(6}Jce1wKdZxWKcvq05?P*gRFCB&a%e60*xBvge))!mFU?=uq$5ghz
zbFDrpJv_g$dDo>di^TJB3!Vk>BreXq8>s%o@t};}pPko*jwIK<`l>(m>+ZK{41z!A
zF1gFrf9Cg(mz9?4l|rhM4Z03zZ0ea@GH1#5@AG}ni+@!=ys7@l{XX~Rx_#aCGygN8
zMDgZTq8*U<F%`E1Ma$$eaYHb@O56-gKNi;m(_B*0ll3Je!EA2{S1>(U!V*lMmv9Et
zqLTJt8l<*J5~8+G5@POoNeif)37B@2vPO#RRw;;W`=q29=S{vPrNpK#4orp&0Lp9j
A@c;k-

delta 660
zcmZoRYck^v@MdP=Vqjq4U<eOU-pJd|$PA<>PiIsF(VKTO@<Rm9GRc7@-Z80wB}AF!
zAQEOQnqYw>mhDVnh79`xh|GQth|*^qyV$@oi}~k)l}vUKg2-eGt!Lx}S`*=VX6CiH
z$;u*{^}-G-x+W=X6<w|rsujBWUQ9LP^dsBeELE(Jf9|NDwftULS=#a61-opfx_)53
z=DF5L$X`jQ;Zc;w*3&0$r-|O1d_Xa{Ni@pQEvq19=KZC2RAQnlHr{G*<<$G&c1rb5
zN=ko*keBRz=aYAiXirh!erp<!?H21S3HuGQ7cxb3GdSx{usFL(AHKlTw`99W%?1<q
z=q+qb!5Rx#TKkSoo)Nc&V_S(ichoblNUt@#cc#oc=~!D-BoG#Ax-xC;mGAPG`@eq9
zw$9QB-K@o@;?L^8gSG9}v;0>JN|pvyP0g;D65()f+3ySP?|yvcmD&A;p+@IGp*HU?
z>(VD056>4i?79?Yk#N2*pjfkQ!{u%7R&ak>kid8S-<@dAM+^6T`8D0^_uVq%297^|
zlk%F=pVfZ*u_bb1jg;^6M3MH3Il}HIbLO29pYMBq@vrX0oA#gbk8gIgzyBis*?yE5
z-n?400~&GScA!|9TrO@1rdNxbf$1mWdSIGcN_w(^gd~{lBjF0Br$|_W=?fChU|LMl
y9!!JO7E40Z_De#{y&!1;l`{d;PEyuLaor{bv2DMUG~?XKx22TW)Wm_QkO2U7BmBhx

