From bade2831982fa26eee0b28822a5495574642b700 Mon Sep 17 00:00:00 2001
From: Viktoria Petrova <vipet103@hhu.de>
Date: Sat, 5 Oct 2024 15:19:55 +0200
Subject: [PATCH] add differential expression analysis assay and protocol

---
 assays/DifferentialExpressionAnalysis/README.md  |   0
 .../dataset/.gitkeep                             |   0
 .../isa.assay.xlsx                               | Bin 0 -> 6907 bytes
 .../protocols/.gitkeep                           |   0
 .../DifferentialGeneExpressionAnalysis.md        |   3 +++
 5 files changed, 3 insertions(+)
 create mode 100644 assays/DifferentialExpressionAnalysis/README.md
 create mode 100644 assays/DifferentialExpressionAnalysis/dataset/.gitkeep
 create mode 100644 assays/DifferentialExpressionAnalysis/isa.assay.xlsx
 create mode 100644 assays/DifferentialExpressionAnalysis/protocols/.gitkeep
 create mode 100644 assays/DifferentialExpressionAnalysis/protocols/DifferentialGeneExpressionAnalysis.md

diff --git a/assays/DifferentialExpressionAnalysis/README.md b/assays/DifferentialExpressionAnalysis/README.md
new file mode 100644
index 0000000..e69de29
diff --git a/assays/DifferentialExpressionAnalysis/dataset/.gitkeep b/assays/DifferentialExpressionAnalysis/dataset/.gitkeep
new file mode 100644
index 0000000..e69de29
diff --git a/assays/DifferentialExpressionAnalysis/isa.assay.xlsx b/assays/DifferentialExpressionAnalysis/isa.assay.xlsx
new file mode 100644
index 0000000000000000000000000000000000000000..528516b27e7f3beb6541e892d58d9400da2a441d
GIT binary patch
literal 6907
zcmai3by(Ev5(cS7x|dGrZk0x4X=zwGmhMJEq<bk5q!B?<=?*FB4gnSEmXZ$dA_w(&
z&b{~hW1oF?=ly1$cV=hi_wFM(1jO5LaBu)P4J#?_*qIhoZFo4i9Yi=dJlLl?lJ<5k
z5IYwGHBSeKvmU#Ltxa))f?X>ocF>Wq)FPWKx}KW4RBLucFJb;SxKR%YR<fDBq~;lS
zT*d-sssckimSll#uk?0erK%{I2_WcxN`x{$KI-%clPyv0acXlelqL(H@zjyfxl|H2
ze%?-K)-xwCg>5N2dRSCO1`>twXjuqcqQ=gPeZtS06XJx5mT=TI7r>epWnn_1gQXmq
zr}eI<eG$?NJrch~g4?~X|DntY{xhkb#A2PU&Ot~V1%TMyjijJ54<0R0NXCL?1wN$7