diff --git a/assays/S3_A3_HyperTRIBE_Rrm4_iCLIP/dataset/01_hyperTRIBE_v5_verfied_rrm4.Rmd b/assays/S3_A3_HyperTRIBE_Rrm4_iCLIP/dataset/01_hyperTRIBE_v5_verfied_rrm4.Rmd
new file mode 100644
index 0000000..aad27b2
--- /dev/null
+++ b/assays/S3_A3_HyperTRIBE_Rrm4_iCLIP/dataset/01_hyperTRIBE_v5_verfied_rrm4.Rmd
@@ -0,0 +1,996 @@
+---
+title: "Rrm4-Ada-Gfp analysis for Sankaranarayanan et.al 2023"
+author: "Srimeenakshi Sankaranarayanan"
+date: "`r Sys.Date()`"
+output: 
+    BiocStyle::html_document:
+    toc: true
+    toc_float: true
+    code_folding: hide
+    theme: Flatly
+---
+
+In this analysis, the validation of Rrm4-Ada-Gfp analyis were carried out by comparing the hyperTRIBE editing events with the available iCLIP data.
+
+For this purpose, both iCLIP datasets from Olgeiser et.al.(2019) as well as Stoffel et.al(2024) (under preparation) were used. But only the results from Olgeiser et.al. (2019) were used in Sankaranarayanan et.al(2023).
+
+```{r setup, include=FALSE}
+knitr::opts_chunk$set(echo = TRUE, message=FALSE, warning=FALSE,
+                      results = TRUE, crop=NULL)
+```
+
+```{r, message=FALSE, warning=FALSE}
+#Loading all the required libraries for the analyses.
+library(BSgenome.Umaydis.ENSMBL.UM1)
+library(ggplot2)
+library(reshape2)
+library(dplyr)
+library(GenomicRanges)
+library(magrittr)
+library(ggvenn)
+library(colorspace)
+library(ggpubr)
+library(ggpointdensity)
+library(lookup)
+library(rstatix)
+library(ggpmisc)
+library(ggrepel)
+library(RColorBrewer)
+library(tibble)
+library(stringr)
+library(gprofiler2)
+library(tidyr)
+library(stats)
+library(DESeq2)
+library(rtracklayer)
+library(ComplexHeatmap)
+library(GenomicFeatures)
+library(GenomicRanges)
+library(magick)
+library(magrittr)
+library(gridExtra)
+library(IRanges)
+library(Biostrings)
+library(ggpmisc)
+library(ggrepel)
+library(ggpubr)
+library(ggseqlogo)
+library(rtracklayer)
+library(circlize)
+```
+
+
+```{r}
+#Theme for ggplots
+myTheme1 <- theme_bw() +
+    theme(axis.text = element_text(size = 8, colour="black"),
+          axis.title = element_text(size=8, colour="black", face="bold"),
+          axis.ticks=element_line(color="black"),
+          axis.ticks.length=unit(.15, "cm"),
+          panel.border=element_rect(color="black", fill = NA),
+          panel.background = element_blank(),
+          plot.background = element_blank(),
+          legend.text = element_text(size=12),
+          legend.position = "top")
+```
+
+
+
+```{r, colours}
+#Define colors for plots
+# different target sets
+# high-confidence from hyperTRIBE
+tribe.col = "#3EAE96"
+
+
+# Khd4 & control
+Rrm4.col = "#3EAE96"
+ada.col = "#D7D7D7"
+
+
+### with the functions lighten() and darken() from the package colorspace you can modulate the colours e.g. in Venn diagrams
+```
+
+# Preparing *U. maydis* gene annotations
+
+First, we will import gene annotation and sequence information Here I used the genome annotation of *U. maydis* from Ensembl. Note that in contrast to Pedant, the chromosomes are indicated by integer (eg: 1,2 etc) as opposed to character (Um_chr1 etc).
+
+```{r}
+# Define GTF file location
+ann = "C:/Users/Sri/Documents/annotation/genome/Ensembl/Ensembl_annotation/Ustilago.gtf"
+
+# Target gene assignment
+##make TxDb object for storing transcript annotations
+annoDb= makeTxDbFromGFF(file=ann, format="gtf") 
+## import the gtf file as GRanges
+annoInfo = import(ann, format = "gtf")
+## get genes as GRanges
+gns = genes(annoDb) # genes() retreives the positions of all genes 
+## matching the positions of gene_id in annoInfo
+idx = match(gns$gene_id, annoInfo$gene_id) 
+## add Metadata from annoInfo to gns 
+elementMetadata(gns) = cbind(elementMetadata(gns),
+                             elementMetadata(annoInfo)[idx,]) 
+
+# find all duplicated genes. In case of U. maydis genes its only tRNAs that were duplicated
+dup = gns[duplicated(gns)]
+##all tRNAs with their duplicated annotation
+dup_tRNAs = subsetByOverlaps(gns, dup, type = "equal") 
+##only tRNAs with UMAG_Ids using the string "UMAG"
+dup_UMAG_tRNAs = dup_tRNAs[grepl("UMAG", dup_tRNAs$gene_id)]
+##remove all annotation to tRNAs from gns
+gns = gns[!(gns %in% dup_tRNAs)]
+##combine tRNA annotation having UMAG number with gns 
+genes.GR = c(gns, dup_UMAG_tRNAs) %>%
+      sort()
+
+
+# remove objects from workspace
+rm(dup, dup_tRNAs, dup_UMAG_tRNAs, idx)
+
+```
+
+```{r}
+
+#### Since we manaullay extend the genes by 300 nt on either side for UTRs, the following code removes genes that are bothersome to the analysis (MAY BE NEEDED TO CHANGE THIS IF IMPORTANT FACTORS GET LOST)
+
+# remove genes in the first 300 nt of chromosomes (6 genes)
+sel = start(genes.GR) < 300
+cat(sum(sel), "genes were removed because they were to close to the chromosome start:", paste(genes.GR$gene_id[sel], collapse=", "), fill=TRUE)
+
+genes.GR = genes.GR[!sel]
+
+# remove genes in last 300 nt (12 genes)
+chr.length = seqlengths(Umaydis)[as.vector(seqnames(genes.GR))]
+sel = end(genes.GR) + 300 > chr.length
+cat(sum(sel), "genes were removed because they were to close to the chromosome end:", paste(genes.GR$gene_id[sel], collapse=", "), fill=TRUE)
+
+genes.GR = genes.GR[!sel]
+```
+
+```{r}
+# define transcript regions
+tx.regions = GRangesList(
+  UTR3 = flank(genes.GR, 300, start=FALSE),
+  ORF = genes.GR,
+  UTR5 = flank(genes.GR, 300)
+)
+
+# extend genes by 300 nt on both sides
+genes.GR = genes.GR + 300
+```
+
+# Import iCLIP dataset
+
+In order to compare the specificity of hyperTRIBE with Rrm4, the comparison with the existing iCLIP data is critical.
+
+```{r}
+# loading the recent iCLIP data of Rrm4-Gfp
+iCLIP_NKS= import("C:/Users/Sri/Documents/Khd4/DGE_analysis_SM_PhD/Kathis_lab/hyperTRIBE/Rrm4-Rscript/bdsWTmerge.gtf", format = "gtf")
+
+#loading iCLIP data of Lilli
+iCLIP_lilli = import("C:/Users/Sri/Documents/Khd4/DGE_analysis_SM_PhD/Kathis_lab/hyperTRIBE/Rrm4-Rscript/iCLIP_lilli/new_peaks_Rrm4G_SOB_0.bed")
+# find overlaps
+OV= findOverlaps(iCLIP_lilli, genes.GR)
+#assign gene id
+iCLIP_lilli=iCLIP_lilli[from(OV)]
+iCLIP_lilli$gene_id= genes.GR$gene_id[to(OV)]
+
+# make a column for Rrm4 binding site
+genes.GR$rrm4_bs_nks = countOverlaps(genes.GR, iCLIP_NKS )
+genes.GR$rrm4_bs_LO = countOverlaps(genes.GR, iCLIP_lilli)
+
+```
+
+# Characterise editing sites
+
+Note that a few editing sites needed to be removed for different reasons: - 6 sites were not on A - due to the gene extension by 300 nt, a handful of editing sites overlapped with 2 genes
+
+## Import hyperTRIBE data
+
+```{r}
+hyper.dir = "C:/Users/Sri/Documents/Khd4/DGE_analysis_SM_PhD/Kathis_lab/hyperTRIBE/Rrm4-Rscript/bedgraph_rrm4_5%"
+
+# get all bedgraph files
+hyper.files = list.files(hyper.dir, pattern="bedgraph", full.names=TRUE)
+
+# assign sample names (ATTENTION!)
+names(hyper.files) = c("Rrm4_rep1", "Rrm4_rep2", "ctrl_rep1", "ctrl_rep2")
+
+```
+
+First, a list containing hyperTRIBE files was created. For simplicity, only the integer in "no.reads" was kept. The strand  information was added from the annotation file.
+
+The hyperTRIBE pipeline generates the list of all genomic coordinates overlapping with the corresponding editing events. To resolve this overlapping problem,  all duplicated editing events were removed from the analysis.
+
+```{r}
+hyper.list = lapply(hyper.files, function(i){
+  # import data
+  hyper = read.table(i, sep="\t")
+  
+  # keep only first 8 columns
+  hyper = hyper[,c(1:2,4:5,8)]
+  
+  # assign column names
+  colnames(hyper) = c("chr", "start", "perc.editing", "no.reads", "gene.id")
+  
+  # extract number of reads
+  hyper$no.reads = strsplit(hyper$no.reads, "_") %>% sapply(., "[[", 2) %>% sub("r", "", .) %>% as.integer(.)
+  
+  # add strand (from annotation)
+  pos = match(hyper$gene.id, genes.GR$gene_id)
+  hyper$strand = as.vector(strand(genes.GR))[pos]
+  
+  # add id
+  hyper$id = paste(hyper$chr, hyper$start, sep="_")
+  
+  
+  return(hyper)
+})
+
+#head(hyper.list[[1]])
+
+# CHECK FOR DUPLICATED SITES -> overlapping genes due to extension
+# these genes are removed at the moment (could also be resolved differently if needed)
+sapply(hyper.list, function(hyper) table(duplicated(hyper$id)))
+for (i in seq_along(hyper.list)){
+  hyper = hyper.list[[i]]
+  dupls = hyper$id[duplicated(hyper$id)]
+  #print( hyper[hyper$id %in% dupls,] )
+}
+
+# REMOVE DUPLICATED SITES
+hyper.list = lapply(hyper.list, function(hyper){
+  dupls = hyper$id[duplicated(hyper$id)]
+  hyper = subset(hyper, !(id %in% dupls))
+  return(hyper)
+})
+
+# check the duplicated events
+sapply(hyper.list, function(hyper) table(duplicated(hyper$id)))
+
+```
+
+For those gene that  are removed from the gene annotation, if they contained  editing events, their strand information will be marked with  "*" which were also removed. 
+
+```{r}
+# convert editing sites into GRanges object
+hyper.GR = lapply(hyper.list, function(hyper){
+  gr = GRanges(
+    seqnames=hyper$chr,
+    ranges=IRanges(start=hyper$start, width=1),
+    strand=hyper$strand,
+    id=hyper$id,
+    gene.id=hyper$gene.id,
+    no.reads = hyper$no.reads,
+    perc.editing = hyper$perc.editing
+  )
+  return(gr)
+}) %>% as(., "GRangesList")
+
+
+# how many rows have * for granges (this is expected because, genes at the chromosomes boarder are removed from genes.GR)
+hyper.GR_star_strand = lapply (hyper.GR, function(i){
+ star = which(strand(i) == "*")
+  return(star)
+})
+
+# remove rows with * for strand
+hyper.GR= lapply(hyper.GR, function(i){
+  i = subset(i, strand != "*")
+  return(i)
+})
+```
+
+Although the pipeline specifically detects Adenosine, a minor fraction of editing events were from nucleotides other than A. All editing events observed in nucleotides other than Adenosine was removed.
+
+## Get sequence of editing sites
+```{r}
+# get sequence of all editing sites
+seqs = lapply(hyper.GR, function(gr){
+  seq = getSeq(Umaydis, gr)
+  return(seq)
+})
+
+# check distribution
+sapply(seqs, table)
+
+# REMOVE INDIVIDUAL SITES THAT ARE NOT ON A
+hyper.GR = lapply(hyper.GR, function(gr){
+  seqs = getSeq(Umaydis, gr)
+  gr = subset(gr, seqs == "A")
+  return(gr)
+})
+
+# check that only A's remain
+seqs = lapply(hyper.GR, function(gr){
+  seq = getSeq(Umaydis, gr)
+  return(seq)
+})
+
+sapply(seqs, table)
+```
+
+To this end, challenges related to editing event detection, including overlapping genomic coordinates, were resolved. Subsequently, editing events that demonstrated reproducibility across two biological replicates were identified and utilized for all subsequent analyses.
+
+# Compare between replicates
+```{r}
+# Reproducibilty of editing events between two biological replicates
+# rrm4-ada-gfp
+venn.list = lapply(hyper.GR[1:2], function(hyper){
+  return(hyper$id)
+})
+pl1 = ggvenn(venn.list, names(hyper.GR)[1:2], fill_color = c(lighten(Rrm4.col, 0.2), darken(Rrm4.col, 0.2)), set_name_size = 2) +myTheme1+
+  labs(x = NULL, y = NULL) + 
+  guides(x = "none", y = "none")
+
+# control-ada
+venn.list = lapply(hyper.GR[3:4], function(hyper){
+  return(hyper$id)
+})
+pl2 = ggvenn(venn.list, names(hyper.GR)[3:4], fill_color = c(lighten(ada.col, 0.2), darken(ada.col, 0.2)), set_name_size = 2) +myTheme1+labs(x = NULL, y = NULL) + 
+  guides(x = "none", y = "none")
+  
+# ggarrange to arranging multiple ggplots in the same plot
+vennrep<-ggarrange(pl1, pl2, 
+          labels = c("A", "B"),
+          ncol = 2, nrow = 1)
+vennrep
+
+# ggsave
+ggsave(vennrep, path="C:/Users/Sri/Documents/Khd4/DGE_analysis_SM_PhD/TRIBE_data/Editing_events_all/Rrm4/Plots_new_revision", filename="FigEV3B_rev_minor_changereps.pdf", height=2.6, width=3.2, unit= "cm")
+
+```
+
+```{r}
+# Keep only reproducible editing events were kept.
+# merge rrm4-ada-gfp replicates
+rrm4.tab = merge(hyper.GR$Rrm4_rep1 %>% mcols(), hyper.GR$Rrm4_rep2 %>% mcols(), by=c("id", "gene.id"), all=FALSE, suffixes=c(".rep1", ".rep2")) %>% as.data.frame(.)
+# select only sites from overlap and add combined info of both replicates
+sel = match(rrm4.tab$id, hyper.GR$Rrm4_rep1$id)
+rrm4.rep = hyper.GR$Rrm4_rep1[sel]
+mcols(rrm4.rep) = rrm4.tab
+
+# merge control-ada replicates
+ctrl.tab = merge(hyper.GR$ctrl_rep1 %>% mcols(), hyper.GR$ctrl_rep2 %>% mcols(), by=c("id", "gene.id"), all=FALSE, suffixes=c(".rep1", ".rep2")) %>% as.data.frame(.)
+# select only sites from overlap and add combined info of both replicates
+sel = match(ctrl.tab$id, hyper.GR$ctrl_rep1$id)
+ctrl.rep = hyper.GR$ctrl_rep1[sel]
+mcols(ctrl.rep) = ctrl.tab
+
+## NEW GRANGES OBJECT WITH ONLY REPRODUCIBLE SITES
+hyper.rep = GRangesList(rrm4 = rrm4.rep, ctrl = ctrl.rep)
+
+# number of reproducible editing sites
+elementNROWS(hyper.rep)
+
+# number of genes with reproducible sites
+sapply(hyper.rep, function(hyper) length(unique(hyper$gene.id)))
+
+elementNROWS(hyper.rep)
+```
+
+# Studying the editing events
+
+In this analysis, the editing events were analysed for their distribution and reproducibility between two biological replicates. The correlation of determination was used to study the editing reproducibility as it indicates the distance of points between 1:1 line, on the other hand magnitud. And therefore, both  pearson (the analysis is independent of magnitude, in our case, editing percentage ) and  spearman (as the editing relationship is not monotonic) was not used.
+
+```{r}
+# distribution of % editing
+pf = data.frame(
+  perc.editing = c(rrm4.tab$perc.editing.rep1, rrm4.tab$perc.editing.rep2, ctrl.tab$perc.editing.rep1, ctrl.tab$perc.editing.rep2),
+  sample = rep(c("rrm4.rep1", "rrm4.rep2", "ctrl.rep1", "ctrl.rep2"), rep(c(nrow(rrm4.tab), nrow(ctrl.tab)), each=2)),
+  condition = rep(c("rrm4", "rrm4", "ctrl", "ctrl"), rep(c(nrow(rrm4.tab), nrow(ctrl.tab)), each=2)))
+  
+# rrm4-ada-gfp
+# density
+####FigS4B
+pl1 = ggplot(pf, aes(x=perc.editing, fill=sample)) +
+  geom_density(adjust = 1/5, alpha=0.5) +
+  scale_fill_manual(values=c(rrm4.rep1 = lighten(Rrm4.col, 0.2), rrm4.rep2 = darken(Rrm4.col, 0.2), ctrl.rep1 = lighten(ada.col, 0.2), ctrl.rep2 = darken(ada.col, 0.2)))+ 
+  xlab("% editing")+
+  ylab("density")+
+  myTheme1
+
+# histogram
+pl2 = ggplot(pf, aes(x=perc.editing, fill=sample)) +
+  geom_histogram(aes(y = ..density..), position="dodge") +
+  scale_fill_manual(values=c(rrm4.rep1 = lighten(Rrm4.col, 0.2), rrm4.rep2 = darken(Rrm4.col, 0.2), ctrl.rep1 = lighten(ada.col, 0.2), ctrl.rep2 = darken(ada.col, 0.2)))+
+  myTheme1
+
+# scatter plots of % editing in overlapping sites
+# rrm4-ada-gfp
+#### FigS4C
+pl3 = ggplot(rrm4.tab, aes(x=perc.editing.rep1, y=perc.editing.rep2)) +
+  geom_pointdensity(adjust=0.1) +
+  ggtitle("Shared sites in Rrm4.ada") +
+  theme_bw() +
+  theme(aspect.ratio = 1) +
+  expand_limits(x=c(0,100), y=c(0,100))+geom_smooth(method = "lm", size=1)+
+  stat_regline_equation(label.y = 95, aes(label = ..eq.label..)) +
+  stat_regline_equation(label.y = 85, aes(label = ..rr.label..))+ 
+  labs(subtitle="FigS4C")+
+  myTheme1 
+pl3
+
+# control-ada
+#### FigS4D
+pl4 = ggplot(ctrl.tab, aes(x=perc.editing.rep1, y=perc.editing.rep2))+ 
+  geom_pointdensity(adjust=0.1) +
+  ggtitle("Shared sites in Ada.ctrl") +
+  theme_bw() +
+  theme(aspect.ratio = 1) +
+  expand_limits(x=c(0,100), y=c(0,100))+geom_smooth(method = "lm", size=1)+
+  stat_regline_equation(label.y = 95, aes(label = ..eq.label..)) +
+  stat_regline_equation(label.y = 85, aes(label = ..rr.label..))+ 
+  labs(subtitle="FigS4D")+
+  myTheme1
+  
+# ggarrange
+figEVC<-ggarrange(pl1, pl2, pl3, pl4,
+          labels = c("A", "B", "C", "D"),
+          ncol = 2, nrow = 2)
+figEVC
+
+# ggsave
+ggsave(figEVC, path="C:/Users/Sri/Documents/Khd4/DGE_analysis_SM_PhD/TRIBE_data/Editing_events_all/Rrm4/Plots_new_revision", filename="FigEV3c.pdf", height=23, width=16, unit= "cm")
+
+```
+
+To check the distance between the editing sites and iCLIP binding site, I will use distancetonearest() function in GenomicRanges.
+
+```{r}
+# Using the iCLIP data of Nina
+dis_df = lapply(names(hyper.rep), function(i){
+  
+  hyper = hyper.rep[[i]]
+  head(hyper)
+  
+  # calculat distance to nearest iCLIP site
+  dists.rrm4 = distanceToNearest(hyper, iCLIP_NKS)
+  
+  # keep only pairs on same genes
+  
+  sel = hyper$gene.id[from(dists.rrm4)] == iCLIP_NKS$geneID[to(dists.rrm4)]
+  table(sel)
+  dists.rrm4 = subset(dists.rrm4, sel)
+  mcols(dists.rrm4)$BS = "iCLIP"
+  
+  # make df
+  df = rbind(mcols(dists.rrm4)) %>% as.data.frame()
+  df$set = i
+  
+  return(df)
+})
+
+# rowbind the list objects
+dis_df = do.call(rbind, dis_df)
+
+# distance between editing sites and iCLIP binding sites
+# density
+pl1 = ggplot(dis_df, aes(x=distance, fill=set)) +
+  geom_density(adjust = 1/5, alpha=0.5) +
+  coord_cartesian(xlim=c(0, 2000)) +
+  scale_fill_manual(values=c(rrm4 = Rrm4.col, ctrl = ada.col)) +
+  theme_bw() +
+  facet_wrap(~BS)+myTheme1
+
+# histogram
+pl2 = ggplot(dis_df, aes(x=distance, fill=set)) +
+  geom_histogram(binwidth = 100, aes(y = ..density..), position="dodge") +
+  coord_cartesian(xlim=c(0, 2000)) +
+  scale_fill_manual(values=c(rrm4 = Rrm4.col, ctrl = ada.col)) +
+  theme_bw() +
+  facet_wrap(~BS)+myTheme1
+
+# ggarrange
+nks<- ggarrange(pl1, pl2,  
+          labels = LETTERS[1:4],
+          ncol = 2, nrow = 1)
+nks
+
+# ggsave
+ggsave(nks, path="C:/Users/Sri/Documents/Khd4/DGE_analysis_SM_PhD/TRIBE_data/Editing_events_all/Rrm4/Plots_new_revision", filename = "Fig3D_rev.pdf", height=22, width=16, unit= "cm")
+
+
+
+```
+
+```{r}
+# using the iCLIP data of Lilli
+dis_df = lapply(names(hyper.rep), function(i){
+  
+  hyper = hyper.rep[[i]]
+  head(hyper)
+  
+  # calculat distance to nearest iCLIP site
+  dists.rrm4 = distanceToNearest(hyper, iCLIP_lilli)
+  
+  # kepp only pairs on same genes
+  
+  sel = hyper$gene.id[from(dists.rrm4)] == iCLIP_lilli$gene_id[to(dists.rrm4)]
+  table(sel)
+  dists.rrm4 = subset(dists.rrm4, sel)
+  mcols(dists.rrm4)$BS = "iCLIP"
+  
+  # make df
+  df = rbind(mcols(dists.rrm4)) %>% as.data.frame()
+  df$set = i
+  
+  return(df)
+})
+
+# row bind the list objects
+dis_df = do.call(rbind, dis_df)
+
+# distance between editing sites and iCLIP binding sites
+# density
+pl1 = ggplot(dis_df, aes(x=distance, fill=set)) +
+  geom_density(adjust = 1/5, alpha=0.5) +
+  coord_cartesian(xlim=c(0, 2000)) +
+  scale_fill_manual(values=c(rrm4 = Rrm4.col, ctrl = ada.col)) +
+  theme_bw() +
+  facet_wrap(~BS)+myTheme1
+
+# histogram
+pl2 = ggplot(dis_df, aes(x=distance, fill=set)) +
+  geom_histogram(binwidth = 100, aes(y = ..density..), position="dodge") +
+  coord_cartesian(xlim=c(0, 2000)) +
+  scale_fill_manual(values=c(rrm4 = Rrm4.col, ctrl = ada.col)) +
+  theme_bw() +
+  facet_wrap(~BS)+myTheme1
+
+# ggarrange
+lilli<- ggarrange(pl1, pl2,  
+          labels = LETTERS[1:4],
+          ncol = 2, nrow = 1)
+lilli
+
+# ggsave
+ggsave(lilli, path="C:/Users/Sri/Documents/Khd4/DGE_analysis_SM_PhD/TRIBE_data/Editing_events_all/Rrm4/Plots_new_revision", filename = "Fig3D_rev_lilli.pdf", height=22, width=16, unit= "cm")
+
+```
+
+# Enrichment of Rrm4-Ada-Gfp targets in iCLIP
+
+In this analysis, I compared the overlap between high-confidence Rrm4-Ada-Gfp targets and Rrm4-iCLIP targets. 
+
+```{r}
+
+# comparing the reproducible editing sites between rrm4-ada and control
+#### Fig2B
+venn.list = lapply(hyper.rep, function(hyper){
+  return(hyper$id)
+})
+
+pl1=ggvenn(venn.list, names(venn.list), fill_color=c(Rrm4.col, ada.col))+
+    ggtitle("Fig2B")+myTheme1
+
+
+# define sets
+rrm4.vs.ctrl=list(
+  rrm4.specific=hyper.rep$rrm4$gene.id[hyper.rep$rrm4$id %in% setdiff(hyper.rep$rrm4$id, hyper.rep$ctrl$id)],
+  shared=hyper.rep$ctrl$gene.id[hyper.rep$ctrl$id %in% intersect(hyper.rep$ctrl$id, hyper.rep$rrm4$id)],
+  ctr.specific=hyper.rep$ctrl$gene.id[hyper.rep$ctrl$id %in% setdiff(hyper.rep$ctrl$id, hyper.rep$rrm4$id)],
+  all=genes.GR$gene_id
+)
+
+
+# iCLIP_lilli vs hyperTRIBE genes
+tab.Rrm4Bs_LO = lapply(rrm4.vs.ctrl, function(i){
+  df = genes.GR$rrm4_bs_LO[genes.GR$gene_id %in% i]
+  tabGn = table(df>0)
+  return(tabGn)
+}) %>% melt(.) %>% set_colnames(., c("with.bs","no.of.genes", "set"))
+
+#### FigS4F
+pl3 = ggplot(tab.Rrm4Bs_LO, aes(x=factor(set, levels=c("rrm4.specific", "shared", "ctr.specific", "all" )), y= no.of.genes, fill=with.bs))+
+  geom_bar(stat="identity", position="fill", color="black")+
+  scale_fill_manual(values=c('TRUE' = "skyblue", 'FALSE' = "lightgrey"))+
+  myTheme1
+
+
+# iCLIP_NKS vs hyperTRIBE genes
+tab.Rrm4Bs_NKS = sapply(rrm4.vs.ctrl, function(i){
+  df = genes.GR$rrm4_bs_nks[genes.GR$gene_id %in% i]
+  tabGn = table(df>0)
+  return(tabGn)
+}) %>% melt(.) %>%set_colnames(., c("with.bs","set", "no.of.genes"))
+
+# Not used for publication
+pl2 = ggplot(tab.Rrm4Bs_NKS, aes(x=set, y= no.of.genes, fill=with.bs))+
+  geom_bar(stat="identity", position="fill", color="black")+
+  scale_fill_manual(values=c('TRUE' = "skyblue", 'FALSE' = "lightgrey"))+
+  myTheme1
+
+# ggarrange
+Nks_lO_HT<- ggarrange(pl1, pl2, pl3,  
+          labels = LETTERS[1:3],
+          ncol = 2, nrow = 2)
+Nks_lO_HT
+
+# ggsave
+ggsave(Nks_lO_HT, path="C:/Users/Sri/Documents/Khd4/DGE_analysis_SM_PhD/TRIBE_data/Editing_events_all/Rrm4/Plots_new_revision", filename = "Nks_lO_HT.pdf", height=22, width=16, unit= "cm")
+
+```
+
+The significance of mRNA target enrichment in comparison to all mRNAs present in *U. maydis*  was carried out using the Fisher's exact test
+
+```{r}
+# make data frame 
+bs_enrich = data.frame(rrm4.uni = c(683,130),
+                       shared = c(377,79),
+                       ctrl.uni = c(430,157),
+                       all = c(4461,2470)) %>% 
+  set_rownames(.,c("with iCLIP BS", "no iCLIP BS"))
+  
+# Fisher exact test
+# rrm4-ada-gfp unique
+chisq.rrm4bs=bs_enrich[,c(1,4)]
+fisher.test(chisq.rrm4bs)
+
+# overlap
+chisq.sharedbst=bs_enrich[,c(2,4)]
+fisher.test(chisq.sharedbst)
+
+#control-Ada unique
+chisq.ctrlbs=bs_enrich[,c(3,4)]
+fisher.test(chisq.ctrlbs)
+```
+
+# separate Rrm4-Ada-Gfp specific and control-Ada specific
+
+In here, we will select editing sites that are specific to Rrm4-Ada-Gfp and control-Ada. *Note that some mRNAs could be still present in both data sets.*
+
+```{r}
+#hyper.rep
+# Rrm4-Ada-Gfp specific
+Rrm4_spe= hyper.rep$rrm4[!hyper.rep$rrm4$id %in% hyper.rep$ctrl$id]
+
+# editing events shared between Rrm4 and ctrl
+Rrm4_con_sh = hyper.rep$rrm4[hyper.rep$rrm4$id %in% hyper.rep$ctrl$id]
+
+# control-Ada specific
+con_spe= hyper.rep$ctrl[!hyper.rep$ctrl$id %in% hyper.rep$rrm4$id]
+```
+
+# Find mRNAs specific to each category
+```{r}
+#venn list
+venn_mRNAs = list(
+  Rrm4Ada_mRNAs = Rrm4_spe$gene.id,
+  controlAda_mRNAs = con_spe$gene.id)
+
+# isolate mRNAs specific to each data set
+# rrm4-ada-gfp
+Rrm4Ada_txspe = Rrm4_spe[!Rrm4_spe$gene.id %in% con_spe$gene.id]
+# shared
+sh.ada = Rrm4_spe[Rrm4_spe$gene.id %in% con_spe$gene.id]
+# control-ada
+conAda_txspe = con_spe[!con_spe$gene.id %in% Rrm4_spe$gene.id]
+
+```
+
+# Study the distance between editing sites and iCLIP binding sites in mRNAs specific to each datasets
+## iCLIP data of LO
+```{r}
+# find binding sites with motif
+# UAUG bindinsites
+uaug = DNAString("TATG")
+uaug.gr = vmatchPattern(uaug, Umaydis)
+ov= findOverlaps(uaug.gr, genes.GR)
+uaug.gr = uaug.gr[from(ov)] 
+uaug.gr$gene.id = genes.GR$gene_id[to(ov)]
+
+# assign uaug motif to the iCLIP binding sites
+ov = findOverlaps(iCLIP_lilli, uaug.gr)
+# make a new uaug column
+iCLIP_lilli$uaug = NA
+# find the binding sites having UAUG motif
+iCLIP_lilli$uaug[from(ov)] = uaug.gr$gene.id[to(ov)]
+
+# UCUC bindinsites
+ucuc= DNAString("TCTC")
+ucuc.gr = vmatchPattern(ucuc, Umaydis)
+ov= findOverlaps(ucuc.gr, genes.GR)
+ucuc.gr = ucuc.gr[from(ov)] 
+ucuc.gr$gene.id = genes.GR$gene_id[to(ov)]
+
+# assign uaug motif to the iCLIP binding sites
+ov = findOverlaps(iCLIP_lilli, ucuc.gr)
+# make a new uaug column
+iCLIP_lilli$ucuc = NA
+# find the binding sites having UAUG motif
+iCLIP_lilli$ucuc[from(ov)] = ucuc.gr$gene.id[to(ov)]
+
+
+# CAUG bindinsites
+caug= DNAString("CATG")
+caug.gr = vmatchPattern(caug, Umaydis)
+ov= findOverlaps(caug.gr, genes.GR)
+caug.gr = caug.gr[from(ov)] 
+caug.gr$gene.id = genes.GR$gene_id[to(ov)]
+
+# assign uaug motif to the iCLIP binding sites
+ov = findOverlaps(iCLIP_lilli, caug.gr)
+# make a new uaug column
+iCLIP_lilli$caug = NA
+# find the binding sites having UAUG motif
+iCLIP_lilli$caug[from(ov)] = caug.gr$gene.id[to(ov)]
+```
+
+### mRNAs specific to each hyperTRIBE dataset vs iCLIP site with UAUG
+Here, the distance between editing sites and UAUG-containing Rrm4-iCLIP binding sites were calculated in mRNAs specific to each set. 
+```{r}
+# make a list 
+hyper.rep.mRNA = list(
+  rrm4 = Rrm4Ada_txspe,
+  ctrl = conAda_txspe
+) %>% as(., "GRangesList")
+
+# only those Rrm4 bs with UAUG 
+Rrm4_bs_UAUG = iCLIP_lilli[!is.na(iCLIP_lilli$uaug)]
+
+## DIstance between bs with uaug ( iCLIP data of lilli) and editing site
+dis = lapply(names(hyper.rep.mRNA), function(i){
+  
+  hyper = hyper.rep.mRNA[[i]]
+  head(hyper)
+  
+  # calculat distance to nearest iCLIP site
+  dists.rrm4 = distanceToNearest(hyper, Rrm4_bs_UAUG)
+  
+  # kepp only pairs on same genes
+  
+  sel = hyper$gene.id[from(dists.rrm4)] == Rrm4_bs_UAUG$gene_id[to(dists.rrm4)]
+  table(sel)
+  dists.rrm4 = subset(dists.rrm4, sel)
+  mcols(dists.rrm4)$BS = "iCLIP"
+  
+  # make df
+  df = rbind(mcols(dists.rrm4)) %>% as.data.frame()
+  df$set = i
+  
+  return(df)
+})
+
+dis_df = do.call(rbind, dis)
+
+#######Not used in publication
+pl2 = ggplot(dis_df, aes(x=distance, fill=set)) +
+  geom_density(adjust = 1/5, alpha=0.5) +
+  coord_cartesian(xlim=c(0, 2500)) +
+  scale_fill_manual(values=c(rrm4 = Rrm4.col, ctrl = ada.col)) +
+  theme_bw()+
+  myTheme1
+
+### Fig2C right panel
+pl3 = ggplot(dis_df, aes(x=distance, fill=set)) +
+  geom_histogram(binwidth = 150, aes(y = ..density..), position="dodge") +
+  coord_cartesian(xlim=c(0, 2500),ylim=c(0, 0.002)) +
+  scale_fill_manual(values=c(rrm4 = Rrm4.col, ctrl = ada.col)) +
+  theme_bw()+
+  myTheme1
+
+# ggarrange
+HTrrm4_UAUG<- ggarrange(pl2, pl3, 
+          labels = LETTERS[1:4],
+          ncol = 2, nrow = 1)
+HTrrm4_UAUG
+
+# ggsave
+ggsave(HTrrm4_UAUG, path="C:/Users/Sri/Documents/Khd4/DGE_analysis_SM_PhD/TRIBE_data/Editing_events_all/Rrm4/Plots_new_revision", filename = "Fig3D_rev_uaug.pdf", height=16, width=16, unit= "cm")
+```
+
+```{r}
+# calculate median distance iCLIP site with uaug
+# rrm4-ada-gfp
+med_rrm4bs = median(dis[[1]]$distance)
+# control-ada
+med_ctrlbs = median(dis[[2]]$distance)
+```
+
+### mRNAs specific to each hyperTRIBE dataset vs all BS
+Here, the distance between editing sites and all Rrm4-iCLIP binding sites were calculated in mRNAs specific to each set.
+```{r}
+# distance a-Gbwtween editing sites and all BS in mRNAs specific to Rrm4-Ada-Gfp and control-Ada
+
+dis = lapply(names(hyper.rep.mRNA), function(i){
+  hyper = hyper.rep.mRNA[[i]]
+  head(hyper)
+  # calculat distance to nearest iCLIP site
+  dists.rrm4 = distanceToNearest(hyper, iCLIP_lilli)
+  # kepp only pairs on same genes
+  sel = hyper$gene.id[from(dists.rrm4)] == iCLIP_lilli$gene_id[to(dists.rrm4)]
+  table(sel)
+  dists.rrm4 = subset(dists.rrm4, sel)
+  mcols(dists.rrm4)$BS = "iCLIP"
+  # make df
+  df = rbind(mcols(dists.rrm4)) %>% as.data.frame()
+  df$set = i
+  return(df)
+})
+
+dis_df = do.call(rbind, dis)
+
+#######Not used in publication
+pl4 = ggplot(dis_df, aes(x=distance, fill=set)) +
+  geom_density(adjust = 1/5, alpha=0.5) +
+  coord_cartesian(xlim=c(0, 2500)) +
+  scale_fill_manual(values=c(rrm4 = Rrm4.col, ctrl = ada.col)) +
+  theme_bw()+
+  myTheme1
+
+### Fig2C left
+pl5 = ggplot(dis_df, aes(x=distance, fill=set)) +
+  geom_histogram(binwidth = 150, aes(y = ..density..), position="dodge") +
+  coord_cartesian(xlim=c(0, 2500)) +
+  scale_fill_manual(values=c(rrm4 = Rrm4.col, ctrl = ada.col)) +
+  theme_bw() +
+  myTheme1
+
+HTrrm4_spemRNA<- ggarrange(pl4, pl5, 
+          labels = LETTERS[1:2],
+          ncol = 2, nrow = 1)
+HTrrm4_spemRNA
+ggsave(HTrrm4_spemRNA, path="C:/Users/Sri/Documents/Khd4/DGE_analysis_SM_PhD/TRIBE_data/Editing_events_all/Rrm4/Plots_new_revision", filename = "Fig3D_rev_all_BS_specificmRNA.pdf", height=8, width=16, unit= "cm")
+```
+
+```{r}
+# calculate median distance all iCLIP site
+# for rrm4
+med_rrm4bs = median(dis[[1]]$distance)
+
+med_ctrlbs = median(dis[[2]]$distance)
+```
+
+## In the iCLIP data of NKS
+```{r}
+# UAUG bindinsites
+uaug = DNAString("TATG")
+uaug.gr = vmatchPattern(uaug, Umaydis)
+ov= findOverlaps(uaug.gr, genes.GR)
+uaug.gr = uaug.gr[from(ov)] 
+uaug.gr$gene.id = genes.GR$gene_id[to(ov)]
+
+# assign uaug motif to the iCLIP binding sites
+ov = findOverlaps(iCLIP_NKS, uaug.gr)
+# make a new uaug column
+iCLIP_NKS$uaug = NA
+# find the binding sites having UAUG motif
+iCLIP_NKS$uaug[from(ov)] = uaug.gr$gene.id[to(ov)]
+
+# UCUC bindinsites
+ucuc= DNAString("TCTC")
+ucuc.gr = vmatchPattern(ucuc, Umaydis)
+ov= findOverlaps(ucuc.gr, genes.GR)
+ucuc.gr = ucuc.gr[from(ov)] 
+ucuc.gr$gene.id = genes.GR$gene_id[to(ov)]
+
+# assign uaug motif to the iCLIP binding sites
+ov = findOverlaps(iCLIP_NKS, ucuc.gr)
+# make a new uaug column
+iCLIP_NKS$ucuc = NA
+# find the binding sites having UAUG motif
+iCLIP_NKS$ucuc[from(ov)] = ucuc.gr$gene.id[to(ov)]
+
+
+# CAUG bindinsites
+caug= DNAString("CATG")
+caug.gr = vmatchPattern(caug, Umaydis)
+ov= findOverlaps(caug.gr, genes.GR)
+caug.gr = caug.gr[from(ov)] 
+caug.gr$gene.id = genes.GR$gene_id[to(ov)]
+
+# assign uaug motif to the iCLIP binding sites
+ov = findOverlaps(iCLIP_NKS, caug.gr)
+# make a new uaug column
+iCLIP_NKS$caug = NA
+# find the binding sites having UAUG motif
+iCLIP_NKS$caug[from(ov)] = caug.gr$gene.id[to(ov)]
+```
+
+### mRNAs specific to each hyperTRIBE dataset vs iCLIP site with UAUG
+```{r}
+# make a list 
+hyper.rep.mRNA = list(
+  rrm4 = Rrm4Ada_txspe,
+  ctrl = conAda_txspe
+) %>% as(., "GRangesList")
+
+# only those Rrm4 bs with UAUG 
+Rrm4_bs_UAUG = iCLIP_NKS[!is.na(iCLIP_NKS$uaug)]
+
+## DIstance between bs with uaug ( iCLIP data of lilli) and editing site
+dis = lapply(names(hyper.rep.mRNA), function(i){
+  
+  hyper = hyper.rep.mRNA[[i]]
+  head(hyper)
+  
+  # calculat distance to nearest iCLIP site
+  dists.rrm4 = distanceToNearest(hyper, Rrm4_bs_UAUG)
+  
+  # kepp only pairs on same genes
+  
+  sel = hyper$gene.id[from(dists.rrm4)] == Rrm4_bs_UAUG$geneID[to(dists.rrm4)]
+  table(sel)
+  dists.rrm4 = subset(dists.rrm4, sel)
+  mcols(dists.rrm4)$BS = "iCLIP"
+  
+  # make df
+  df = rbind(mcols(dists.rrm4)) %>% as.data.frame()
+  df$set = i
+  
+  return(df)
+})
+
+dis_df = do.call(rbind, dis)
+
+pl3 = ggplot(dis_df, aes(x=distance, fill=set)) +
+  geom_histogram(binwidth = 150, aes(y = ..density..), position="dodge") +
+  coord_cartesian(xlim=c(0, 2500),ylim=c(0, 0.0035)) +
+  scale_fill_manual(values=c(rrm4 = "grey30", ctrl = "grey")) +
+  labs(subtitle = "Rrm4-Ada-Gfp vs UAUG-containing iCLIP2 BS",
+       y="",
+       x=" ")+
+  theme_bw()+myTheme1+
+  theme(axis.text.y=element_blank())
+
+
+```
+
+### mRNAs specific to each hyperTRIBE dataset vs all BS
+```{r}
+# distance a-Gbwtween editing sites and all BS in mRNAs specific to Rrm4-Ada-Gfp and control-Ada
+
+dis = lapply(names(hyper.rep.mRNA), function(i){
+  
+  hyper = hyper.rep.mRNA[[i]]
+  head(hyper)
+  
+  # calculat distance to nearest iCLIP site
+  dists.rrm4 = distanceToNearest(hyper, iCLIP_NKS)
+  
+  # kepp only pairs on same genes
+  
+  sel = hyper$gene.id[from(dists.rrm4)] == iCLIP_NKS$geneID[to(dists.rrm4)]
+  table(sel)
+  dists.rrm4 = subset(dists.rrm4, sel)
+  mcols(dists.rrm4)$BS = "iCLIP"
+  
+  # make df
+  df = rbind(mcols(dists.rrm4)) %>% as.data.frame()
+  df$set = i
+  
+  return(df)
+})
+
+dis_df = do.call(rbind, dis)
+
+pl5 = ggplot(dis_df, aes(x=distance, fill=set)) +
+  geom_histogram(binwidth = 150, aes(y = ..density..), position="dodge") +
+  coord_cartesian(xlim=c(0, 2500),ylim=c(0, 0.0035)) +
+  scale_fill_manual(values=c(rrm4 = "grey30", ctrl = "grey")) +
+  labs(subtitle="Rrm4-Ada-Gfp vs all iCLIP2 BS",
+       y= "",
+       x="")+
+  theme_bw()+myTheme1
+
+HTrrm4_spemRNA =  ggarrange(pl5, pl3,
+          ncol = 2, nrow = 1, common.legend = TRUE)
+
+HTrrm4_spemRNA = annotate_figure(HTrrm4_spemRNA, left = textGrob("binding site density (nt)", rot = 90), bottom = textGrob("distance to iCLIP2 binding site (nt)"))
+
+HTrrm4_spemRNA
+
+ggsave(HTrrm4_spemRNA, path="C:/Users/Sri/Documents/Bioinfo_analysis/iCLIP_course/iCLIP2_Methods_Stoffel_etal_2023/", filename = "iCLIP2vHT.pdf", height=8, width=16, unit= "cm")
+
+# calculate median distance all iCLIP site
+# for rrm4
+med_rrm4bs = median(dis[[1]]$distance)
+med_ctrlbs = median(dis[[2]]$distance)
+```
+
+# Session Info
+```{r}
+sessionInfo()
+```
diff --git a/assays/S3_A3_HyperTRIBE_Rrm4_iCLIP/dataset/01_hyperTRIBE_v5_verfied_rrm4.html b/assays/S3_A3_HyperTRIBE_Rrm4_iCLIP/dataset/01_hyperTRIBE_v5_verfied_rrm4.html
new file mode 100644
index 0000000..8c00219
--- /dev/null
+++ b/assays/S3_A3_HyperTRIBE_Rrm4_iCLIP/dataset/01_hyperTRIBE_v5_verfied_rrm4.html
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:784e7f7a5430bcf09e1f9ecb85df8483427e6d92ceb3e54d99b8e4a2cb9d0fe4
+size 1064189
diff --git a/assays/S3_A3_HyperTRIBE_Rrm4_iCLIP/isa.assay.xlsx b/assays/S3_A3_HyperTRIBE_Rrm4_iCLIP/isa.assay.xlsx
index 61e58e4e367aeba21c3783c02cd54dff69d02346..e6dae7cb9b54f0de6b72f52442011b06a8c3435c 100644
GIT binary patch
delta 1910
zcmZWqc{JNu8;*!HT5Ig0K@+<)8C!+gqSkaFD)z0S2i3-)r<RgwZ7r>YA6?W|RMnui
zh^4fSMs?ayTVv1$Rfdn4E|ybTA92R{`py04dGCFfd(V0A`#isyw3vvy5QQQ8K_Cze
zq(VX0i>C_-ZzFJ9NPPzz+l3@|4>(|?z`+Nj1r9l3<gUX6q9eW?>FG|gd6)wRfi{5%
z2!<AY!I1zty;K?wn1n5uE&VAXQw_Fn2AVfk+D(Zw%_Sp}j-&gE>5W#4iwmvi$~xZI
zS6OP|GM&)hNbU{1*%|KlC3eQKp3j}rH4Anp{ZrIE*bf(-<{gG$K`6*qO|6^E?tGG)
zN$H2P70`j;a&p@T`Frt1PKn6l38Ej-i>87NeGzghD~0(3W;?>vXWQqspZvNC8z}uK
zKXl}#%IoWI^HjSo`dabRGD#PO4<RXfOPR?zm3rI&R>$DxeRh9R8XkKpf*YH@OnH>&
z$}Cjp2b3;9#Xr!oBW1h8pH8~0IA)q@aqBvRtV6R~)2V(rRxziq=P!FFJS^&j(OS>z
z_qh@dF&k?Z*+=RXFlkZnr~Hj-Z|<Cdp9dBZ<Xr7>GH2%K^E4lSinoQGXWTO{<a!V?
zNF24yHoO%$_;KpbbC*HwV$ExI1p|rM190rI!noHT>bE}Kd68_`&%Us!h*15H0eX!{
zzl86*m;U!Gl4{vUB!p+jKAAazp>2+yxm<1M$Ui`5smx()V~KQ@@>~reR*!x=>&qZx
ztm21RCQo+FU8=_++0+pjbvUW-4>RodkkovOty7!P+t9p)gW#c^6vlD2WFujo;T_LS
z21GrvF!0QGTZYRdLPTc2HN$O^C?X?o%^*)Eur-q=8Bq1agwYfW{azY!cD!42G00{W
z$3w2ZMJ_C52=g+QeW@YTQu44wip+hwd0jgzJn~XY1~QjfWzJNd_&e3I$tBraCn5X|
zYVBcNyE@7H%vJtG4qy}Zdu!9W!RnT)V(5|N=QY<Je2J;2=tO;DoDIRlaicmCR$A4b
zn5B+y7`^cpi+9HT`!v#Rp<gdY>iq!!^u0aF{1p5hArPnt0s_f`0GyIME${Sr#yCzY
zaoIyGiJIHt;#}X+l6gY-p3x|uP<&OF9(?6+t^MIoJP(PGFhp>U1E;_++CI8`eZE|7
zli)Czk8bm+L0O|BP@G?`caE?(=+cb2im5-8kC#g8#5?oY$B^I=7x=~ZYsHGFf%~&f
z4Ho%~u$rNX^fGgUg@d1IX=cYB%e4nQw!(29T(=(WT1U6hZUo{!&;8a<y<((!x5tuG
zrMrPNEbfWezbOj;B;DK_7FjtETloUH<<JqOf#7#*Pnts(Tzkp;=N;-WF;}J*qQ2nw
z(M!!)PirNI|1zQw)J|}r?KWH1mkzKRl4W2a{;wMsoEYw_rhO7LGT%T=EdC~}+s}Pk
zp3^vtKrhR!4Sk!tl6o3uUW=`mcFXr%iR?v61iWvK)-Fss+B<ifQ{*)LyJ5sdQcPQ=
zm6ynBoY!RxE6$6v#@pAJejs+Lt1H^zhmG8zpYZq}P!s$3mvR{Jm&pX?wb4scg_v{G
zw}Gv~{`{U)3^rJMjI68lKFv6@Wl-0*HpYHpx|aC9fa$p&ILP~_cc2|=0y<#3%rgUP
zg9<3<zGM+tz)1x7t|tusSV(k-i>3!E!U6zwSsfZ+t(rk#jAgiG>&gvR9pU;v)2PQJ
zg!S^caZ=VFhsXQ+7GqWW&ZalOlAf788p(ZLb`4U}B2PMBL17l8OQIuta|2V!I1OV{
zgI8383#3}i6YulSN+AldsE?!z6_m_SlJh|x;pIfHUal5*?3S2C6CzxZS1<ksoxu+k
zrS(E=?GfE?#Inj+vX|?O5`3DVSKYKrAgNhBWp|32V9hZe2fSyGdpTE&`{p5E+9XCs
zNs--+t9ojN*Hnk->{mYK;o9zvx)SJq$f;J5w6R$|rdu0H$>NpqQD=QM>QLfeDAv|D
zXqI0*$Wnf?B@g<&(CqV}ss8%pwn4IKP``i4EJ-Y=?EE`dtr?pxmBX8@T=?_g#Dx`X
z-b(w@S&;O4Vfi~K{q@HBd>mdY4z2;<GP*+>ZU8X_<*c>h6a5M+THOt_8D5q{a#Cj|
z?e5mkBh^?bcWqY)3>7Q|-H1{6MSztGCIXyNI4nT8qLBcd6zv3<t%(0W;ovIbRd?F=
z^OSCD)80A=V3kmUn7yNILv(K=wQbD-zbYvTZn&X@085AhkCX&j25^)RLa%^%B^9%s
zOZIa9RUiTm0#T^JE>YCTXsioS2rLWQ6G*^H86gA!KFX?sR|r1ZHlKXh7C!0!tq8IM
X?kcMZUh!l*V+a^kJ_Pku*a`VBk;f*~

delta 1945
zcmZ8ic{JPk7XQT>t%wp85=&I=Yp0ezwH2YsRB4A=LOCNT5@M_6q0y8HT?C<cRkWo=
zF<J!C!9j-@TWPh;vy>{T8d6J*tuJD{bK2iOpWnInbHDeVbMO7!M$;ryhznL&<NyEw
zVBo?pN1i}vAYnc-azUtFtZfEC_Y8eP$^r*hNL}EN6IR}Hn2Kma_)L$6>#nS1ApmG+
zkVNz;=4R?Bp^9kN`qOughumFTfXh}2p_vTk=4!J!cDlOw6*SWvVI{TMQm}kyw)&RT
zDMa}OwM`F|IoDJX(5l-#K-+vQmv$4M_}uH&4eB$nU1$&VZ^jV);h}akc<zj?B9V3(
zi5O2!&(Bx1r~gzxq*M!^_aTYtdwfuy=j2f|*lOIo1$J7^$fAE4>o$%An~1sJpqYAD
zzc#NWXxgv8F1=O!wefbNN_FGBm^}%v`}xMTtg`o?2AX|?m?6B{BLDvN{LfUgb?1nx
zn-!lW!zr?fn|+=I&z*FZF;nu$3zkFo4Z8I!7qv1Pd&l~|8nDU#s<7`{tJ<zEw347S
z5%svP7`6I_s)gtB;nMofa_VuGYp(U7y?9o&uW5T2?ssa*#}9G{f@eN)6*k!;%>B}q
zz6mD6;|%g&z!)=K@noJD@)%sDN1YDED@Sgj=Gz~jPR{fE3SyMno7ZBa3e2FBeU{^^
z=7x~TQf0DLzjyM|VP!+5S$(@$3YOjgpRGC-t4nV{&f=BnJM`SRXRlIbXSiEUq%EHe
z5xMxO3$yl3c6rt<Hb$;I=@RK@5rOyTP~B=vCe$<*O*OO4OhN;rLd6MP)W|El0v?h`
zDDpc6fR7zWDD`UxfwK-IJoYoW+Dpx7Icek%g*>HgtPPeE4h2A0Ki{K#<H*MU5#ndT
z%lUYB;mphHoU36+R?6ut;$yLx6t_CJkqR!-<P9^$3SDMfm2D}`OWU-2vn{QyZ)_X0
zq19bn_v&Y_1b7!kw;<5$S|`D-Hje2rB-s@E@@W?RXE+kpWvz*O;>8hP#kw=Y@4ijR
zU8D4>wjf)3tOfH-*&k>Rru3slG6(>yL;wKBx5knTBLn>-@B!zeB7#CMMH<A0kaDsw
zVmpjr&nLEFs6~TF*+W4V^MT<teM2MSMQGCEh|Ny#=r2q%Sx0Ri^Hw>2aZz2fNfSa4
zKgt&OfT3wCgyRoIqVU1@Vo-_N!=K_YgW(jP$e`oND`2NfFWi#mQgeePgWiwsTs5v#
zbU`{2pqv=ypE}&FM`OmL-tSCI0q4`E3iQRisZ;0A<-0d$IBR6rc|B_|`lf9Ux~>)G
zii7cpZ8%s>^^%YMwBu8u^eRzNPUe?J+OpO;s+)SXP8)YHV64KdCO7clFz0|%VF_is
zLZ$+Z2#W3kd4DU$;#M(+MmeXsEZ)ks@(i01+}-sVAB3mzSm$sbW8%&2zo(4fPP>nV
zb|y4+=h;|ow4=q-XpGfn*DO8u@N7cPw8OWZeCUJLq@!OYKGpJQm=sHK@3jBu)rC>9
zND<j0><OoUTNLq*!u5}A%GdWSrrwpFj^1e9l6U=%{uzJWN}kMVNyQFbuK0B0@UnH%
zob0~n0K1~YSOM>83POS<CJ>i5&_W@B+QiB1d5UFz2TAOzj6-k!h%dtfrcIHxDZ8Gf
zS}*rV%}vMc@i;CXl-tQ%C`C~&&f2Q#JQ|OVCUk9vu}<bVED4XCt~w@jR!t^p%FC(#
zukQa6<i;6osPj}gFI#kQSU~<n>8Lu+JN5}D$w9(k3EgvaG$4Q;D1%X&uw##Q>Sk*;
zaBfRl)>#C@t!tD9gJAlB5|nNcJ2awWP%^!w0hUm6+|j#EjCx+HSR^I=Pez_^9hezq
zcF=1E<B6$+jAj?IZ4)CRq}|<2$_Z63zp4z=SC@$v!CG#$I#TLqMb9>h{>GUh&lg9P
zp8IzWF*e)7X8hsipd)vE6@qMD0TT4u!gV1V7MG{BCI`ZkSVQjSego+)k=no23^Tc9
z2fq~iNxj|~^_G~r*Rryai`g8D{wWE(<(w6I?b1x*+IpR5W`g3GS$`Pq1xePCO)Bh_
zFFG^uVB?1WTk9|6u3B5`iMfk2t@~XOoPyeSa;bX?Pn5S3G^0}9Sb*>3O$Dd`HxQtW
zB7%X3D+vCt!W{(2hM)N1DnJ!ZsO)y|$A#qY<Ub#jaY^CG{);DSz=CCs3dD!t4PCGx
zAsF!gGv$%hZ=!iq3;;S+0YG*?UVyK`j7bHQAd{#?l5aHsA_?<}knc#@43r{rKNHA=
zfm4M0?AFHq(1B0pi-m?T07!oqfs+A%0P?Rc5#+E)L;tX_UD^1tD8X#<qu=v$9{Mg?
iit$2GRZtT_-|h;I&xzu5px<%sFr*P`V(Rj{#{U7#(JL$f

diff --git a/assays/S4_A1_microscopy_DIC_Gfp/isa.assay.xlsx b/assays/S4_A1_microscopy_DIC_Gfp/isa.assay.xlsx
index 7a502c264298a61588d5f9ea6eb391482c9e58b2..d8d196e6bb9b3d6f0ee928489be07a6e4f45efe3 100644
GIT binary patch
delta 683
zcmexk`qz{<z?+$ci-CcGgFz-mWg~ApBQubmJe^SyL~q{B$PW=X%OnSuc*mpymJnr@
zgGiXMXo3ZjShh2P88Ym%ATm2SAW9!_>|z7U%;ld4Rx;U62qKdzw4RX@XidbUi_0?O
zC(DXx)=zej?{b=Ot1Eb-mgtpL=GWs6sBYA)&OCAddZmEF(<`^noqJOue=e<k6Gz<v
ztCd%$99i7KvS5c;Q0}snt#jJ>RSHf_NoWl-P&KtMI-PHn7qm`yPgL%KMJ(bK%1?vx
zmZfxO1bNBccRG3Jg!UBm>$j%y*lv-|lDNN-_kv2-yA00y6D-bd(uXhb^ex#gQnSIN
zI(iFRQ?SMYme#&wi)YN+!m+I+oIC27Po&ox-k7O!Cmm}GiUh(!O;;UTd*!?Q<^H3m
zqph<vLN{yishnr=-^to`>zVe};9WtIwx>;PymS=uFW0_M-v0j=TVHGygPque9aGu<
z&b9ia^zi(~=3SS<EE3PhEqE5hlejqdZlL-T$AdC@e|BCMI+9%b>Z|_Lue;x-F$n&c
zyW}og|C!%EURGMFR|=_4Ht0H>v8iWr$($wIzt8tQFaA~i@TU4F_xs$N>-Kfm&-~AX
z62+UBh;~5YM_=3y6fKhr#0|mp5^*yyeOFu$Ob1FzPu7%>1hZWwT)}j&ge90hDd7yJ
z`6cbabfBaOnC_5-n0Zpt0xB*&SzZcahP9M6Qe@XlnaP8qK26uTE{2hTp@fNnfghL-
Q5n#sTD^f~qisB#<04oXj_5c6?

delta 660
zcmexs`p1+vz?+$ci-CcGgCRUbc_VK-BQubmJe^SyL~q{B$PW=X%OnSuc*mpymJnr@
zgGiXMXo3ZjShh2P88Ym%ATm2SAW9!_>|z7U%;ld4Rx;U62qKdzw4RX@XibFcnVHw(
zCd-Ow)(bnV=$fRkRdl&hs8;Cedok6F(~oR>vsAG@{<))q*7AF0WogHM7woc`>iU8C
zn&(<0A%7*IhDT8zTTh?3ohEv3@&U!*CebKIx2%GcnfI68QHhDJ*m$eKl~eD7+bPvM
zDJlIKLSC}>olo95qCG`@`>km_wp*;TB<wfHUdR;D&ETv*!Q$*DefR=T-;(VjH5*La
zqqnd%1#2u|Y3(~Uc}Cn8j%_98+)>ZGBE8n|-kCD*q+@MSkw93e>B_XVSH8<%?*IBZ
z+d4}lbh8$pia)FW4%W6?&+=a_C|Md*H8s0pN`%9`Wxp@Dzx(l(S7!GYh8mp%h1$Ho
ztV^G0JUn06u<KHoMZ)>MfMU(I4VSmQTfzNlK?2|Pe|MreA1&PX<=1qt-*?N58#w;>
zP0DLde^&eL$Ck*6HB!FM6GhrD<_No=%$avae7^7b#lN}}Z`yy#Kfc+~{{D;jXZulN
zc=J-x4oLJEh}(f;WpbgoA(&n&ZU(0BiR*!BehCvW?Iz(0ru!r;!SpE!XD}@wX%D9P
zC8Q_kN=ky+ostkUPf1$9<rJhKayC-dNO9dD1+i_Xlr-b?$ycS6*c8NpsgMBxcSHRd

diff --git a/assays/S4_A2_protein_expression/isa.assay.xlsx b/assays/S4_A2_protein_expression/isa.assay.xlsx
index 1a843e417b05c8c00befd30f752405068164f993..f0a36b1294269c35ebc0500f7c6cf2dce13633a5 100644
GIT binary patch
delta 680
zcmexi`qPv*z?+$ci-CcGgFz-mWg~ApBQubmJe^SyL~q{B$PW=X%OnSuc*mpymJnr@
zgGiXMXo3ZjShh2P88YnCATnDyAWH9W>|z7U%;cX3Rx;U22qKdxw4RX@XidbUi_0?O
zCrgTG)=zej?{b=Ot1Eb-mgtpL=GWs6sBYA)&OCAddZmEF(<`^noqJOue=e<k6Gz<v
ztCd%$99i7KvS5c;Q0}snt#jJ>RSHf_NoWl-P&KtMI-PHn7qm`yPgL%KMJ(bK%1?vx
zmZfxO1bNBccRG3Jg!UBm>$j%y*lv-|lDNN-_kv2-yA00y6D-bd(uXhb^ex#gQnSIN
zI(iFRQ?SMYme#&wi)YN+!m+I+oIC27Po&ox-k7O!Cmm}GiUh(!O;;UTd*!?Q<^H3m
zqph<vLN{yishnr=-^to`>zVe};9WtIwx>;PymS=uFW0_M-v0j=TVHGygPque9aGu<
z&b9ia^zi(~=3SS<EE3PhEqE5hlejqdZlL-T$AdC@e|BCMI+9%b>Z|_Lue;x-F$n&c
zyW}og|C!%EURGMFR|=_4Ht0H>v8iWr$($wIzt8tQFaA~i@TU4F_xs$N>-Kfm&-~AX
z62+Srh;~5YM_b$u6fKi;#0|mp0&z1ieN$WyL{E~Eo~$Y%2^Mmca0Szy5|&{4sDv|^
z=9aVv(IBN6k`SdWk`PmmN?JgqOu#D5rL2)+x?0Li9u)6sy3Tbmj0_AVObiVCz(j}u
PQzl=KQeu-82Z;ax$fx(?