zJzak2c06(5F)~Ks;zU;zS}(^+;uItvk4aB`4fh#~CPuaCB7%Q52^T;8#zYakEy~5Y
zqI{XoLjg>uZ`<8CCq4_8k9`6Ma#28z<}r4{hXWN*T}iP690bb96qMsFpSgHF1DT~u
zOFs<N0o#OE<zIw$aWIa*>s_Y4tGa(+6G*+@`%)Np>U6!-_&!U}I--u7Xwf|BqrWl%
z_ahT9@_!y=*gFF!h>bJHjm>qo_A+Fq*I?ht-GYNd`)R{|Wmz2ePO*&>U2NN1YVqua
z9SD&1s-7z66Fsj;3!NQlWz@^|fUnzOF=FUZmMGDVn=9tM8~s92>rpC)WazAgB=|_Z
z10e$~y_c4bSj=e1A+#vm4ms#4%Vrnyw6gi#jZkd@P#5y!*yBvsDq)2rmT3GQrCv)3
zropkbP`8%oZv`dWE~njo%Ype-17g#4cV1s`jqusn>DaHuZW(1$nS;-J7)|BL!=8GM
zZKnonE@v@68d}lQn5;h+&PxXkWo1^STHvVWE6(?Vn_bCf^iWp@BjqHjzt@tz2=b?O
z*G4rt=N@4Y81ja@VdS5zA;1{%u=z>ZKMhc?4gQVUK)O<mD`sn9%#!?W=5Fs~ZESCE
zef3MYA=;{q6Z^sT#qH7~up3yGDb|_ksjkiuLSRLeyp4>7fbGSRIw^<@kcE=bUi2aP
zJ!qr<NHA1MehlSJCbKN|s>0jGZG3OunKN_j_GukqMCfgLx({RS8v<m!E96c-bg>FT
zOb&g!QnK8b(h5?ctNRM1Bd_oFj&;B8*LP>sgq+ZgenePDQz|XLJu;v{^@3^sNrU9f
zA+kZh-N@Aw*+9DV;64tLw0ovV(t4(pF_R0La-GhfJDg85gfI(r(6J&kzPL!74KRuB
zG=!ZT6ZS2{aT-u>byM#VFY=yB^}o+2_S{`qr~L0kV_p+<MUArs1mf~%nO27@*9F3e
zY=sdH{D<ui2-g*#&k~jGQ#i5xW{+56W=RDF=%{ZMxG7i4r109N9c}{gif%ouimy65
zs27x5EXf?liWMXk!8~h9-A`F5iNcg1%|G>TVWo~;tt~KZX6YIXIV&Uxi-h=efX5^J
z8vv4aJy<94BhXx&)`x&q1#uGV5LYtN&!N%D$s`Y;Je4El<-m148)P=EC5rXwB>HZe
zuSuKTVQ(k4jb7I!>e}GXx@T82gc7oqCpB3v8V*!MH=|5)UDQyP)T|>vuz|2_MFhmX
zUf39{*SD;)-7U{B8aPhg@)tN(bSjQ4*g|)Fg6DJAubtWfV&0dXCnD1n9?53!Vk_Ea
zjH&7S)PKa@ZGW%eLH}X#MM=5{YOOWvS7lk6%If0H4kAZvHbnwDPvJx5O1nNtU5P$_
ztAp+v|D3fY0#Y;WWa|U`xgLbCdo9st0BfKpd-5=T{PKG*`(0!*ZXjh39TW>f;e1ZL
z-ujYSXnof()t$Vx{?NlERRC+QU-<KZAP2_WD++s&0iD1dLJAJ@6*fr^IcPO-rC7p)
z1zJtE0-=CjLZ5p!j0deOe?70YIoFFpB=DNoTzOC{nIzgI#;LrEorB%rWRbl}-9@v*
z=O0!VLKWL0fJ!e*>92dsfIjK9FJJ`KJHt={4#0ie`;}oUJRt72ccCHQ(?0*0CLvBE
zER3>{)5D>BGaOT_gRQLZ(|BHuwubk2pRJ{BDvX6sKXst}mJhA7E<|<@Qm;^-DELao
z_n|6C<l$@a;sjxo-LNys4;R=>Y+T~*r;J^h731<?Z{YhUEU6X(0qtgz<(^eqBj~jr
zV`Xtrc_117dr=16Qt&j&ft*H_W7<^E^TQ{7R83^fJ)$>Ne%)Y4bC{4VVdGF7HV*Nx
zE7#e=$O&Sq>f&T+XYTx?Y7>-{0>rR8wtd6<KW|M?L~@Bq;^X4!kiJHN(xOA+FI3$L
zRht^+Od`P&)3iLzDE8)`aoMoIrAjVz#bGD?HUq>jdL~9TjW6r^-)sxgV&x)3FghEg