delta 682
zcmexq`ookrz?+$ci-CcGgCRUbc_VK-BQubmJe^SyL~q{B$PW=X%OnSuc*mpymJnr@
zgGiXMXo3ZjShh2P88YnCATnDyAWH9W>|z7U%;cX3Rx;U22qKdxw4RX@XibFcnVHw(
zCQFKF)(bnV=$fRkRdl&hs8;Cedok6F(~oR>vsAG@{<))q*7AF0WogHM7woc`>iU8C
zn&(<0A%7*IhDT8zTTh?3ohEv3@&U!*CebKIx2%GcnfI68QHhDJ*m$eKl~eD7+bPvM
zDJlIKLSC}>olo95qCG`@`>km_wp*;TB<wfHUdR;D&ETv*!Q$*DefR=T-;(VjH5*La
zqqnd%1#2u|Y3(~Uc}Cn8j%_98+)>ZGBE8n|-kCD*q+@MSkw93e>B_XVSH8<%?*IBZ
z+d4}lbh8$pia)FW4%W6?&+=a_C|Md*H8s0pN`%9`Wxp@Dzx(l(S7!GYh8mp%h1$Ho
ztV^G0JUn06u<KHoMZ)>MfMU(I4VSmQTfzNlK?2|Pe|MreA1&PX<=1qt-*?N58#w;>
zP0DLde^&eL$Ck*6HB!FM6GhrD<_No=%$avae7^7b#lN}}Z`yy#Kfc+~{{D;jXZulN
zc=JNh4oLLqh}(f;Wpb{#A(&n$ZU&}riR*!BMk(pZY7&xQwv&V_nC_CW1k=YPoWV4Y
zq&=7hsm+vxsBM*mn0rjp0xD+$rY)qbk>a{W%1j;<^J%)ybuo+#3?)nq4E(@khyar(
NUzAc}lMx4r005h?{kZ@D

diff --git a/assays/S5_A1_HyperTRIBE_Khd4_workflow/isa.assay.xlsx b/assays/S5_A1_HyperTRIBE_Khd4_workflow/isa.assay.xlsx
index 23ac52d656e6ca88e4f16d77b0abd2f36c8401ea..b4344555a9f4c4052462000c043aa82dfe7b3fef 100644
GIT binary patch
delta 677
zcmZoRYcb;u@MdP=Vqjq4V30{s*~r_@$PA<>PiIsF(VKTO@<Rm9GRc7@4seJF#}}pM
z6zijC+$_p02T^Foq6yZS#Il_U%#dMU2$4C!p#m0o&asOP%vi!d53FRes}MvcM`%4G
zC(zo6M;Di6#!pre(X5~BAm8OQ;Z|4hL@m)PtIV&*9Z=n<Tb+60{`E=$ho@I=pF8)a
zLjGJ@`zDUM16C`qPC2r;gJr=Ev7p>#DO=~X^Q#n`n3B*MW}s?nVRSm*C@*N8?w+XJ
z1B+P1E0muG<t<C;&It07z3+7L&I#=)>ep{g<FVZ$oh5O9Bku*3u6G%n^(R=I-J}m+
z;OSekU8H7%Np<uVwx(c>1uU(7#}?0+w}oR{NjP`ZGoMJWHM}uX<xV=*78D7Dg_^E9
zw)V<*`OE!BPe)s4X@qXp;!`=#;=hx%?bb8xt--s3ByCTd+IZ<G<X^6Rp}hV7FSfqe
zDh4~T2Ro*+{he#|N$KJFjm^6*g;^w?k6Z98h$nGz?%hE3CyobY^#1I;E_5Wh_SIMY
zsb6=$O=A%JF?Y#bw*E7}f4r=;RIe0Loovu`IAc@K<dQi{wtt`RdtUsj`r%FWPww}*
zH`nd!uAljz2{q<ci*`U`PTUR@EtAW|4Z-wkaWgReL|hL{b4y82Hjt16vwb97!Soaf
zOE7&w!Wm49N!o*HklJENh}wQhh`AReEueBHVA@H_8Y!~dq#(BKmy%|jKl!$l5}SrN
IFj+DH0C;ct-~a#s

delta 676
zcmZoMYc}Hz@MdP=Vqjq4U<eOU-pJd|$PA<>PiIsF(VKTO@<Rm9GRc7@4seJF#}}pM
z6zijC+$_p02T^Foq6yZS#Il_U%#dMU2$4C!p#m0o&asOP%vi!d53FRes}MvcM`%4G
zC(zmm*E2J(#Z6Wb(X1DCSkW~}VXNqJrBJQV)%Rkm8K)oF_GYPKef)Dr1+C@x%F5D?
z|1Q{NGu8D2^EJ=4Mne8dLJg0iJhq-baXU@)-sA&{!A+u3j&4~6DKqacy`vHnU9s_2
zgDa=r2e(tIcT!UNGlaZk?>nEob3}WJ`u1DXcx<;=XGz#^kiC#8qMN~4e}cu?P5ST!
zp1vj9MQS#fxJPecYYNs_z|z`xZ1Rk_EgaiQ%(<hUc}04y;k`3u-bu&Wq9TE?P}7xZ
zYp;Blzuf=zbGCJsM(AcOJ{5mf{~fGtx1Qy{T2QhysA_6<#gqt#d&_=baDVsXE3eG%
zFAOz02MV=$e_5A4(Rg^iuwmDwFpGrqeF4RqZ5u9cd$)r7(}D!P>;LXVb3R(Q@5`_0
zUcc{_88>kJ@tc&_oc^r#+m9`g6KkY=pC^j6U(6A9KbbS{jQD)t^NW9VC*HLGlz)7)
zqy7CC@z3_7M%)_F4oLKvi`#)>WpahMA(&nxZU&~GitB-C9x3U`h7yuswy%UMn4T(O
z38pVfID=_%NqaC2Qd=SkQ9D5rV(vvr3#gn4n0A)3MvCipDTr+cq@)?=O}-<g#HKC|
HOqC1(EpGp`

diff --git a/assays/S5_A2_HyperTRIBE_motif_analysis/isa.assay.xlsx b/assays/S5_A2_HyperTRIBE_motif_analysis/isa.assay.xlsx
index cc6aa3f7d1cbe837e884ebb24b0d90eddb30823b..afafed3d44dd7af11e647b8ed3d5f210b5b94f7a 100644
GIT binary patch
delta 653
zcmZoLYc%5x@MdP=Vqjq4V30{s*~r_@$PA<>PiIsF(VKTO@<Rm9GRc7@-Z80wB}AF!
zAQEOQnqYw>mhDVnh79{Wh|FFNh|(t<yV$@o3;E}Pl}vULg2-eFt!Lx}S`+c;;<C*6
z$%-PH^^+asyPPK6>I$ByC3<C*`SrL1svC8yGf&*VUMb-4^vdmX=iXGvpG#}s#8G#^
zYUR}_M;3RmEZ89yl)Eft>zsCem4Xvf5?aFyR81|6PUjot1+CNF6P0^l5sP?*^3$Na
zWhvbmL0+==olf34p*=<Y`mJd^wp*mLB<^qIy`a+dE`ziF1dFqq^x+FUeM`2B)NC-R
zj^4u76s)m;rM2(a;u-U{aBM3H=Z<>j6X~^vH)g8bNyplPB7v|_(^bdTUimJ6x&P?t
zXzMJE(9K$WD(6}Jce1wKdZxWKcvq05?P*gRFCB&a%e60*xBvge))!mFU?=uq$5ghz
zbFDrpJv_g$dDo>di^TJB3!Vk>BreXq8>s%o@t};}pPko*jwIK<`l>(m>+ZK{41z!A
zF1gFrf9Cg(mz9?4l|rhM4Z03zZ0ea@GH1#5@AG}ni+@!=ys7@l{XX~Rx_#aCGygN8
zMDgYoq8*U<F&4K2Ma$$8aYHb@Lfi~YKNQyk(?Sv^VA@l{6--Z*umsa*C7i*uu%tbh
v4wZzc>yd<*cUIB@EY2YX5x1AJMvCNSDTpn5q@)?=Ouiwd#HK0^OnwXi4?y)3

delta 660
zcmZoPYcS&t@MdP=Vqjq4U<eOU-pJd|$PA<>PiIsF(VKTO@<Rm9GRc7@-Z80wB}AF!
zAQEOQnqYw>mhDVnh79{Wh|FFNh|(t<yV$@o3;E}Pl}vULg2-eFt!Lx}S`*=VX6CiH
z$%-PH^}-G-x+W=X6<w|rsujBWUQ9LP^dsBeELE(Jf9|NDwftULS=#a61-opfx_)53
z=DF5L$X`jQ;Zc;w*3&0$r-|O1d_Xa{Ni@pQEvq19=KZC2RAQnlHr{G*<<$G&c1rb5
zN=ko*keBRz=aYAiXirh!erp<!?H21S3HuGQ7cxb3GdSx{usFL(AHKlTw`99W%?1<q
z=q+qb!5Rx#TKkSoo)Nc&V_S(ichoblNUt@#cc#oc=~!D-BoG#Ax-xC;mGAPG`@eq9
zw$9QB-K@o@;?L^8gSG9}v;0>JN|pvyP0g;D65()f+3ySP?|yvcmD&A;p+@IGp*HU?
z>(VD056>4i?79?Yk#N2*pjfkQ!{u%7R&ak>kid8S-<@dAM+^6T`8D0^_uVq%297^|
zlk%F=pVfZ*u_bb1jg;^6M3MH3Il}HIbLO29pYMBq@vrX0oA#gbk8gIgzyBis*?yE5
z-n>$@0}?$Z;&z}|nOrJv2&Pwxn}O*^;(B13Q%ZWWo`fWr?Iqy~rYA{Qg6VS-&R|+Z
z(jH8M)D}uY)b>h3%snS*0hKcW(+*PBNO9dF1+i_flr-b)$v35x*i^)UsgMBxKWY4j

diff --git a/assays/S5_A3_GO-term/isa.assay.xlsx b/assays/S5_A3_GO-term/isa.assay.xlsx
index 3d8e665c492589c4d5a2a60e777ea3e22c73e466..71367fa008f350f6e44ceb64e32f4c6947b2bc5b 100644
GIT binary patch
delta 677
zcmext`o)wtz?+$ci-CcGgFz-mWg~ApBQubmJe^SyL~q{B$PW=X%OnSu*uWto9AA{0
zQ>>4oakD7197LfRizZlS63ccbFhhoYB1C2bhYDEWI>#<HFk=e;Jg}0<ra};z7@_ry
zoIq<M9$j3P89!M>M6-UfgM63Mgj-#~6SYLItTMkIcR+QcZgu8~``0T49G+geeeT?w
z3i)$s?VC924p^<cI_1dX4weNw#Da2{rEHzk&aYB%VoE}5n1QOPh0*DJqr9MXx_hE>
z4=iF4uTXv(l(#IUJ0r+T_P*1}J14ZKs9(P|jmLJ2be6>Zjl36By541Q)}LT;c9TAQ
zfv0cDc9EJ5Ce_hf*qVYh7O=GT9a}tO-WHB+CE?sr&wL`i*6_wml{@KJTTmnr7HYcc
z*xD=K<uCUiJsoYGr4hPWi%;b|i~mm6wp-7%w+8PDlC(W-YU8D&kbk-Mh4S|Qzu5X>
zs~GIW9_*OP_IIw;C#8qyH#YCO6lRflK5oIYAfCj<xpxEApEw?r(fhOWy3mp2+E-uo
zr+(f2HjP2>$J`}%+4|4?{_(QXQoT}0b+SR%;fzf^lS}3-+5UaL?|JdB>W4SgKe^xM
z-dwk@yME?>Ce)alE!qKzA2o41P_#@=7dHgcv&GH8^c8VEF#TInda{CqB$#a@;R>c(
zBrL)70SRX?%_eCNra@|xB_V3-B_ZY>khFlxnSf~{DQl$2E|Y@Twq8n_v48SuDJ3=u
JabU7!001oP``Z8j

delta 676
zcmexj`q`8>z?+$ci-CcGgCRUbc_VK-BQubmJe^SyL~q{B$PW=X%OnSu*uWto9AA{0
zQ>>4oakD7197LfRizZlS63ccbFhhoYB1C2bhYDEWI>#<HFk=e;Jg}0<ra};z7@_ry
zoIq<MT+htB7B^W$M6+JlVMW&@g{`8?l|r>bSKo`NW}JRx+nc3|_3_Ug6||P$D=SMo
z{<~n8%~aP9%-1~E8VUI;2{k;5^4NO%#O*ZEdy@|+1~-XDIl5&Pq|Cg(^o~kQbj8M7
z4X&JeAKXr<-bqR6&k*vGz3+VT&Jpb?>f3Kk<FVahoh4zvLH0tXh;9aF{RtLlH|fI{
zc>0!X7pd7`;vT()ttnVz0ZVJ&vB@*yws34KG3SnY<`wC+hWE~tc_$rfi;4uoLQPku
zt-bPH{&N4<&)L>l8ljuD_*DE^{dcgo-FlY)YC*};psK0a6;mP{?k)R$!TsHjue>t5
zzcAG394OT0{bgPHMC0N4!iHU!!YmTb_XQMdwr#k)?cECQPYV+GuK&9e&G~5IzAwL~
zd;Pv!X57H>$8S<zbNaK|Z$Gv~POOpgeV!=NelbVb{bbI(Gvf1o&oBPfop{s!Q~vSI
zj`sIo#6R1Q8gX+(J0Q`cE^Y^kmB|_6hG2S*xEYwfDy|2n|42$tR+Nwgvu!0@!E~#H
zC73=a;S8qPCGEj9NNtKFL~Vm4#N30D7En18Fl{VljTG1AQV`oVNJ%sHO+F)~#3n8d
HOqC1(;eG+W

diff --git a/assays/S6_A1_RNAseq_data/isa.assay.xlsx b/assays/S6_A1_RNAseq_data/isa.assay.xlsx
index fc66a729a17e6bfc62447ac904a42d8de88036dd..22b55df2f9f642111210a769dcff2b1f23237f26 100644
GIT binary patch
delta 661
zcmexr`puL#z?+$ci-CcGgFz-mWg~ApBQubmJe^SyL~q{B$PW=X%OnSuc*mpymJnr@
zgGiXMXo3ZjShh2P88YmXAu^jdAWCm?>|z7UOyi#iRx;UK2qF_Fw4RX@XidbUi_0?O
zCyR+_)=zej?{b=Ot1Eb-mgtpL=GWs6sBYA)&OCAddZmEF(<`^noqJOue=e<k6Gz<v
ztCd%$99i7KvS5c;Q0}snt#jJ>RSHf_NoWl-P&KtMI-PHn7qm`yPgL%KMJ(bK%1?vx
zmZfxO1bNBccRG3Jg!UBm>$j%y*lv-|lDNN-_kv2-yA00y6D-bd(uXhb^ex#gQnSIN
zI(iFRQ?SMYme#&wi)YN+!m+I+oIC27Po&ox-k7O!Cmm}GiUh(!O;;UTd*!?Q<^H3m
zqph<vLN{yishnr=-^to`>zVe};9WtIwx>;PymS=uFW0_M-v0j=TVHGygPque9aGu<
z&b9ia^zi(~=3SS<EE3PhEqE5hlejqdZlL-T$AdC@e|BCMI+9%b>Z|_Lue;x-F$n&c
zyW}og|C!%EURGMFR|=_4Ht0H>v8iWr$($wIzt8tQFaA~i@TU4F_xs$N>-Kfm&-~AX
z62+V6igrNaM?>5W6fKi8#SOvqTyZlneN9{sO#hXXo~$Gx31-_#xPs|62}>}2NWvLR
zb4c2QX^`4fNr>7;Nr<_JBrTwFCSck`${H!ME2JQ{ZIqH`oH+TcloFeiI4~J9008L9
B`B?w}

delta 682
zcmexn`qh*-z?+$ci-CcGgCRUbc_VK-BQubmJe^SyL~q{B$PW=X%OnSuc*mpymJnr@
zgGiXMXo3ZjShh2P88YmXAu^jdAWCm?>|z7UOyi#iRx;UK2qF_Fw4RX@XibFcnVHw(
zCX0z^)(bnV=$fRkRdl&hs8;Cedok6F(~oR>vsAG@{<))q*7AF0WogHM7woc`>iU8C
zn&(<0A%7*IhDT8zTTh?3ohEv3@&U!*CebKIx2%GcnfI68QHhDJ*m$eKl~eD7+bPvM
zDJlIKLSC}>olo95qCG`@`>km_wp*;TB<wfHUdR;D&ETv*!Q$*DefR=T-;(VjH5*La
zqqnd%1#2u|Y3(~Uc}Cn8j%_98+)>ZGBE8n|-kCD*q+@MSkw93e>B_XVSH8<%?*IBZ
z+d4}lbh8$pia)FW4%W6?&+=a_C|Md*H8s0pN`%9`Wxp@Dzx(l(S7!GYh8mp%h1$Ho
ztV^G0JUn06u<KHoMZ)>MfMU(I4VSmQTfzNlK?2|Pe|MreA1&PX<=1qt-*?N58#w;>
zP0DLde^&eL$Ck*6HB!FM6GhrD<_No=%$avae7^7b#lN}}Z`yy#Kfc+~{{D;jXZulN
zc=J5b4oLK9irax=Wpb9dA();gZU&~Wi|c{uf0ELZl_ey>Y<me;Fx@U;38oKAID=_U
zNqaC2Qky0TQQIU5G54^f1ys%iOq)tsBgJ*4l$ksz=F@bY>tYxg7)qEJ82Ew75CJAk
NJ}0HbCMgaQ0RVF~0BZmM

diff --git a/assays/S6_A3_RNAseq_analysis_yeast_vs_hyphae/isa.assay.xlsx b/assays/S6_A3_RNAseq_analysis_yeast_vs_hyphae/isa.assay.xlsx
index b580dd4344d4e098e6ed31ccb065861cfd6ac1f4..065148d2b1fb70b93e9bb5dd247070aaadd0d69a 100644
GIT binary patch
delta 677
zcmZoRYcb;u@MdP=Vqjq4V30{s*~r_@$PA<>PiIsF(VKTO@<Rm9GRc7@4seJF#}}pM
z6zijC+$_p02T^Foq6yZS#Il_U%#dMU2$4C!p#m0o&asOP%vi!d53FRes}MvcM`%4G
zC(zo6M;Di6#!pre(X5~BAm8OQ;Z|4hL@m)PtIV&*9Z=n<Tb+60{`E=$ho@I=pF8)a
zLjGJ@`zDUM16C`qPC2r;gJr=Ev7p>#DO=~X^Q#n`n3B*MW}s?nVRSm*C@*N8?w+XJ
z1B+P1E0muG<t<C;&It07z3+7L&I#=)>ep{g<FVZ$oh5O9Bku*3u6G%n^(R=I-J}m+
z;OSekU8H7%Np<uVwx(c>1uU(7#}?0+w}oR{NjP`ZGoMJWHM}uX<xV=*78D7Dg_^E9
zw)V<*`OE!BPe)s4X@qXp;!`=#;=hx%?bb8xt--s3ByCTd+IZ<G<X^6Rp}hV7FSfqe
zDh4~T2Ro*+{he#|N$KJFjm^6*g;^w?k6Z98h$nGz?%hE3CyobY^#1I;E_5Wh_SIMY
zsb6=$O=A%JF?Y#bw*E7}f4r=;RIe0Loovu`IAc@K<dQi{wtt`RdtUsj`r%FWPww}*
zH`nd!uAljz2{q<ci*`U`PTUR@EtAW|4Z-wkaWgReL|hL{b4y82Hjt16vwb97!Soaf
zOE7&w!Wm49N!o*HklJENh}wQhh`AReEueBHVA@H_8Y!~dq#(BKmy%|jKl!$l5}SrN
IFj+DH0C;ct-~a#s

delta 676
zcmZoMYc}Hz@MdP=Vqjq4U<eOU-pJd|$PA<>PiIsF(VKTO@<Rm9GRc7@4seJF#}}pM
z6zijC+$_p02T^Foq6yZS#Il_U%#dMU2$4C!p#m0o&asOP%vi!d53FRes}MvcM`%4G
zC(zmm*E2J(#Z6Wb(X1DCSkW~}VXNqJrBJQV)%Rkm8K)oF_GYPKef)Dr1+C@x%F5D?
z|1Q{NGu8D2^EJ=4Mne8dLJg0iJhq-baXU@)-sA&{!A+u3j&4~6DKqacy`vHnU9s_2
zgDa=r2e(tIcT!UNGlaZk?>nEob3}WJ`u1DXcx<;=XGz#^kiC#8qMN~4e}cu?P5ST!
zp1vj9MQS#fxJPecYYNs_z|z`xZ1Rk_EgaiQ%(<hUc}04y;k`3u-bu&Wq9TE?P}7xZ
zYp;Blzuf=zbGCJsM(AcOJ{5mf{~fGtx1Qy{T2QhysA_6<#gqt#d&_=baDVsXE3eG%
zFAOz02MV=$e_5A4(Rg^iuwmDwFpGrqeF4RqZ5u9cd$)r7(}D!P>;LXVb3R(Q@5`_0
zUcc{_88>kJ@tc&_oc^r#+m9`g6KkY=pC^j6U(6A9KbbS{jQD)t^NW9VC*HLGlz)7)
zqy7CC@z3_7M%)_F4oLKvi`#)>WpahMA(&nxZU&~GitB-C9x3U`h7yuswy%UMn4T(O
z38pVfID=_%NqaC2Qd=SkQ9D5rV(vvr3#gn4n0A)3MvCipDTr+cq@)?=O}-<g#HKC|
HOqC1(EpGp`

diff --git a/assays/S6_A4_analysis_specific_targets/isa.assay.xlsx b/assays/S6_A4_analysis_specific_targets/isa.assay.xlsx
index 01411e9b70f81c655a66e784884861d8e3796baf..968e0c695b9a15013ae732eb01fd2dbb61bdc61e 100644
GIT binary patch
delta 661
zcmexo`rni{z?+$ci-CcGgFz-mWg~ApBQubmJe^SyL~q{B$PW=X%OnSuc*mpymJnr@
zgGiXMXo3ZjShh2P88Ym1ATql-AW9!`>|z7U%;%p6Rx;T^2qKd%w4RX@XidbUi_0?O
zC(Day)=zej?{b=Ot1Eb-mgtpL=GWs6sBYA)&OCAddZmEF(<`^noqJOue=e<k6Gz<v
ztCd%$99i7KvS5c;Q0}snt#jJ>RSHf_NoWl-P&KtMI-PHn7qm`yPgL%KMJ(bK%1?vx
zmZfxO1bNBccRG3Jg!UBm>$j%y*lv-|lDNN-_kv2-yA00y6D-bd(uXhb^ex#gQnSIN
zI(iFRQ?SMYme#&wi)YN+!m+I+oIC27Po&ox-k7O!Cmm}GiUh(!O;;UTd*!?Q<^H3m
zqph<vLN{yishnr=-^to`>zVe};9WtIwx>;PymS=uFW0_M-v0j=TVHGygPque9aGu<
z&b9ia^zi(~=3SS<EE3PhEqE5hlejqdZlL-T$AdC@e|BCMI+9%b>Z|_Lue;x-F$n&c
zyW}og|C!%EURGMFR|=_4Ht0H>v8iWr$($wIzt8tQFaA~i@TU4F_xs$N>-Kfm&-~AX
z62+UBiFQEZ$57l36fKjB#0|mpGI297eP3J;ObbYufN6ILS1{c#VF{*BOE`mRK}mZs
zEg&I1IZsj&%<hten0Z>#0xqX01(CCrvPO#RMk$DGyQHKUXHC8)rNpKz4orp&0R6xB
Ag8%>k

delta 660
zcmexw`p=X%z?+$ci-CcGgCRUbc_VK-BQubmJe^SyL~q{B$PW=X%OnSuc*mpymJnr@
zgGiXMXo3ZjShh2P88Ym1ATql-AW9!`>|z7U%;%p6Rx;T^2qKd%w4RX@XibFcnVHw(
zCd-Rx)(bnV=$fRkRdl&hs8;Cedok6F(~oR>vsAG@{<))q*7AF0WogHM7woc`>iU8C
zn&(<0A%7*IhDT8zTTh?3ohEv3@&U!*CebKIx2%GcnfI68QHhDJ*m$eKl~eD7+bPvM
zDJlIKLSC}>olo95qCG`@`>km_wp*;TB<wfHUdR;D&ETv*!Q$*DefR=T-;(VjH5*La
zqqnd%1#2u|Y3(~Uc}Cn8j%_98+)>ZGBE8n|-kCD*q+@MSkw93e>B_XVSH8<%?*IBZ
z+d4}lbh8$pia)FW4%W6?&+=a_C|Md*H8s0pN`%9`Wxp@Dzx(l(S7!GYh8mp%h1$Ho
ztV^G0JUn06u<KHoMZ)>MfMU(I4VSmQTfzNlK?2|Pe|MreA1&PX<=1qt-*?N58#w;>
zP0DLde^&eL$Ck*6HB!FM6GhrD<_No=%$avae7^7b#lN}}Z`yy#Kfc+~{{D;jXZulN
zc=K}64oLJEiQ9o<Wpc5&A(&n+ZU&|wi0grAK?xHu?IGa`rYA^Pg6T67&R|+d(jH6;
zN=Q%6my`svyCorJo{_YG%PC1g<m{xZk>a{Z3S!%CDQU);ldnrDu_=iIQy~KYtiAnL

diff --git a/assays/S6_RNAseq_analysis_khd4D_vs_wt_hyphae/isa.assay.xlsx b/assays/S6_RNAseq_analysis_khd4D_vs_wt_hyphae/isa.assay.xlsx
index b29d16640ed9f81f2d9626184ff1456fb4f73316..302fac396c7060b7409ebd25ab51023e6bdf88b7 100644
GIT binary patch
delta 683
zcmeA$>onsH@MdP=Vqjq4V30{s*~r_@$PA<>PiIsF(VKTO@<Rm9GRc7@-Z80wB}AF!
zAQEOQnqYw>mhDVnh79{Mh|EzAh|)J4yV$@oEBWVvl}z>$g2)sKt!Lx}S`+c;;<C*6
z$(kaX^^+asyPPK6>I$ByC3<C*`SrL1svC8yGf&*VUMb-4^vdmX=iXGvpG#}s#8G#^
zYUR}_M;3RmEZ89yl)Eft>zsCem4Xvf5?aFyR81|6PUjot1+CNF6P0^l5sP?*^3$Na
zWhvbmL0+==olf34p*=<Y`mJd^wp*mLB<^qIy`a+dE`ziF1dFqq^x+FUeM`2B)NC-R
zj^4u76s)m;rM2(a;u-U{aBM3H=Z<>j6X~^vH)g8bNyplPB7v|_(^bdTUimJ6x&P?t
zXzMJE(9K$WD(6}Jce1wKdZxWKcvq05?P*gRFCB&a%e60*xBvge))!mFU?=uq$5ghz
zbFDrpJv_g$dDo>di^TJB3!Vk>BreXq8>s%o@t};}pPko*jwIK<`l>(m>+ZK{41z!A
zF1gFrf9Cg(mz9?4l|rhM4Z03zZ0ea@GH1#5@AG}ni+@!=ys7@l{XX~Rx_#aCGygN8
zMDgYgq8*U<u@<)jMa$$GaYHb@LEH>XzZBO4(*jb`lT9Tg!R$Z@S1>(O!V*khm2d{r
z(vtRI8l<*D5~6mBB*fgSk`_=o6EN*AWsMZs-BM=qpr}vNb*_tHWMC*^VqoA0rb7f+
OGWmg&5}U3#NCW_%H~7c^

delta 682
zcmeA)>oDUD@MdP=Vqjq4U<eOU-pJd|$PA<>PiIsF(VKTO@<Rm9GRc7@-Z80wB}AF!
zAQEOQnqYw>mhDVnh79{Mh|EzAh|)J4yV$@oEBWVvl}z>$g2)sKt!Lx}S`*=VX6CiH
z$(kaX^}-G-x+W=X6<w|rsujBWUQ9LP^dsBeELE(Jf9|NDwftULS=#a61-opfx_)53
z=DF5L$X`jQ;Zc;w*3&0$r-|O1d_Xa{Ni@pQEvq19=KZC2RAQnlHr{G*<<$G&c1rb5
zN=ko*keBRz=aYAiXirh!erp<!?H21S3HuGQ7cxb3GdSx{usFL(AHKlTw`99W%?1<q
z=q+qb!5Rx#TKkSoo)Nc&V_S(ichoblNUt@#cc#oc=~!D-BoG#Ax-xC;mGAPG`@eq9
zw$9QB-K@o@;?L^8gSG9}v;0>JN|pvyP0g;D65()f+3ySP?|yvcmD&A;p+@IGp*HU?
z>(VD056>4i?79?Yk#N2*pjfkQ!{u%7R&ak>kid8S-<@dAM+^6T`8D0^_uVq%297^|
zlk%F=pVfZ*u_bb1jg;^6M3MH3Il}HIbLO29pYMBq@vrX0oA#gbk8gIgzyBis*?yE5
z-n>z?0}?$p;&z}|nOrMw2&OlRn}O+9;(B0OP)d5TnS>;m9VFojre{f5g6V4#&R|+b
z(jH8M)K*GD)J~Ozn0rmq0xD+$rah#rk>a{X%1j;<^J%)ybuo+#3?)nq4E(@khyaTx
NKa^5p(-8-W007D1{+j>*

diff --git a/assays/S7_A1_microscopy/isa.assay.xlsx b/assays/S7_A1_microscopy/isa.assay.xlsx
index 74d64fcfa09884cae09240a3e6733e25e57f9c79..e4e64663ad458259d2ce8d7b35a7c2edd22b1692 100644
GIT binary patch
delta 672
zcmexr`qh*-z?+$ci-CcGgFz-mWg~ApBQubmJe^SyL~q{B$PW=X%OnSu*vKIw9AA{0
zQ>>4oakD7197LfRizZlS63ccbFhhoY5=3SrhYDEW2FEToFk>qJJg}0<W<n5|SfTZd
z96)O$9$j3PIax$Rp+4`Bfxw>c+DiAECp*Y@IZe3L6+BT(^vWvp>v0EEH|kbrp16O#
zQo!NqmD}gey{V8tm)5?Cqwav!%Bxe3Ebd@gutO{;cUj8TIqm!^1t+E?w1yd|npzm0
z&Ns>nTBo}wD)+!57V!$@r$KqkQo1vOykze?oxF2Gdy4w?Thn-Kw@7EzOWfbcdqJh^
zT?Xd~7H2o<!xwn^mTVWP*<ex~y@jnQSYrW8Yu~ZOGv;mK*j5tG9res7(rXQG%v8CP
zj<p3v0%4)1tB$R`@?HLN|IyRY)>#^%o3;2<&a?RMWNo|kOnYnat{_R<)223FItuxh
zYhNgD|No1vFSd%oPVB*ssce7eT4jGydU$?g^R7!_7U$y@JPYDUT%3D1Q2mMHK^eV2
zJFg2JNv?hMRe$Q&-EY$v1b@t3a+j_D%<msBD=pP4g;XaSbREvv)HAtc&XVol=lh-)
z|Ehj?Q~i_seeTV5`?~9A{%1ms!nvXykciR{w*$q`<V<lxFg;h?3`}1W*8|gkC8Z}T
zNl1d(b`q{&x=q3oOdpbP2Gbmp_Fx*MHdPX$wowvd?jcDFsGJFyHj%PM#Co}uIaqL`
GlnVg5zWwL`

delta 672
zcmexr`qh*-z?+$ci-CcGgCRUbc_VK-BQubmJe^SyL~q{B$PW=X%OnSu*vKIw9AA{0
zQ>>4oakD7197LfRizZlS63ccbFhhoY5=3SrhYDEW2FEToFk>qJJg}0<W<n5|SfTZd
z96)O$(u0?EP8JbSsP{W;Ah74N=*0J(leaO6EM3X6LS0KSkmXU@o80VKH>T}XJ$wJL
z%`CG;>Uq}In;+L&M9Z93`oZ{mNm%hD7eh{mLfs{|&YiqnC3$c10ma}Z(WrxSt~@xQ
zwEyG|&z;*oByDBv7K(Y$JH>nF%*nEgJT*&e*j0-shHLoeZPAsi%GiFT-e6yP^n%G2
z`<ALI2=hqh@;Dn?Ou85J;ov2ioQqN%ehV9fM671HaN1@I=Db`dw&hIgrYRB9JG5*k
zHvf9@L}AS;tyRm`Uim)%LjTpz+16Pap_{e%RL-;b?__Pe^(;SYeaTXzs)^YZQz9Jh
zE&F}J{oRMJyfVALFx2QADAeZtWnG&6MC0N4jqSTGg;|{M3n<oX+i-Q;yA{Tt79{Y6
z|GOj2`Dmft_g~Xb{kmIb+`#e2?^0f~`m@?!Keoh8suA)}OPtg4v1IO%mnGBAy|bG=
z&;4uq;Z5~V?)RxT*X_Hw|4cn2Y81{D?SMp-hPWLlekNy%8-nS%;$~p_nz$aA{wpax
zSxG_?%(jzo1=DR3mSFmjgfp1tkhBNWAhoHI5Vehx5OWVnT0rGYz_f{!H6qr_rOd&C
H8>L(TR!j#N

diff --git a/assays/S7_A2_Kat_protein_level/isa.assay.xlsx b/assays/S7_A2_Kat_protein_level/isa.assay.xlsx
index ad5d45abf8b31ba4ba7c34ea665fdcceb0714fc8..d365691194a2b286a60e6d646fdbc454c1e7c212 100644
GIT binary patch
delta 676
zcmexm`pc9zz?+$ci-CcGgFz-mWg~ApBQubmJe^SyL~q{B$PW=X%OnSuc*mpymJnr@
zgGiXMXo3ZjShh2P88YnCAu`)IAWH9Y>|z7U%;KL1Rx;UI2qKdtw4RXzXidbUi_0=6
zONuDe=N&Q-*z;Xm>3;KM2l+0i3Aeg}Cu)gaS!I4b?ttn>-RjH}_pet9I6S>_``o!V
z74qlO+Bb339k5z?b;^;&9V`oWhy~>?OW8W7onNKk#FT{AFauRn3!~HdMtMQ&boWH%
z9$3U8UZMOnC~sLxcSewx?0u(`cTQ+eQNMm`8jtN3>8yH*`x|*LsC2!{;5@<N>?VEq
z0#DzP?IJZBOsb=|ur&p1EMRHvJGOYnye%BtO2WCLp7}(2t>KNCDtFScwxCELEYx(>
zv9(ve%U|w4dOF%VOCxl%7N5#_7XO{BZMU9jZw=lRBx!rv)W%CkA^&pi3+3(qf3fw&
zRx#L#J=igo?eAQx`cFy^&u?trbt%l^eB6R(K|G0zbMFSKKXE)LqxWa$b)h54wXeSF
zPyM?4Z5o5%kGV_kvh|<&{o`e&rFx~1>STki!x@`;CYQ`vvi<vf-}B;M)emo~e{#Ri
zy}52*cm2%&Oek?3k*4ch7sJTFP{PE(zz<9T6*>Bww~3ZOB2QP`4ismT^TZ9o^dfOH
zFnwEG4@~<@N>5gokOZ@xC0xODw}d5_J}%)5rg<gp!L+}m37Bq^gqV3;(gG?jJy})?
UVuq!ZH6kU{NST8bY?E>U0R7?p0{{R3

delta 676
zcmexm`pc9zz?+$ci-CcGgCRUbc_VK-BQubmJe^SyL~q{B$PW=X%OnSuc*mpymJnr@
zgGiXMXo3ZjShh2P88YnCAu`)IAWH9Y>|z7U%;KL1Rx;UI2qKdtw4RXzXiY?V@UqUy
zk|GNAeuoVN_Iwtd_`Y-UHYSm!D_K^kYbge@JW6|$n?38sw7sfl??1MgWwuB?&)RzP
z<64VonbS%?7+)_5E1u+H$mvk1yX4lnleeoR?@d0S7~CWpb#Ts=2Pc&FpWNZObK8fc
zt&H75F%NpDc<-D!S$2`9W@!z(YVpKy4gb6?x{_5H+pp9c>`RYcFxg_?QdI?E9?4uD
zXJd;=_kungyd;xzQHsNFVS|u})hriI+iby{m+Qo~oN3)OB|>_KmhHsmUoW00tXZYC
zYT4Q=-{)WGzxp}bI!hyTvlgGqc^3bjtZlcR<!7xgS!z@@F}q?)gu}gMzc0AI`|y=l
zX7?9{8l3}$+PuH4OY5I#JUqX#eb=Qhi}QT}#hPs!u5Np`!uZpI1itWpcceKVEwuao
zYx=2Qcgu_$IR5xu%4=4CR{QJ6mbghZLjGxqb6P%@%suk5WZJoRcC+WXe@#EUss73R
zKK16heHZtisb@rq>xeX6=eih128I$Q1_pj$3aH4@-@Hw<1QL0=;&z}oo17<Z2&NZ_
zn}O-u;(B1(Us8Iqx`ZT{?JVI6rn@C9!SrznXE4nxX%D9TB~8F|n<T`{<B}Foap}pj
VQV=sNrK}Mtp+?FatYDjz3jiTr1~UKv

diff --git a/assays/S7_A3_Kat_mRNA_level/isa.assay.xlsx b/assays/S7_A3_Kat_mRNA_level/isa.assay.xlsx
index f37832ab8c29e5e3f8dbfe5c82e73af9878ffece..5fb9c73a6ae521207c49cd50b34cbd451e826fdf 100644
GIT binary patch
delta 656
zcmexq`qPv*z?+$ci-CcGgFz-mWg~ApBQubmJe^SyL~q{B$PW=X%OnSuc*mpymJnr@
zgGiXMXo3ZjShh2P88YnCATnDyAWH9W>|z7U%;cX3Rx;U22qKdxw4RXzXidbUi_0=6
zONc1c=N&Q-*z;Xm>3;KM2l+0i3Aeg}Cu)gaS!I4b?ttn>-RjH}_pet9I6S>_``o!V
z74qlO+Bb339k5z?b;^;&9V`oWhy~>?OW8W7onNKk#FT{AFauRn3!~HdMtMQ&boWH%
z9$3U8UZMOnC~sLxcSewx?0u(`cTQ+eQNMm`8jtN3>8yH*`x|*LsC2!{;5@<N>?VEq
z0#DzP?IJZBOsb=|ur&p1EMRHvJGOYnye%BtO2WCLp7}(2t>KNCDtFScwxCELEYx(>
zv9(ve%U|w4dOF%VOCxl%7N5#_7XO{BZMU9jZw=lRBx!rv)W%CkA^&pi3+3(qf3fw&
zRx#L#J=igo?eAQx>`zJ$&u?trbt%l^eB6R(K|G0zbMFSKKXE)LqxWa$b)h54wXeSF
zPyM?4Z5o5%kGV_kvh|<&{o`e&rFx~1>STki!x@`;CYQ`vvi<vf-}B;M)emo~e{#Ri
zy}52*cm2%&Oek@^d7)?rB%*Z0?LhG}Iak~eOfM8S1Jk#}^}sZvl=NgZ2}v;9Nx~IO
ycS%@+>0=VkV46qL9!!JOW=cZTwn{?GJtk=Zl`{d;7E;!TSg)2c2McbMasdGE4fvV>

delta 656
zcmexq`qPv*z?+$ci-CcGgCRUbc_VK-BQubmJe^SyL~q{B$PW=X%OnSuc*mpymJnr@
zgGiXMXo3ZjShh2P88YnCATnDyAWH9W>|z7U%;cX3Rx;U22qKdxw4RXzXiY?V@UqUy
z5+VxqeuoVN_Iwtd_`Y-UHYSm!D_K^kYbge@JW6|$n?38sw7sfl??1MgWwuB?&)RzP
z<64VonbS%?7+)_5E1u+H$mvk1yX4lnleeoR?@d0S7~CWpb#Ts=2Pc&FpWNZObK8fc
zt&H75F%NpDc<-D!S$2`9W@!z(YVpKy4gb6?x{_5H+pp9c>`RYcFxg_?QdI?E9?4uD
zXJd;=_kungyd;xzQHsNFVS|u})hriI+iby{m+Qo~oN3)OB|>_KmhHsmUoW00tXZYC
zYT4Q=-{)WGzxp}bI!hyTvlgGqc^3bjtZlcR<!7xgS!z@@F}q?)gu}gMzc0AI`|y=l
zX7?9{8l3}$+PuH4OS7M7JUqX#eb=Qhi}QT}#hPs!u5Np`!uZpI1itWpcceKVEwuao
zYx=2Qcgu_$IR5xu%4=4CR{QJ6mbghZLjGxqb6P%@%suk5WZJoRcC+WXe@#EUss73R
zKK16heHZtisb@rq>&**AJ0KCIBW?$ZpUJu6hG2T3xEYwfC9Vgi8KtBrt4T<L*-jF!
zV7g1f5=<YHa0b&nlJ;O4q&8C$qPA5MV(u|X3#gn4n6{9zM#OrxlsQ;%tCR}>eR~1Q