z=X)2KY4%t_7#$4<zE3z1)!D2vlRv#gP3ydeAtF?lmf0xzI$!D=IIP3lmxUM9rVY8j
zVA7=JFhP7WJlCc~9R{M0RT?RipQV|L2cZXT)8Krw2@*?_jOr}6ZGOMcSS6LG4OR!W
zWlhzMZm+TrCssKVl+pCQSJx>5n>_n;fLC=X{=A0dnZBXb%NDE+Vif26m}2pa<KQfX
zd1Zc#I!+u^=KF#D6c~BPYD#f|bV=mhQ{uyOi+FAPQ}ir*&yAlEEY$=lbeSZ*;|Yw3
zx_ctIG?ErjY}%h5Nv1nWmlR}CAY(ilT*$eFs;G2XpD}U3S#6nXnG^S=&4Hn|l{wXS
zG`5D$Ft4uEC2R)^)bu|({a=mT#R6gr`PuKUGZ;6(#}EmdpY2rF3k_@_T$}xP{n2)|
zw3X~<`0>9p`+qGl)!EC)v@_~;8|An3@7x-qr5z<Sk>v$3hbiL&r$^ZlkX_o?5!_~s
zfEtEK8k=QUc$pm&KB2-gm$cJrDOHxkMvibPIlkMw?~f=b4cZGQl_agmOxOVtV6&5O
zTN1&&sh9@~iJtaD9DMSUAbboQ2##Gc4{P7XWJxv~@fU1TD)KP4F>VB=Je|Zl-oS_R
zw^QZ;=}|ze*g$ql9m!}#F>6q9xb0*Sc5D|f4Zi<K<8bKl2Ou4D|EoQUpf{j!)0VvR
z7A5mOxttGkIjQHN$vcb!(KxoroP#lG=sWqm7~z3|C~TvOqPebH1(o>OWn%mclS-n_
zwY4n{Dl$vQ#|})Zf+ecf90!`*7b!LRjhY+diKi-Xdp=s0+AquXcT?~3qx8HW`Sj^=
zHCSWk?!`EU_l&|NzPD?TJO9o_Q+1gUW&+<QjD{IYx4Hsf_n<enUpCz8H^vCOZ{KDN
zqbIePDOPXnuzDVY^Ku64G3t7H&_mWFp<TP$vq-CrZ%uvAxB<&=tQHj46;sYcK~3pE
zk-Zp$XA%;L0BB$ePx3RWH$K{8_GWmZI4vt2Ud7oXV=meB0VsP6Y+W&B)>&p7vRbC%
zFlZ3;IzQjs-8NTBPZhp&6*<cN$RFP6Svx7}vp<MsK=S1K;lf7V?D{SZ^vOZ5=9|mo
zeTDT`5*zjAZ_-7*PA(>&T%4;R*gLx<g<yd~gB(#ZfbQA=v@v-<tdn{f^ji<`QSsqa
z5H`ET;6Eo*7qq#)wQ4;h;|{{~pcPT6p+FQ$e1OnE9(dc~IoGt2Zhh)Zx9-VO`>>Yi
zUFd#IJ%D^;`EY{lV?-YI-h;dmw6_w@8UEG7Kxr+KZXW)3TC|6L*c~PH?JM$cV|gjC
zUj~Fu&>=W69!Sj4AvX89Aif(9w{_blC4cC;UVp45)mkN{mWQj_5h?J9Rrxg}QsRa5
zS1RIF5Jg|j8=x*|=NnMf>|3xFAgzxggUQ8SGI+S&=lOsHLHC{H)tLLCr9x%B^!k3S
z`H4JX{z8YjNn)WiCK)npsJUNba<F{Gl(Xu$@mObVb!G$5bFg9-W%^uoZt=K^4y*!<
z()ReVo^4JqKOiMf^C${D#O%aR%cSn?Y)rW)l)^2%rUP&K%(ke!pDm};Y6SY$kDDpq
znm7861nLxmkQtJ<o4IwEd2lxNE=|8Xy;aw@FA1Z$Bf{%S32L$)WtInYhYvyrUb%{j
z$!gv4$%0N2LqEGhpY{!Vb$xM9eA@17H-nDdaq34*#mMQhM)<(E5mc6@QmVxwpdzr<
zgE0Ya#EV-k?id75E%?4DTX{(!L}ajz|0?0&RvzGplGVD7G5U}zmF~HEKSX{1Ns(3f
z;U0v|S-V$vf;*!qQTrK(#wD9l!5vobB_5gtiZ0@g`!sCch?^Hil*prs%oW~kycn5x
zGZf!N-Ibj|Hs3>|2?&5wFnZy1uT85@9U8<1xh2a`{>UBtxMPl;)a>Qb-ux?i097qX
z$cQx;X3&eiht>z<Gxe`dD+CBVZ`l=mJEwDs&!;OO!97?%0VQlj7!QxVwMdw4Z|(6!