diff --git a/assays/S8_A1_microscopy/isa.assay.xlsx b/assays/S8_A1_microscopy/isa.assay.xlsx
index cfee95c266daee817e3851a4ebfaeab48f7feb4c..c8a7d3a5109f4d18f5073758696024073f31c086 100644
GIT binary patch
delta 672
zcmexr`qh*-z?+$ci-CcGgFz-mWg~ApBQubmJe^SyL~q{B$PW=X%OnSu*vKIw9AA{0
zQ>>4oakD7197LfRizZlS63ccbFhhoY5=3SrhYDEW2FEToFk>qJJg}0<W<n5|SfTZd
z96)O$9$j3PIax$Rp+4`Bfxw>c+DiAECp*Y@IZe3L6+BT(^vWvp>v0EEH|kbrp16O#
zQo!NqmD}gey{V8tm)5?Cqwav!%Bxe3Ebd@gutO{;cUj8TIqm!^1t+E?w1yd|npzm0
z&Ns>nTBo}wD)+!57V!$@r$KqkQo1vOykze?oxF2Gdy4w?Thn-Kw@7EzOWfbcdqJh^
zT?Xd~7H2o<!xwn^mTVWP*<ex~y@jnQSYrW8Yu~ZOGv;mK*j5tG9res7(rXQG%v8CP
zj<p3v0%4)1tB$R`@?HLN|IyRY)>#^%o3;2<&a?RMWNo|kOnYnat{_R<)223FItuxh
zYhNgD|No1vFSd%oPVB*ssce7eT4jGydU$?g^R7!_7U$y@JPYDUT%3D1Q2mMHK^eV2
zJFg2JNv?hMRe$Q&-EY$v1b@t3a+j_D%<msBD=pP4g;XaSbREvv)HAtc&XVol=lh-)
z|Ehj?Q~i_seeTV5`?~9A{%1ms!nvXykciR{w*$q`<V<lxFg;h?3`}1W*8|gkC8Z}T
zNl1d(b`q{&x=q3oOdpbP2Gbmp_Fx*MHdPX$wowvd?jcDFsGJFyHj%PM#Co}uIaqL`
GlnVg5zWwL`

delta 672
zcmexr`qh*-z?+$ci-CcGgCRUbc_VK-BQubmJe^SyL~q{B$PW=X%OnSu*vKIw9AA{0
zQ>>4oakD7197LfRizZlS63ccbFhhoY5=3SrhYDEW2FEToFk>qJJg}0<W<n5|SfTZd
z96)O$(u0?EP8JbSsP{W;Ah74N=*0J(leaO6EM3X6LS0KSkmXU@o80VKH>T}XJ$wJL
z%`CG;>Uq}In;+L&M9Z93`oZ{mNm%hD7eh{mLfs{|&YiqnC3$c10ma}Z(WrxSt~@xQ
zwEyG|&z;*oByDBv7K(Y$JH>nF%*nEgJT*&e*j0-shHLoeZPAsi%GiFT-e6yP^n%G2
z`<ALI2=hqh@;Dn?Ou85J;ov2ioQqN%ehV9fM671HaN1@I=Db`dw&hIgrYRB9JG5*k
zHvf9@L}AS;tyRm`Uim)%LjTpz+16Pap_{e%RL-;b?__Pe^(;SYeaTXzs)^YZQz9Jh
zE&F}J{oRMJyfVALFx2QADAeZtWnG&6MC0N4jqSTGg;|{M3n<oX+i-Q;yA{Tt79{Y6
z|GOj2`Dmft_g~Xb{kmIb+`#e2?^0f~`m@?!Keoh8suA)}OPtg4v1IO%mnGBAy|bG=
z&;4uq;Z5~V?)RxT*X_Hw|4cn2Y81{D?SMp-hPWLlekNy%8-nS%;$~p_nz$aA{wpax
zSxG_?%(jzo1=DR3mSFmjgfp1tkhBNWAhoHI5Vehx5OWVnT0rGYz_f{!H6qr_rOd&C
H8>L(TR!j#N

diff --git a/assays/S8_A2_relative_fluorescence_level/isa.assay.xlsx b/assays/S8_A2_relative_fluorescence_level/isa.assay.xlsx
index 9713d55d00fce86a34e4baa7de16cd43ed8a77fd..2a57df1dff4d4cab7b38b6aec8a7905fa2241052 100644
GIT binary patch
delta 676
zcmZoPYc%5x@MdP=Vqjq4V30{s*~r_@$PA<>PiIsF(VKTO@<Rm9GRc7@-Z80wB}AF!
zAQEOQnqYw>mhDVnh79{Wh|FFNh|(t<yV$@o3;E}Pl}vULg2-eFt!Lx_S`+c;;<C)i
z3L*;id4~)H_I%e?y5Bt6LB7jr!mY00iCUspR+(RqJD|Ezw>tC0{p*zi4o|P#K6ma-
zh5Wg+_Dvjh2dq|JopNMx2g`yTVnMmfQnt=%=T|8>F(sij%s|!D!sv9qQC`qG-91sc
z2Nto2S13OX%3GGwoe|_Ed*A8gofFzq)UV%~#$&rhI;&pd{zl#lDqZg~I8U%RyGb9u
zz|*&6yGYFjlj`U#Y)!!$3s_qFjxC-sZwtq^l5p;*XFic$Yj|U(%AItqEhrKQ3pHJJ
zZ0(ir@|XLMo{qN8(g@wG#iw$f#eXMj+pTBXTZ4B6N!p$^weiwX$iH0sLV5fDUu=D`
zRSb4w4|Yst`#aaF{*%(f^BbFYT?(@}AGhFH5KrRb+`ED5PaF@*=>6GwUFb-1?W?c)
zQ@`$ho5mpcWA2i>Z2f0`|9Dwxsa`3hI@zG>aK@&d$t81^Z2vyr_q_O5^~0O$pWN?r
zZ?4<dT|e_b6G~i1r0F`>#V|53lrS+c@B>poMUMXFy`m+M$TJbQ1I5|oQgK5ty;9r^
zOg|FW1Jj&R(v$ThB*APi30E*ZNx~9LpObI~(;|}gU>c;hP!giHR}y0GIY|qsoC%nA
Rkg`Ukgk~vou;5-P7XavQ{4oFk

delta 676
zcmZoPYc%5x@MdP=Vqjq4U<eOU-pJd|$PA<>PiIsF(VKTO@<Rm9GRc7@-Z80wB}AF!
zAQEOQnqYw>mhDVnh79{Wh|FFNh|(t<yV$@o3;E}Pl}vULg2-eFt!Lx_S`(2TysUGw
zf`~%B-(drRJ)cD<zVDp8jY(wbN|qJsT8e=zkJ8@cX3x4YZLjLt`;TpAnJrS!v$o#+
zxYi<C=Csle#@9>2iYK`kayk_1F1dB?<n1cSdy@|+1~-XD9h`IJ!3m}PCwF-6-1Z@9
zD`U4%%!A%3-aBVbmR;njSz5!cT0Aja!#{6}u4Gll_AB)U`_iKqOt#p!R8>KkM>3bk
z+1O&zy`T>VFUjOwl;ZGP*dQcgHOqz5Hd`>~<vOt~XIeK+iICo*WjnF?*NZ0#YgTEk
zTDJDe_xTt4uYS(9&e90oti`8tp2dGBYul}7`C02rmKs$}%&wRc;c#!+?+fnlK78es
z+5Lr~M(04GHt#R%()uSF56^FG-*qX>;(T8~v1Z$btJ~hKF#fb4fiL{u9cj)-3+=xD
znttln-7@0_jz4~v@|xA3)&BaiC2mrUkbhd@oR*IzbC0|%nRf1--RybpU(*k7s(*67
zPrbQr-^KlB>KReuIwDQixh{s0fuV$nfq@^G0xEL!H}4fKfkd8(xE(0YCYOpEg6Wmw
zW?=e}xE`41l#-sTCm{)Ddr7#0=}8inVEUYdGnf{Uv<K55wS|%pwY`!MbI(ayK;=xp
Tw1bp2A|*6SnS%xQO1S_43G@YF

diff --git a/isa.investigation.xlsx b/isa.investigation.xlsx
index 0a4e38e7491fd9ee4915e111a6bfd3bbdee9b612..d1b5cacbe5d8aad87ab3d8837a44c9a592692267 100644
GIT binary patch
delta 682
zcmZ4Cw9<(;z?+$ci-CcGgFz-mWg~ApBQubmJe^SyL~q{B$PW=X%OnSuc*mpymJnr@
zgGiXMXo3ZjSgtaI8CDz%*uYBf@<Eic@b3Z(Y(6MDj|nW3Bmt4>l-SJ33A85S(Zyw%
z@snMpH0vij$agtSxYZRrQA_m7D)Z}c2UIueR%f2Lf4x$`;pvsz=gz&UkUy8!zKNsm
zfYr*YQ;sa|U|Fz3EGTzb%GNpU{3-<}rX;k68K|0C7@f{H$_rYjyC*95z#<m$3gxFk
zdCO9|GlINi?>n8mb3%KH`t@7Wcx<;wXGz@O$a_Jh>s<zC{RtLlH|fI{c>0!X7pd7`
zQXRd8ttnVz0ZVJ&vBfjyZQ<Bf63!j<%qP-o4R6d;xs#5y1w{g3p{A>jt-bPH{&N4(
z)6v#h8ljuD_*Blb`0r$GyY)<aYw)fhN!!z=HeNak`Il>7C~yD&i>)uVios6o!H%hH
zf9G0#QhIoPWAm;{VHSz!;}$#%;z?YbdpA)1iQ_>Ty+1pz3mr+Wef3p;>et<G(-;JQ
z%w2Mqt^dsLA1^B{)hmTmCmVDf&e+s5xn$0g?ceA7o)`bBet1*;lly({&2{^_>u3IF
zLW$zdXQX=|F&8as2ab(7vW8&#f~*;s=9JR|(*_FClSAbs!R$ggS1`R(&Js+2m2(Eu
z*7EjX8l-lHJVfmld5F1R<t?CcCSW>U!5S&DS1XvwgQC8x=Gp25Mh1o&CI$w6U^+yA
N1Ctb$*nDL{0suu2`+fib

delta 682
zcmZ4Kw8Duuz?+$ci-CcGgCRUbc_VK-BQubmJe^SyL~q{B$PW=X%OnSuc*mpymJnr@
zgGiXMXo3ZjSgtaI8CDz%*uYBf@<Eic@b3Z(Y(6MDj|nW3Bmt4>l-SJ33A84{^~}s`
zag$x8H0y;OR&-5L*ebeQDO4+T^}U#C#_314y;-VQAOGA@L2LQFva+<}zYBKROm+Rh
ze9d#Mk&wTVP{X4rkFBRq+)fj{H~D~KaFb}1qgz%%%FO#q@2JE?S8Tl1;L54@!R?gl
zos^XR3?VPs`_3ot9MPVlzWvrT9@{O}SrYaeWG`fj=w@)%pI~uzlRkWbr*Fx2k(v!A
z?$KM=nu0YJu(b9an>-_K3&*w+bMB~TUXfmFc<)S^cha%8s7N3z)O2Oq+AH7XFZX}_
zoNb+@5xQB6PsN|re+O&Zt!MeK7L+Uvs+yWzF(ty`-m>2p+~589$}6+`3qy_0fkJKG
zU)H5hG#;KWY}j=v%p&1@UqG>D+lI^A-mT#Nv><`+`oBBToR1dn`|@kL*YCS!#tj^Q
z{3hi!r$4Lx_G3%r#2P8z=ZPZi7juN&Pv*=!BR=2v{Ni8Ti8t*(<saYdXn+4j{ImTi
zF}(S#bPpurVr1>Wkug`+5KLc`H3QRJa(ZCeP(gZfn4Bb-T_ooUrgzC%g6VH^&S2U`
z-X2VY)XtQLsNE_LG54Fi1ys%iOlK%qBgOR^1v7b2%y-p1Tb;njz)-`)z`zeoh6u2K
NGNYmrn~y9=1ORGH0bu|D

diff --git a/studies/S10_membrane_trafficking/isa.study.xlsx b/studies/S10_membrane_trafficking/isa.study.xlsx
index 5f9a9f180351650462f4a39f1d3ef08bbd0da8f8..b5ff08c1d6b5a236c22ad97af38a7b678fc9817e 100644
GIT binary patch
delta 676
zcmeCR>9yev@MdP=Vqjq4V30{s*~r_@$PA<>PiIsF(VKTO@<Rm9GRc7@-Z80wB}AF!
zAQEOQnqYw>7BLnuqng8$8Lad;H$>?>?p<tPnbkt`n7}eVq7a#4(G83oKx-l%U0jwq
zSzBD8KJSo$z@G2gO81*5JIHrAO}Nz+JW)&Z$}02gaR*d4>Q-l-xPQG;z~SkY+vm=`
zsgOUH*1n0O?ts<Gt5c3F?qFH4Lo6tFS<2Qq?ffbQC#EE{h8d`uS{R+qH_8iIr@JRA
z_rM|+@e1XqL3ztkx-){jWbZqjymLZ(iu(0i(|ByRNN3ec+~3H1L8a?m2ImPDXE*7?
z7kK)XY!|87U{W2ug{>)AV*yKR-?7Cr=568FRuaw~^~@*IYYlJARJoImwFN~2VWFn0
zj;+1&UH)?a(bLh^SsJ06wfI!dv-t01ZM*eMdu#BnAW7TPrZ!$W3i+37Unp<?|BJ0J
zwu-?{?7@zyY=7rk)qhfYcz$E^u1jGS=i?SU3*t#!oO?G={fXm28NEL{uL~VXu6^}Y
zf9luWZ_^kAf6QHSm#zQI?;kHKE!8W9R3{sB9nRR)Gr45WlI`E;`<@s7s(yG={geBB
z?#*@ky6b2DXF`eV2re5F*H}gdh7u+Q27X`)sL0XZd_tlW60HtWcHpRLlrjX<Tcymv
z^gAg%FfA`_0;a>HUBUD`X-hDDOWGMsE6CV`X?bbs$+a?)VD?NIh?%!!EZ}kmvJg2R
RS!+Z}=$ADID>y0Z0sy1H{Hy=~

delta 676
zcmeCR>9yev@MdP=Vqjq4U<eOU-pJd|$PA<>PiIsF(VKTO@<Rm9GRc7@-Z80wB}AF!
zAQEOQnqYw>7BLnuqng8$8Lad;H$>?>?p<tPnbkt`n7}eVq7a#4(G83oKx-n>gO_zq
z))rT&_d9GLu;;Vr#P^+(w=sz<UCFXST}v^L<x$$3-0WF5rtMWdd;hV`EVD)GdDhmO
zAJ<w$%bZsF!T5SfSn(tmLr#Z6-6glqoxEKod2jLo#o#8<sDpE^JUF4W|KtwOo!dSn
zZDs5hih0mG#e3(>$+C+)HA`#QRf{KvYxw7F(Uq*q*nXwnU|)Llg2@*9mZ~ZU^GN3M
zI2&6`x)=1};3b)yi&7kZ3mb$)tY*1z+GY#pyj&-?<xK0QDG|~;v}`9f|9bI6Va+P7
zRm;|1`9A+b|JBdg)>#^%o3;2<&a?RMWNo|kEI(^~$x@@LiP;rXA{_25`+dRv-G{Hd
zGP}Pp)aV>2)aLzVU0VM{<Kg*@?Yl08S)A_+DAsJ-aCO_e6~><yB=Cj*yCco{XrbNr
zU(-+hx?5)4!12fLQeLzAv)W%jw!}@U5%Nz<oYV5LWbTodCDYEmvztB7{cHN+P4!Ri
z_o+A6?Yp@DOg$q?Tt{%(n7GC=GBA`dF);80Q$R(I{^k=BrI2WKkg@|uRil(4nBFR7
z2BzOh>49l^X%jFVChZEQ=Sf?F>08pyU|K=O9!$$iOHZzqkp#16%0SG#C1U}XGmwSI
S`N&!$QbND1Iat9-Sr-7xb_Lu3

diff --git a/studies/S1_characterization_khd4D/isa.study.xlsx b/studies/S1_characterization_khd4D/isa.study.xlsx
index 20ffcc7d5d56a303314004d850963c23d5b382be..e11c4b82042a34658150c881fb10fe6d228f0ab8 100644
GIT binary patch
delta 676
zcmX?WbJm78z?+$ci-CcGgFz-mWg~ApBQubmJe^SyL~q{B$PW=X%OnSuc*mpymJnr@
zgGiXMXo3ZjSS(q<jCmYs%wVPLJP@UNJiFMyGOvZ^F@a@zL?JSpMK>^V0Ii95ba7ec
z<ZN+;`n*F10(-t|E8TCN>>%IeG~rfP@I)=qE33?}#~o1Js9T+R;{NqY0f(noZl62%
zrb7N)TKguBx&u}#uTD9#xPxWE4zZxzWhq<dwDYSJoS2f(8fKtsYGHIb-zYC=o$j8f
z+yjeP#4D7a2IVbF>COo9lD+SA^3DnEDeBj6P2;iMBArz)aepK41(mLM8Js6roZX}k
zU*PFmvR$NRgGqJt7Ph8fjRh>Nea9Bhn74&vTS+)~)H9z*uQj|eQ{_%N))o{AgoT=}
zI=1%8clpcxM^8svXK93P*5Xq+&*Hz6we8k3?XAJPf+THEo7#BkDCA$ReWASl|1Y+_
z*eV7)u?IV*vi+TFRsTup;rWftyDo)UoR3@ZEQlv@aqitf^(T%8W%T~+ye@Pkx%Smp
z{i$DfzfEHh{4saQUAF!+zkj@}v{bJYQk`tjbvR>F&*YLhOSXTX?|WYStNP(h^-u2i
zxi{DC>#m>qp9v+dBe-l#Tw@s-7)qEJ82EuHpdv?qGlyg;Bw8D!?7&fVP|6TYf0Z%=
z(|Xc+U^-sf1WZqpb_LV-q%Fa;l#DZ&PLQz&)A7>MllRI<g4s7^AZAL*TEOKBWFc}r
Rvet-{a9-9NtbkL_1ptIE{MG;f

delta 676
zcmX?WbJm78z?+$ci-CcGgCRUbc_VK-BQubmJe^SyL~q{B$PW=X%OnSuc*mpymJnr@
zgGiXMXo3ZjSS(q<jCmYs%wVPLJP@UNJiFMyGOvZ^F@a@zL?JSpMK>^V0Ii8g4_?+e
zIa^$z-tVx1z@E>d6W@1E-o_-dbS29QbuGm}mPcuCa<gaMn6_8-?ES|!v&<H$=UH2C
zeq3u2EpuAw2jlA{Va1bN3^^SNb(h>ack*_X<h{uU6oZ>YqYlow^5BHh{*yaAcW(QT
zw3V@2DCR-$6z`ogC(ADK)GV!GS1q0xuHm1zMOU&aWBZkQgMI1I3np9aTdJxc%p;l0
z<7{j(>0Z!>gO_A-E=qCuEo=}Hv6|(=X`3yW^KzZomNTuJrbI~Z(6XJ_{OiRNg*B_R
zRxMk5<@@{#{Z~I{TW4v6Zr0*cInUz1leO*Ev;3^}B}<K}CT3SmiEy~L?DqxtcOSm;
z%IyBaP@{98P@DIcb!q(*jfdwqw(q(WW^ukRpjfkQ!_{r?Rv3R;kiZxI?~XL*qlI?g
ze@#F2>u#BG1IHh~OL@)e&uV}D*b+CXM#w)caZby}lDS7-mP|YM&TjTR_pj-PH`PD6
z->2SOx9{TqGxdxpaUH>BW8xai$iPs-#K6E0OaT=+`kOf<OCizPAY})Rs)JI7VEU_+
z8JO0S)&tY=(k5VfnzSpJz9(%7rln+@!E}O*J(!M{mY%#<MiR`vDFZQ6O4b4{S0D?K
S>yfoaq=fUb=3oV!axMU><pu@-

diff --git a/studies/S2_characterization_HyperTRIBE_Rrm4_constructs/isa.study.xlsx b/studies/S2_characterization_HyperTRIBE_Rrm4_constructs/isa.study.xlsx
index efc129cad32a7b060fb2db637b293e044f314ff3..5f43db6a0b3cf95bb89f83a8bf500150fe9b43ea 100644
GIT binary patch
delta 676
zcmdmQv)_g{z?+$ci-CcGgFz-mWg~ApBQubmJe^SyL~q{B$PW=X%OnSuc*mpymJnr@
zgGiXMXo3ZjSd>`6jCPKEX0Xzq+z_P-JiFMyGIxdMF@a_3L?JRuMK>^V0Ii95ba7ec
z<XCZq`n*F10(-t|E8TCN>>%IeG~rfP@I)=qE33?}#~o1Js9T+R;{NqY0f(noZl62%
zrb7N)TKguBx&u}#uTD9#xPxWE4zZxzWhq<dwDYSJoS2f(8fKtsYGHIb-zYC=o$j8f
z+yjeP#4D7a2IVbF>COo9lD+SA^3DnEDeBj6P2;iMBArz)aepK41(mLM8Js6roZX}k
zU*PFmvR$NRgGqJt7Ph8fjRh>Nea9Bhn74&vTS+)~)H9z*uQj|eQ{_%N))o{AgoT=}
zI=1%8clpcxM^8svXK93P*5Xq+&*Hz6we8k3?XAJPf+THEo7#BkDCA$ReWASl|1Y+_
z*eV7)u?IV*vi+TFRsTup;rWftyDo)UoR3@ZEQlv@aqitf^(T%8W%T~+ye@Pkx%Smp
z{i$DfzfEHh{4saQUAF!+zkj@}v{bJYQk`tjbvR>F&*YLhOSXTX?|WYStNP(h^-u2i
zxi{DC>#m>qp9v+dBe-l#Tw@s-7)qEJ82EuHpdv?q^Dl`~NVFD7*@2^Kvy>s2elBGO
zrWK_1z;vLr37GDXb_LTHq%FZTkBl>z4wA74(}B{`lh?~gg4w5KAZGH&TEOL!WFc~O
Rvet-{a8TA9tl+n-3jnrD{xkpp

delta 676
zcmdmQv)_g{z?+$ci-CcGgCRUbc_VK-BQubmJe^SyL~q{B$PW=X%OnSuc*mpymJnr@
zgGiXMXo3ZjSd>`6jCPKEX0Xzq+z_P-JiFMyGIxdMF@a_3L?JRuMK>^V0Ii8g4_?+e
zIaXYu-tVx1z@E>d6W@1E-o_-dbS29QbuGm}mPcuCa<gaMn6_8-?ES|!v&<H$=UH2C
zeq3u2EpuAw2jlA{Va1bN3^^SNb(h>ack*_X<h{uU6oZ>YqYlow^5BHh{*yaAcW(QT
zw3V@2DCR-$6z`ogC(ADK)GV!GS1q0xuHm1zMOU&aWBZkQgMI1I3np9aTdJxc%p;l0
z<7{j(>0Z!>gO_A-E=qCuEo=}Hv6|(=X`3yW^KzZomNTuJrbI~Z(6XJ_{OiRNg*B_R
zRxMk5<@@{#{Z~I{TW4v6Zr0*cInUz1leO*Ev;3^}B}<K}CT3SmiEy~L?DqxtcOSm;
z%IyBaP@{98P@DIcb!q(*jfdwqw(q(WW^ukRpjfkQ!_{r?Rv3R;kiZxI?~XL*qlI?g
ze@#F2>u#BG1IHh~OL@)e&uV}D*b+CXM#w)caZby}lDS7-mP|YM&TjTR_pj-PH`PD6
z->2SOx9{TqGxdxpaUH>BW8xai$iPs-#K6E0OaT=+`kQ}AltQAlNXiZzRhy*@!Sr(}
zGcc_ntp}z9rA@$ehqNo0z94N0rg>zX!E}&}J(v!ZmY%#`MiR_EEdw!=N7e!^mm~|3
StCO`xq=bXA=3oWCWnBQ>0S9CN

diff --git a/studies/S3_HyperTRIBE_Rrm4/isa.study.xlsx b/studies/S3_HyperTRIBE_Rrm4/isa.study.xlsx
index d7b184394944957d506903292ddf73aa4d77bd2b..92e06844f1b257c57f73fe7246fd090c6b646bd0 100644
GIT binary patch
delta 2762
zcmZ8jc{tSj7ye=_WgD_(#(M2L$&#f)*D}VQecy_VEsDVmQ8CHVWW?awtBZbi*HVp)
zvJ+XdGzix&#3<X3(OtUVf8Oso=RKeEd7krm&U<z=$~2kHU^Jl9001xmP*0Hx=KEAM
zM~F?Q5<14JMk>}5M>jP;C9p~@LJ4rv@Sg-!K$6TyOxr2wjn6wY0APvr0|}wclSkFS
z^k2xk9Oj=Io43`#Agh=8zo)Gh4mg>TvzS?I;nQu3eq`<ajAhx(!o=FmXg&9xv7ov8
zv8rpY>)^qPsPY$M#nW!7V#Oun&9~kmzLSSd*Q|Y%;wm*BKV0fkiBi%1jv{x?wSNm}
zX@8PJjP@TXehU5`ienyZubxGJnM4k>;zqyKGOhOsROOM2H4|NY@y2po;X}Aum<#*R
z!8IjEr?HM@r%-=5x3f-@PY3w^#Vo&zO~o~Xy~LWL!&|GQt1nhOhy@70Fn-;E!m=Tk
zr0mUEk2CVSjnS3JZhlr&d;ns0Vsh~d`166leDbiP=M^sOEqv@ln?Q8-77>rcqrgj1
zuMDaty!XC54N5`p%(yOYjK^J^7`Wz<{1m*FYI5c_%fpqffI0Wfk!m>iz)b<Cb2$+G
z25rr?ZnM^Jqs8{5hLQBVaYR#u(R9~?u=L#xq(H0v__t5fmlxIM7r%dGU8h<908W-~
zY!z!<R<YxBQC!4{o9Cb-rA_lSgE}E&s8+-V$^|o!t`qJ%l#XnapZrQI!Rj3~r4sd8
zzPnzWcXpP%8EoR5w1FdU;<D;(^P2|!<N_UnUjL8t+Oo8xsa_0M7J-@`vm4{yEL=@U
z)vGv_W7K6KA#718EUpw2Z&hlLXbeu1kLFB}J(a&h3&Rq!Kxp&BJG4fw=I&SY<m^&;
zk_2ZMxcFjL4BjNUPO;f0i+nY}@h5B<=p=hCr2a6~?HU=h9u?`E;3WR-rm%>}$!>#E
z{T{BA{pz%6LAzR!+M;Jqp*YzDgyd<R=1eX>So^nXWBY_mYnkxVotAoNxHL}l?yO{f
zF()kN%?5}0fKiaQJ)9q!UM2p-XQ@>4qKU(Uk4~A@)aE`IFMD{7W`dEW%)n_p-J)Su
zjj&WH*Ru`J=T~iI&1TyzO3LkXJFrLIW%l?D5DrF=i`i+XrC^vV)rp-=H-urZO&0qK
zz*vnB@Mtz<bP;_yKYYK=bAhT<|I80_o(jiLKq}|a+aiIb_i_B){RI{L@cH*LTD<=?
z+fQj_7U_Fvspsi$ZmWplAt&sdtiA#}r1B8<3{n}E{1zGPi;t(!YAlKUSP!jlj;8li
zAn4tV>nQpC_qTNWpCFkqRdX&XD(}e6Tb~=lIt82<UPNhK$k=e*+maaaTX782YI6=g
zRGJzW?-^4g1Zjlfw|nSaM!~P4y@yNgx>ai{p@UMnZRwTq_1vFh%T|?{)(h)bmx!Gu
zh@HiQiu-}Qbw=-6#!$<lppS@)kz@fg80WucitT&(cDU%#WSGV#GC<KbPL|UO98qMO
z@dd25!C)wKm@3PjxWYs|z;!LsT?gOaRcxqgIC!uNZ)PoYv2xC>|MS!M%|}`H4ptm=
zrf3-r)gU~7zC1^xz!+vQf^?PHTVJT5vJm1D?l{ZOqmFyK^5vO)5p{OQ3?V+vD8Sf~
zPSGS~d7a}NU&0>-DgDW4cSMJkD@O;9N1EB@^zw3tG1!d`r0L=7>bS2W=rQARZ-pFl
z!($}fbHqls*CjD$x0rXk+kG<1%*&0%BtAo!tvR3Lux1bY)OP2^&D*a-t_0gTHH%}W
z7yB4GFQr)dIBf&8YmkimOPzTMhBD6OihG%?ZTc?k)>%UFUjYfU$dIk!Bpb&*Vf{&I
zL|{;`m1efR(1ob@{>2Z>C_HO|MvVwG!p<n7Trwy;`0Lj5xoNMGxHk6$w>T^2sqor-
z5rEq=QN$leI@PLh#ZXcv)b_SNZcsHr@1<}S`O~vV=|R~co?pp1n+me8{Dw1j&kdJ2
zovrkqT#~e>n)FCTM{|P0VCYQI63mK4_T0KL$o^nAD70m>b%IzSOUi)Xu%Gb7VBl7J
zD58*B!L9l0bJek>#;uNoID<hJ|B?Ad1yiB4cHJN+Vp*sEK$zdhEe*Fs>LSr+qYp^H
zmV+04-(9$5*~5FY;X^l>8DU0`TMD#8GYARVhiUuTLPltvG69EJjA9!H{irx~{>B@N
zX?e1_TD+?Bs8_Ar3|>lkz8t&6EgRf194>kl5hPgQO`wL?>E^A<NHK<pDLyseTx%2y
zE4z^|+@uI!iX^F~|Icynp#*w@XP(Z^Cs*UVoY8r(u5!8_zjMJ13FdB^6%LEJZ5eXy
zpeqNy2t}I*w$hkDSXRUf4@OY2A(eT-?qj~_;twQ-?Nr9Pp4S(_rehErM&G13YeS!9
zq2QHVbbcG^dvn8xrs38^%JbNU@yi0`uOj9J*h)&@dyj1UEiT!ZPRI>OEi8x|knTX#
z0?a*xSz@%<qtspX*z}e@5gaC8zS0=@m8dxsiC2x#nf=@dse5Ba^26_z=f|7f;q7VR
z`ZE}VmqviIhiV_&)Z`Q&V3qb*|59e)Sedbvj3>hTk+Fe}qQE%z9BPUrt8$)1oH@&>
z7>=cQ`hBqvmWx{u?f*sr+(ecZCdFbe31D<mMlqJDQk)-tR~>dHh*ro(__UFR!@-wk
zKaBPCEQbm7c;ByNKoKrHAAC$KhzI5V!DWFc_N>Xe&ngnw_Sp5VwSwq*HKon~C4Y+-
zvQ72~LOzH)?3Y;!|6<Pv*DZ|rNILD~ZPJg$hevTtTGbF=G!LnQxlaVMdi_)zNcUGr
zOCM8GVI4<gxpIU<HQgOciCoa#q_+i6a;h0>Lu?rB=Zx))N|_zg_}ec>1qOqyub%(?
zZP^F1z(8_qr-O#C#MLS(7Li_%X+7<|(K+cF%La?HTAk-LjbsD^2BPMFsXP2mm*j*5
zw7Dk#NTb`&zHnnhc&fJ|wxQozt=Bns&VtFU05M@MK6AMlDz{fZ%ue)(THKOP+iG0#
z2H1A83n%E3yLNXL!qvsY*+sDmn3n66iP(^=!aDMA@LujM@s>*T3@J%J7WL`@I^&S~
zul`Urr>ft05>6H(X<ltgTl{zxDVWQvLcx!`a>w|H4}ukioTa!fL#|LT0iyn&9jX_i
zE_mF^zh@^C0B{^_Y5#n&4A@i#F03|`>Bp(+ql^F$<|iL=-3#F*Zw8~H<^cX)>}((P
zoEJ}|0|25R0G#>fl%qc?CTt#5NZ_~{twyx-EouOuIU+LuM0$mtf<k{3qH@7P`FNZt
zFKvI?<t`Nfh#if0@J|W%I03*jz{4y!An>NVTVSAE7{c$rcRGHjE=Sp)k4m!rl&y|U
g<rAb_>9nTu6{jOk$PtJ2C(b);AD=LtIq$La|3bOUrT_o{

delta 2609
zcmZuzcUaR`7fwQCD65enB<vL_MJP(yAcBd84MG%A3JORPVq}95WDg}kkW@f+Sb~CR
zNT7^bWr)ZqGc>X(qog2VlvxR1pFZFB_5Sld?>*<9-+i8Qf9HLxjkXMh>`*-5;{X7F
zAK>DoR4bGK<oSYR3Q*w?>l%R~M;qNBS#E$0QsxH4d1Q|Qy5Q47Uoz3xXjH@^4*(!Z
z#)1`y)}%3AQQnDgVq8JEv#Nfksk<T46D-gRvdk&+er`2tp=@8^gQvALzoKCt!bEia
zwcL~YQJ1sZGZ>KvO}LkJLNRMBRY{RLqdK?Q&F6;L&n+#HVf7t#3fX>m>G4tPeQd(+
z-UelzEHWNn{8}3YWYu(%v^Sm=ovJLxbrV-6!pEq2%!Hx01A+-2^D*akRtspSXRyu^
z)daWwjGE)7<jE!Gm7w3AIbs^OAP}slNA~{RfW4LMA!pN*!`Um#11-<)kCi1NhUr^I
z@pD&QtD9j4avwa&Ham>~$0je*Be^M8mt&?|1|}u+1GVjG{WB@I(=%vGO(^fX4C3O|
znswC!dFRG^S(0Px^tCcV1~C?k$N2kB<?k=l1txe}Z6berV*0KvaO1mhn)M=crfz{o
zYL=>hq~o@n9~@NPzs{Vwb~9n*i4SdQBL8K;tYt%26XRDzEhIQK#~Ark)y-{VFD(d}
z6F*>r_g<R%(M|Hoc1bxV&m#15HPI;P^V@Uy-*?0}J9j)!e?%Xjt;nez81n>rYnX-J
z)sbNTvf19B8(w68Bh>W8%*<mrKGGEbks;xqSx;w3(D9+fs$<^l6W47m9%$-6K*8W_
zzGSJCUO@!pooa}>HmWcY*_oW%0akRVRn-3Wyi+s4S(&DsI3=lJ4f2Or5cf_<z#mv9
z9s5e(+tNcXI!y^30H!Gk7)Hk-+>JAOm9B;<4=D*4XHXFyM|5Up)N(#u!}#9kL`4oV
zOEzg8X->Mekd7uP|0{(r4kjKRPVOy6hlvdpms8ZUWaHN1<|K~=do+=x$bnb!eR`Pt
z<L*LEecBzo{_>vQ@>ARJ;9qVO8HsmM-)M^4=OxcNd`~gUEc0MEji}hocHXO~K^43w
zb9W!B9VR`1+qyHrze5t`g8vVV2LVe!bCDWO>r9JeAs;#nu+$eT>%IW2LJ&`eMN#=`
zWUcp7ZXfc$>3pAtvGh{kz)jyQ*+=U><|MC$J~T;{<MR(C4+@x*=BjP2B;fqU*;It5
zu}UGLj^k5RrhJr^87te}UtF7)(d+n<lZmzseO6|6BECs~WZYVh?$;shN;<zltc;_)
z>s$@z>}`F+`izh(#@}>BU^aBGU#sxK{4tFw4(Z(MYIDs0bD|&IuEMhZv?Cfr(3Z)i
z9V|H_>Xulu6|ZA&>r=Wi!)Xc)i#F|Py38)7l|d8p-HUy>dQv-q;g7vB>~uy4{v5*`
zI{^IG5J5ZQ_^A2&AOIkmoXrm-Qc(C}Ezzhy_QWO1HhO!5p0O)0JJ>@Skawb^ss<cq
zqApdP)5YY_c6ZJdib!iIcdPug)~$7h^mLMix!kHV1=2D2R+CSX*X*o^c4<y}t>DwO
zo4lfs{!@^PeI4*LEq0sQ1qEfhN~ebpt20Nd?<D)AIKX)|E;wC+v^l~DiAv)?C{FXY
zd8DLSC4~kO2%e>)jyx6`W%q9Vx_j2lX0-)2ia+sPTL^q51m1q0o@*pztuLEB`(~`@
z!!(GlT?A1(wHm+Mz8IXYAiK@p3z%KwG_cGQRn9LL2|&JTf8rE6%JZI%x8zlNEG+(m
z*{+n-bk8PmmrVg+E-D}gh@iAIe41F4N&$y2*C0d(;Nq<|`wK(-=d}c7j0<b^u?cdI
zq0)LM&HEN0NcDM-jfv@UE%;A^cSRc7KbTbrjC2iy5v>UD`3DAOd?&$kTDZhG$k#pH
zUK`dL69r<DF)oTXpg~>IF`Z}c%FWGEmK$%-S9ox@SK_1Xnu;U=M1`r-HAVbaCVSQb
zSpAyIzQC@~l77=brp!jxrp_?UJXm{}er;AP%i3u_(n9;L+TQ%F$&Cxnn)MH3q$FO-
zv3)oO5=gi|0Um61FOV6bAEe<rE+G7{<nnpfGm$_}wF6ITQfc9kWV|?dh^%@X#gC3c
zyk5GO>hSu&a2MxIBoUgr%n@SeSfZA$@A=2Xno`+??K`8s6F%P=gKme)22L_7cu}i<
z<yR>?{<!rwTjQ}c6jsz&dNt2;uj$I~c^r_(AH18?m0k;sTYj>%ekufdZC~;FNXipG
z4}$8|x5)O=Z8Of`K{V`~YIbtO;J#g7{>aWu|8Vzk@RV&JQE9QzsN+gjiHFD~mq+_H
z7dHk)KBjc{Td`Q>Mjc(!5oQsa^Y~*!zQy<gW=d#zDzBU5GmVPjo`MEy(A(?w!gC4k
zB(%&YF_d5uJGQE|qG2q<=FM1TNMl5F_p&R+l~CoE$BIN>iWZ2M*(sd5f6=a<DnoF>
zLBnwCX9x2|6IY3U{~v%uktP3j;z&b<1siy|V%i1C198<AD}EFqi`M}84^`FMu{4Q{
zl9VUf{H!JV<C=K-A4y~yNQ_zmE>}}mum?|h{f@(Ak7PBebdOIPW$PBH`57A4O-Jat
z!nzc<fJ-IL{uvh90%nA7N|+xz$HJsOky{lUqs6cNlshodq1e(%zr>)ec)SLtK(0?b
z%0w}qkY$Q4oesRur{bUP0=M;h^^H`RPyGN<tJ&MNfUMU{Rgpg_D1{Tepre=Z$zkQE
zei*h-n%|}{3L<8ZZ6RQc`3k%6T;kP-xR;q|C|%t+J!X4;M!u?2y|T1=U^Bm$G`NN_
z^o3ukQx{h50oyW;#WUydzApl(--e}QLNd{2pGtRn5$u(9Ay^{^a9^X9@U_skVIXk^
zKG{>7(9rL!*OO}Je>%Qqkj5_8`CQ;G?6UtWRA8#mWOJMHew!7f6UD!4)9)9fHW#tI
z_3B2(eTc2s_qnmF0Z-p91Y~_=o8;sn*1dmzNt_u^Rf~yi?rZr#1peJ0t_eaPH#%$S
z1_S^CzKk%DFV-jod!}ywRN#@{ahEpXwyIECn~Q_ex?B{7YI4yOdX|epP)ja0L-qg1
zAAw=|@`t^3#QkSV3IYIPUq18C3gjo}^Gk@>p@1MUz@a%idN-y}D3D6dgPr0QX277J
z4=2b&Fa<8%hC$_%Al%FP2ZUm8`)h{au>V#;oop|2Q~@gk1=^DnW#s;OYA<9YfM9Z)
Wj6ApI!k2^$@-bOOUYPXZCH?|7d#cj_

diff --git a/studies/S4_characterization_HyperTRIBE_Khd4_constructs/isa.study.xlsx b/studies/S4_characterization_HyperTRIBE_Khd4_constructs/isa.study.xlsx
index 3deeab54a15dcc7d518d48b95b8d973d11252c14..01563f2651d944961f214e4cc4f92eaae84b50f2 100644
GIT binary patch
delta 675
zcmaE4{m7a(z?+$ci-CcGgFz-mWg~ApBQubmJe^SyL~q{B$PW=X%OnSuc*mpymJnr@
zgGiXMXo3ZjSj1SsjA{-!X0XyZ+z_RQxp%RFWg3L$F@a?iMIkaCq8k`FfYwAjy0|QJ
zlDI;B-XQ~lJ>RvJ?l(_%kneJuaH}hLqL%2DRp!^@4ybO_t<F4g|9Yi>!_zCb&z*Zy
zA%8BdeG^CB0jrf)ryN<_!Lne7SWxb=l&y2x`Be%|Oi5@BGf*|PFgl%Ylozy4cTZIA
zfkiCh70OS8@|LA^X9Ri4-gi2A=Y;kY_3O8$@z`#W&Z?KVzmfNXO4qv#&J!%oZqkP@
z@boR&E>g3>q&j*FTT`&c0+!akV~c0Z+rqJ}B%C|ynNOtG8s3<xawi>Y3yK87LQPj4
zTYKfZ{N?_mr=zX2G(tCP@u{3=@!!eXcI%n;*5F-1lD4N!ZM<|8@-NrEP~QIk7h7L!
z6@#7FgB?@Z{?4_k|D^Qr{Kn>8m%=R0$1Qjk#FMx<_imv26UT!xdVh9a7dnz$`|7Ly
z)UUhWrZEWqn7iaITmPBgKVDW^s#glBPB!Q|oUy5Aa><+}+rQ8EJum)M{qUyxC-?i@
zo9p&<*U$XVgc8*eTs9`Iv5X81B}@zq{J;cIk)ywPu0$y$Rz;=kz%dmjWeBFbq|Ctd
zVJST@{Ypl9GQYGWn5`}C3Z{#tEy479X=gC~RoWg*gVYAeK-A{RK+Ih)V*!;j0n>`I
R*6@TdIYrhSEI3cr1punb{NVrq