z!el_WW8bF7V1hV@Of4*bp3u$F;5C=d&YfGg8E)pOu+l129Mct)B1=OQ3{OU}(MGhn
zVWzsh9-jEHahJ>6)^-`0Bwu&|@lbahiBIH3RUgjzC}O|E?b8Qw`Pk&rY@^SeC7YGZ
zlAWmQL5RexJ_*I5bhyp|aoEPf+sGuvHP2XF&-U+3R)~uBYHuiZzQj3%yz44J8|1z-
zoks~!yvK?>g7R*sT`-5MIilr}U1KWH0TieUb_RK{*Jx_!%4zNwzt*iPs$$F@h3i*J
z@a7);V(BHrP#vAHc3QxihKlw6B0|u0mc1g87Y#G!u@T{!M~HW{y82+x_;Q_Do9{l;
z?i`9lG+0upxFAo%#ZA{xJSL??!?0R5OF(poR|^Ve(bUXsjMA}n^FWN94YK0PRWapw
zub6dyNO%;hO%IYLnp#pL;bLIh&)TXYe>4C1PW{}Wtm1g797eSsTcut#_-iesekNb&
z*2^v`*7~WBKF8)61Iy13*N!_od}<gg-yE}6Xn|35@*N&K8kFE0d?ZC=-G8gGCQ#U~
zSUgr#b#^Cj#xmiBezEHMM8o6i*@KS{%fEN=MytLZEqSb1JjpoTldkDx<tEWQ%sQSX
z`)X@!CMtc@m$#a)$a}Y*)4pe8y7}+x2hx2%eK*+Ri~t*87=NuFE}k}!AA85E1U=Zc
zj32yx#KJnOih#iy=4WLYu9ly|%op#r;U`mcia<OXt8lh`9~l?dbvpO3=lvUK#{MZ!
z?OKi)M<1_lAwG(x$U}L8x<#w!^KVi<rkIRr705DI7&D2yMV>XKjO(O8^qS@|!@*XI
zpKq)@h>OYnz$25wqQ`?o`;0#hy!wLN(yGm3szyd7X6VR-hDp<diWRaeiY?Rctm74w
z$XDszi&Pzw9u&)(cy#|2#;4m3(?~qvO!iO(kD?*DH{l?C;HT9defWgcf_WsbEmv{E
zKtep!xAwG1IJ<2|bJ{AF5K^^O4ebv;nfF6_&0jSae#E%z*wqs!fo2;Mq|(=o=)znp
zm`TK}LUu1ppcPr%=|i~wITt`&RC?H?m5spLx(2WNQI<W)7bj}P5(y!I_AOGoWaYaq
zLqK~>z9eM_K4kffBj{#YRtQz(0R1<Nu}@a2t?H?V3yhF3!)HOL!P|!=m38!XL*Ngq
ztW0-5SxN;-QkX}=8=}#-$Jf7^EkJYAq#p0loj&94aM=B{4y6W?w88VZkbO_(e>)o`
zrRUl$nsp{Y^esO8qfG8`gcqr?M5b+T(9$|q@KbHK_(|Wfy7x}nNWeRV7A%{~yh-y+
zmwmFIdv+2Ix(q7F%X5$4rKw@plN6O>MQ!Pfk)+ROxEDer4)iD<J3rw&GMi-GBOJEc
zk}97Wf1Ji~KGb~SdT2GfYxX__IR-*Y)f*W>-Y=>E4j;T1aN+yC<*@ch3V4>0-Ey>N
zExKdImFBg7d~a`$5iq%H<4UwNoP4wz)f}kgZ^%u_#`av^p@V(Pen4H2ZuJs^v*>|q