delta 675
zcmaE4{m7a(z?+$ci-CcGgCRUbc_VK-BQubmJe^SyL~q{B$PW=X%OnSuc*mpymJnr@
zgGiXMXo3ZjSj1SsjA{-!X0XyZ+z_RQxp%RFWg3L$F@a?iMIkaCq8k`FfYwB$2QTZK
zB(6~Jci2E+&u7tz?>i@NV-i`ql4XUumSP~wqqH}<*|Tm;+pBu^{$rb2W{cGGtgSac
zuC<7kIj!`A@%56h;z=%soDPM$OKzPzdAmyT-sA&{!A+u32j^UQa6)PS$sL|Mw|z+3
z%GfOw^PqQ%_s*G<WfysBme#PV7EcV<@Xy<#D_NDX{Yt&TzVzq?lP&fwRaFq?k<8_B
zHnx~_FX+R;OENhZr8xW+HVBDW&2r(i%@)jgxlU}$nbu8HBBXa{*-mW!_2P-bnpIk>
zmaV<=eg1|1tDm#2vou0CYw@X^XYt?3+IH(%e%AVurAAc~vn!@VINV$I`-1zs4_|p@
zc7I{0(K%44&HKx`wEl_4!}A;4cU=mzINujgtl75V>b7?)j6W?%;0ynEN1F4|Lc8z3
zrl0zCx6HVK<B#8^yk_-hwZDFBiJMd-<e!!}r{!bG+#@ebrk#6dH+!D@*Yv}i>Yv>2
zQ*W-@cX9ujdPbC}j^MH}agAkUU?^c?VBiNPfQlUb&2uG6A+ahdWe1L_FeyVY-6drP
zrVmT$f$3K=(v$h6CBbZMX;&~^ENuy<*GoHt>95lEU>c-0NCu)dPX=P{dKn9-oC%m#
Sl(mK@gvlwg=3v2jvMvD1qXrQG

diff --git a/studies/S5_HyperTRIBE_Khd4/isa.study.xlsx b/studies/S5_HyperTRIBE_Khd4/isa.study.xlsx
index 46585fa76f7662ac04abbc4044bc918c1be46f4e..d120caf4f00bdff954e39304301efb80372d7808 100644
GIT binary patch
delta 656
zcmexi^TUQWz?+$ci-CcGgFz-mWg~ApBQubmJe^SyL~q{B$PW=X%OnSuc*mpymJnr@
zgGiXMXo3ZjSY%nij3$n?%wVNPJP@UkJiFMyGGfB>n7}gIMIkcxL^m*U0Ii95ba7ec
z<Z0px^?8R31onK_R=VFj*+IU`X~M0p;E7tIS5}!{k2|2cQMWqt#Qp1)0uE2F+&*{i
zO@;iqwDwILbqB0gUY&AeaR<wS9b!Sb%Tl(^Y3EldI58!mHOxTO)WYa=zENJ#I^8`{
zxd#@ph*u~-4a!@V(w!0HC41lL<ed}RQ`E2Dn#N<hMLMfq;{Hb73o2djGB{7LIJ-$7
zzQEJBWV=Ys29xUOEo@D}8Vguj`;IN1F>edUwvuq}sAoQrUTb(`rpldktSu-K2n#h`
zb!_dG@A8-XkDiXU&e90oti`8tp2dGBYul}7+FOHn1xebTHns86QOLhs`$Bp9|6go<
zu~iIqVh?sqW&1nVD*Kbt!}A-PcU=mzI3Ks*SrAX+;@rD|>Q5XG%IN*sd0ps8a_y_H
z`cuE|ew)T1_+##pyKMbue*bt`X{lZ*q&nH4>u|=Vp2;P1mTdn%-}k)uSM|f2>Yv>2
zb8oKO*IhsJKNCt^Z<d$rghb(LDLZhqypb{l(+bjNU^-G-4@@`6N>5%YEeU2Hly(Kv
xoHCYR+EvCGOn1xJgK3c37cvmFEV2-DU1cqxawcGUyR0=L)_=*Gg9T0GTmT)_`au8y

delta 656
zcmexi^TUQWz?+$ci-CcGgCRUbc_VK-BQubmJe^SyL~q{B$PW=X%OnSuc*mpymJnr@
zgGiXMXo3ZjSY%nij3$n?%wVNPJP@UkJiFMyGGfB>n7}gIMIkcxL^m*U0Ii8g4_?+e
zd78LFz29L2fjyr^C%*5Typ2g@=}MLr>RO6{ERWLO<Yv#hF>SBv+53-eW|=Kg&$G7P
z{J7R4TIRIU560I^!ip!k7;-uk>Mpr;?&R$%$$OIzC<Zr)Mjf1U<-rN1{U>*L?%ehv
zX)9y5P|SngDc(D0PL^HdsaaaXu39`XT*E(ai>_o<#`Y`q2K&;Z7fiO;w^UU@m`5^~
z$Jy9o(!HP$2QSIwT$JMQTi75ZVl~T!(>7Z$=jA%FEoWLcO^J}+p=CR<`PYjl3Tswr
zty;GB%J=yf`mcV@w$9QB-K@o@a-PM1Cu`fSXZcy{OO_f{P0X&C65()f+3ySP?>>Cx
zmD&A;p+@IGp*HU?>(cBe8V}EJY~OV$%;J1sK(S`qhO67&tuX$yAb~IZ-yLbrM+@z~
z|C)a4*WEJX297^|m-3p`pVj{Qu_bO&jgWs@;+&R`C3BCwESYxho!#tt?qAanZ>oQC
zzfZlnZr{cIXX+VI;(D{ZWG5sFS4-J}qveg1A(&Q>HUra<(t2RJK~{S5QfWyr`=GQd
znC6tR1k<iE&S1J*#vV+A)V`2`sAZ9bnCmKQ0hKcW)7xdO5wZSD)*LKoBIg1CtTY30

diff --git a/studies/S6_RNAseq/isa.study.xlsx b/studies/S6_RNAseq/isa.study.xlsx
index 782593f8f2db9b589eede20f7e92a56db49ba866..46157e2d5c0b7b91607a37c6024a674d052fe896 100644
GIT binary patch
delta 676
zcmZp&ZL;MJ@MdP=Vqjq4V30{s*~r_@$PA<>PiIsF(VKTO@<Rm9GRc7@-Z80wB}AF!
zAQEOQnqYw>7FiZBqlsfXGgzq&4@7A)&n`BwjDqkyCa}ywQHab7(G83oKx-l%U0jwq
zd4ae>ecmAhfj!@~mF_oBc98FKnsBQtc%qi*l~v}~;|{29)UD1uasPUyfWy-(x6hq>
zQz3sYt$h<m-2tnWSEn3V+`+P7hgeYVvXrfJ+WA!qPE1K?4Kq+RwJ<uJZ<H6bPIpgK
z?tw)t;uXqIgYuT8bY}#4$=-K5dFO=o6!q)3rt#Qrk<O}@xWAG2f=buB49*iQ&Ti6&
zFYxp&*)CGE!K6BR3tLmL#sZeszGI7L%-h1Ttt6Z~>X}cZ*BaiKsd6VBYYU15!a_|~
z9b0?lyZq(;qo<>-vou0CYw@X^XYt?3+IH)i_SWECL6WwoO>Mk%6!I_EzEIx&{})?d
zY!!o@*n=HY+5XP8s{f?)@chQ+U6;Zv&c`iy7Q~adIQMR#`V+^4GJ1b@UKcu&T>I*)
z{?xC#-=;AL{+PSuE?fVZ-#=bfTB=tHsZKWNI-IeoXL8A$CELHx_dPHERsHa$`X~4M
z+?(t6b=S}Q&x8`!5nMJVuCa^^3?)nq4E(?pP?4j**;cX?60KXM?7&g=P0A2VYe}1d
z>11g=Fx@39J$b#fB$$0#+7(O-%UFVGe;H>mJypgYOoP;Zl7Xn@lZBY;FKYpnGXc{F
RWvvk@fkn<7ENCa^0s!HR{Cxlb

delta 676
zcmZp&ZL;MJ@MdP=Vqjq4U<eOU-pJd|$PA<>PiIsF(VKTO@<Rm9GRc7@-Z80wB}AF!
zAQEOQnqYw>7FiZBqlsfXGgzq&4@7A)&n`BwjDqkyCa}ywQHab7(G83oKx-n>gO_zq
zULdYe?|0ZhV9#gKiSIinZ(|Z!x{_sux|U)f%cHb6x!JRBOxvq^_Wom=S!RpW^Q^5m
zKd!ZimN~8TgYor}u;NKBhMW$Cx=U`IJ9)cG^4{bFios2yQ3vN-d2m8$|H&PmJGXsE
z+RE516!V~WiucZ$lVulqYL?cps}@fT*YMBVqAOXIvHeQD!M^n91(PlIEmc(z=8??h
zaW=M?bT8<`!AmkZ7o|A-7B&cpSj}?bw9OXGdAUw(%bC_qQzE2yXxUC|{`KOC!kSfD
ztCp?3@_qh={;Qv}t+O;jH*4{!oM-Xh$=Y`7S$@{~lBGsf6SFI(L^#}A_WOeSyANM^
zWp;mIsL?r4sLlJ!y0rd@#>4X)+jm_GvpC-uP^{Uu;p(<`D~vxaNZ<?qcSoA@(L%fL
zzowu1b+^p8f#Z+grMzbKXSKh6Y>AsxBjlf!IH%=f$=o9^OQxNBXE%GE``7fto9dt3
z?^AEC+jnvQnR-T)xQ^hmF>#G$WMC*^VqoA0rhtkZ{mr(LrI2XdDrE<bs&7(;U|LJs
z3`{3W>w)PmS?S5^r6s}a)6%YBT3E&sO#90?gXyU<_Fx*M_LB@mEuSpJTz^>$sGJFy
SJ}7IANC_-*=3qfPITru}5e2OP

diff --git a/studies/S7_Kat_motif_strains/isa.study.xlsx b/studies/S7_Kat_motif_strains/isa.study.xlsx
index 055bafc29513dba808e2652dc9d9d82476dc2119..00fe6ae03e6270bb722c81ca08a572a49232e6ec 100644
GIT binary patch
delta 676
zcmZ2)v)+a`z?+$ci-CcGgFz-mWg~ApBQubmJe^SyL~q{B$PW=X%OnSuc*mpymJnr@
zgGiXMXo3ZjSY%nij3$m0X0Xzi+z_P#JiFMyGG~S6F@a_BL?JR$MK>^V0Ii95ba7ec
zWM6TG`n*F10(-t|E8TCN>>%IeG~rfP@I)=qE33?}#~o1Js9T+R;{NqY0f(noZl62%
zrb7N)TKguBx&u}#uTD9#xPxWE4zZxzWhq<dwDYSJoS2f(8fKtsYGHIb-zYC=o$j8f
z+yjeP#4D7a2IVbF>COo9lD+SA^3DnEDeBj6P2;iMBArz)aepK41(mLM8Js6roZX}k
zU*PFmvR$NRgGqJt7Ph8fjRh>Nea9Bhn74&vTS+)~)H9z*uQj|eQ{_%N))o{AgoT=}
zI=1%8clpcxM^8svXK93P*5Xq+&*Hz6we8k3?XAJPf+THEo7#BkDCA$ReWASl|1Y+_
z*eV7)u?IV*vi+TFRsTup;rWftyDo)UoR3@ZEQlv@aqitf^(T%8W%T~+ye@Pkx%Smp
z{i$DfzfEHh{4saQUAF!+zkj@}v{bJYQk`tjbvR>F&*YLhOSXTX?|WYStNP(h^-u2i
zxi{DC>#m>qp9v+dBe-l#Tw@s-7)qEJ82EuHpdv?q^DBu`NVFzN*@2^Kv6La0zAj}3
zrUj(+z_g>Z37D>sb_LT1q%FbpA8BVW?IdFlrX8iFC(oCW1haR`K+OCjV*!^7l7-0S
R$yy^)!bVwhu!7gJE&zjX{%rsN

delta 676
zcmZ2)v)+a`z?+$ci-CcGgCRUbc_VK-BQubmJe^SyL~q{B$PW=X%OnSuc*mpymJnr@
zgGiXMXo3ZjSY%nij3$m0X0Xzi+z_P#JiFMyGG~S6F@a_BL?JR$MK>^V0Ii8g4_?+e
z*;ibl-tVx1z@E>d6W@1E-o_-dbS29QbuGm}mPcuCa<gaMn6_8-?ES|!v&<H$=UH2C
zeq3u2EpuAw2jlA{Va1bN3^^SNb(h>ack*_X<h{uU6oZ>YqYlow^5BHh{*yaAcW(QT
zw3V@2DCR-$6z`ogC(ADK)GV!GS1q0xuHm1zMOU&aWBZkQgMI1I3np9aTdJxc%p;l0
z<7{j(>0Z!>gO_A-E=qCuEo=}Hv6|(=X`3yW^KzZomNTuJrbI~Z(6XJ_{OiRNg*B_R
zRxMk5<@@{#{Z~I{TW4v6Zr0*cInUz1leO*Ev;3^}B}<K}CT3SmiEy~L?DqxtcOSm;
z%IyBaP@{98P@DIcb!q(*jfdwqw(q(WW^ukRpjfkQ!_{r?Rv3R;kiZxI?~XL*qlI?g
ze@#F2>u#BG1IHh~OL@)e&uV}D*b+CXM#w)caZby}lDS7-mP|YM&TjTR_pj-PH`PD6
z->2SOx9{TqGxdxpaUH>BW8xai$iPs-#K6E0OaT=+`kP-#ltQ94Ny-i!Rg0wz!Sr=0
zGcYY6tp}zZrA@$eg|sV}J|JxgrvFGggJ~xjdob-NEj@X@j3k)7TLxn09~ld{T#zh8
TE>G4PkrFn_nu8U*mURIDswD@V

diff --git a/studies/S8_Kat-target_strains/isa.study.xlsx b/studies/S8_Kat-target_strains/isa.study.xlsx
index b24e1097ae6264cca06b907652fab84b9a94175e..0187769af736d6a0a4bc9740a034d3378fa3ef25 100644
GIT binary patch
delta 702
zcmX?ZbKHhEz?+$ci-CcGgFz-mWg~ApBQubmJe^SyL~q{B$PW=X%OnSuVB`@IjxS2h
zDb`2PxLK504x-SEMH8$uiA9VB%&6vQW`=520SjpG>|z5mo(j!l0?V|CLS)v8ZeSDw
zS{w1`;<C(mMh1q*ObiTy43i(q3fIpKI-PgOKw!^zZKeColO5!{oF?4r3ZAGXdS#XQ
z^|%A78+EHQPu#y=Dd6z*%I$OK-c-n+OKac6QFp*<<<%)i7I&~L*dZ2_yDVkvoOXVd
zf)i5`TEh%fO)ZR0=Nsh(t<&8Tm3v?ji+F|d)1bU%Dcu=CUb6R{PTo18Jw^Tct!X^A
z^;@K~B<^qIy`a+dE`##~i?f^b;R`%{OSX&DY%r;g-on-ttg(QlweQ&C8S}PqY%2-p
zj(X-3>9vM8W~$st$J&A-fv`~1Rmav|`7VFC|LEyx>nx4X&02ga=UM!BvbNoNroA<I
zSCFLbX;T|79fkbMwJ(&n|Nq6-7hA<(C-z{+RJQuRbFDrpJv_g$dDo>di}P^{o(1tF
zF3!ChsQ$$9pp4$1o!5nqB-g(Bsz3GX?zd?Sf<NXixy#mn=J$`6m6qz2LaLJux(;V-
z>X}?JXUX>O^L@{Ye^o!css73RKKJIjeckml|1+V)X9SmxiEAt{21<Z2zz<9woBvBx
zKq9zG$_^Z9yQK`l^m{2YFs&i22d4dHr6-q2OM=-Gq+P-E4QWd-Eh6I#rlVx+!8Azi
kb{UA;%Q6siMPx0YawcH9P1c$NmL?{jlr;wnGRwID09b4Rng9R*

delta 702
zcmX?ZbKHhEz?+$ci-CcGgCRUbc_VK-BQubmJe^SyL~q{B$PW=X%OnSuVB`@IjxS2h
zDb`2PxLK504x-SEMH8$uiA9VB%&6vQW`=520SjpG>|z5mo(j!l0?V|CLS)v8ZeSDw
zS{sobysR^xk%8ec69a=F!{mpu!u4~5PWv4;5ZLosbmIHY$=jGjmab%3p{}JE$nq%d
zO>XwA8`Jixp1uFrW|r9^^*n3q&5vs>qGe7i{a}2(B&>Lniy@~&q3)7f=T6?PlDs$h
zfMRfyXw<<uS00>D+JAC~=gw^(lD0B-3&lL>o#MT7=49DLo|>gK?5f2R!!`W#w&+S$
z)n{zKVz4hgdckCieM?mpgn1-$d7O<cCfy7AaPX2$&P6E>zl9A#B383pIBl~9b6&0!
z+j6FL)07D59a^>%n}5A{qOfL_)~aP|uY8|>q5taVZ0jtI(9K$WD(6}Jce1wKdX}HH
zzGSIU)x_+IDG?6$mi@lq{_ew9UYXrr7;1D56l(L<|FSN9qVe$j#`ay8!Yt1B1r%$x
zZMeGa-3sGR3ljLk|J{-1e6-N+`>*Mze%&oIZs7RicPXz~{aNj=A6w!k)d=~gCC+L2
zSTgs>%aUp5-r3Eb=l(VQ@TU4F_xseF>-JsTf2N)hB|am#Y)o8ZfiX}5i~)XN^4R=e
zq5=}ZRZ@1~NZT!C2&UglnSp5yX+1FQFDpH{L|PKeo*?ZCrf*1Ff@u*MXD}TlV-Kc5
lYPZWk)Lxc>m@6V{0hKcW(`~ZW9I!Mo`J}8lSddxH1ptLz3cCOR

diff --git a/studies/S9_modelling/isa.study.xlsx b/studies/S9_modelling/isa.study.xlsx
index ba2646f1cfeffe9bfe652d723029778f241ce4ac..6987e03478c144a9efe5376fa9bfef3a71a15c23 100644
GIT binary patch
delta 676
zcmX?Sb<T=6z?+$ci-CcGgFz-mWg~ApBQubmJe^SyL~q{B$PW=X%OnSuc*mpymJnr@
zgGiXMXo3ZjSpG1B8HpTAn7~RoxFJgQxp%RFW!?zRgUIxXKxDRvY+&R7S`+c;;<C)i
zIbsU+d4~)H_I%e?y5Bt6LB7jr!mY00iCUspR+(RqJD|Ezw>tC0{p*zi4o|P#K6ma-
zh5Wg+_Dvjh2dq|JopNMx2g`yTVnMmfQnt=%=T|8>F(sij%s|!D!sv9qQC`qG-91sc
z2Nto2S13OX%3GGwoe|_Ed*A8gofFzq)UV%~#$&rhI;&pd{zl#lDqZg~I8U%RyGb9u
zz|*&6yGYFjlj`U#Y)!!$3s_qFjxC-sZwtq^l5p;*XFic$Yj|U(%AItqEhrKQ3pHJJ
zZ0(ir@|XLMo{qN8(g@wG#iw$f#eXMj+pTBXTZ4B6N!p$^weiwX$iH0sLV5fDUu=D`
zRSb4w4|Yst`#aaF{*%(f^BbFYT?(@}AGhFH5KrRb+`ED5PaF@*=>6GwUFb-1?W?c)
zQ@`$ho5mpcWA2i>Z2f0`|9Dwxsa`3hI@zG>aK@&d$t81^Z2vyr_q_O5^~0O$pWN?r
zZ?4<dT|e_b6G~i1aM_r+#xgQ6lrS+c@B>poMUMVvPKi=Tv^GlGfg|ydq#>C8CTRwy
z^`-Q{bb^!#n4T`>3a0N%S%PV4X=gB<C~Xg>6Qrak?~|4Uvu{a5%#@a~fXfxiK;(L5
QtPv^Uf{Zy>0hg=`07Dl2mH+?%

delta 676
zcmX?Sb<T=6z?+$ci-CcGgCRUbc_VK-BQubmJe^SyL~q{B$PW=X%OnSuc*mpymJnr@
zgGiXMXo3ZjSpG1B8HpTAn7~RoxFJgQxp%RFW!?zRgUIxXKxDRvY+&R7S`(2TysUF_
zj+jEd-(drRJ)cD<zVDp8jY(wbN|qJsT8e=zkJ8@cX3x4YZLjLt`;TpAnJrS!v$o#+
zxYi<C=Csle#@9>2iYK`kayk_1F1dB?<n1cSdy@|+1~-XD9h`IJ!3m}PCwF-6-1Z@9
zD`U4%%!A%3-aBVbmR;njSz5!cT0Aja!#{6}u4Gll_AB)U`_iKqOt#p!R8>KkM>3bk
z+1O&zy`T>VFUjOwl;ZGP*dQcgHOqz5Hd`>~<vOt~XIeK+iICo*WjnF?*NZ0#YgTEk
zTDJDe_xTt4uYS(9&e90oti`8tp2dGBYul}7`C02rmKs$}%&wRc;c#!+?+fnlK78es
z+5Lr~M(04GHt#R%()uSF56^FG-*qX>;(T8~v1Z$btJ~hKF#fb4fiL{u9cj)-3+=xD
znttln-7@0_jz4~v@|xA3)&BaiC2mrUkbhd@oR*IzbC0|%nRf1--RybpU(*k7s(*67
zPrbQr-^KlB>KReuI)cl_#5I<YfuV$nfq@^G0xEL!H*-pqLZY=%(heMnha?Tb^fyT}
zFs(182c{FGOu+PXDOWIkU&<0pOG`V0=|pLJFr6SJJ$awBB$$0m8e*ojj0Ie-PzEB`
RD`SmF2^VC{!3wx!T>xp!2F3sY

-- 
GitLab