zdfHSzdsCqQ{xofBZ}P~=-r>&&!0x3sNFZ#DriVR}W5eqBr<sw1!_^9%7AI~$!wK6_
z&j^CQMy1*@28(HM<&ZwsDut7oS!n5YVO2{+jOB~FIPJ!qzqg@SFC2$8n88#qBe@bz
zfj9MqrBpW|Tg+a<_M!<FT5qqJAtjF9giIu)F&|22cYsnULv3svp|*&q^voi8K~|QV
z%}p#q=+JW{a14HhdkbPgV!gwjG>IwPyHVB<>tXnfZ$i`YHhx~a`rvm`FbdDk@aR{d
zbGn9svC9P9O2!!0M2=Y2-2BG7OjRclwYwG(%Y51*>nh!z`BlhdCC+c{T5y<8CLSFD
z+6MRy@hr#p3#8kq2~3}?6zfII6JcWtK3k>M-eFa&QsuHD3XAu}Tnhp}pudy1%((Ko
zwkqSB6R)YGWda^(;(6%(Ud%P=@~7?Jsq_cJq>;HyDiB4V0;0FE2Pw~3e97woBHND?
z*WraW9d{Jh>kl}-0o~^?frD~QHU+k5s2k_(qqOoEt{Il`q~{xi=M)>|D;I`>VR@rd
z8%zD!=URyicT&A%oAhcf5pEKDy*76TNiP_{GPVHgJ~+Q;%*5Ua@*`y`y;mw=!x0P3
zYye&+LAXTBbhv6PGr?Gaz@&c5ol-V0%dXi;&lta+{OYu{sa=s&c10<Qb3a#=!n<M8
zIH+QdY&p~Y-DZvG=5!8S35K;AoD2klWnEuY>~Kri8o;(K*@#3Qv`e^l%cf8ZTv_s2
z$#);SSP~ejrwP%8EACqXMc<MSIpPZs-HJgCj+_Y2S|gV+XY#POjOMpTN6d?nguhK5
zCCx=%0jP2iKqFa}&;}Kue@sa4*7tELBT9taWoC#PJE9zgj`!;DSTU+MGGo%oAt}`$
z1y7rix<0B?V`}Ug7n1FxwjR-2rFB0)MUJ+uLlGhTQu7S?A`QI9JU8g*S1_g_IH;d>
zs)BBmXFINfut#N%sd@QP2X(%b<ne{vt50?_#A1lP3^Miac=km+AM10-@JDx!az?kV
z`jRWfc_hl`Ww;J%9t0Q-3-8&#FBcb>9dGXQh5vgt%-AG-bz#|Xfn@{hdJg=qLq)|Y
zD8aP8;O+Bp#-n1k0Qm7~89<DiIGG>Io{D=!B1gxX)^}k$=~!$ccE`<jsKI^hVx@^t
z+J_^b)ytArR5DeYhV3-Ft0(iOit!U#_zWA`WDh}3dIm)zK0-E)qJRN+wQe8TtUhiP
zuL?0|%AsAEjh8{~b{`@5G!l|t?WPKD$t%5m{%(8nj0;bIO}3S-C~xjXu%}VuV9;qO
zd68RWYadXi26?Qu%6pOmOUEDP`3A}wsn<^3r8Kgx*-&*9j`ci4v8@bG_fA=kJS9BI
zo23~Hpa1C8XjS>{XnzbTa0lJ(wQ&xo*jni@YKp9r!h-0oCY9S<(`ay7y;M_-_QgIf
zhcfR63G)$_!WXOOxxIxAj5%N8P#5IJq#p@~gnU#c_tD`hNih?|vs24K74ZX{?&8r!
zlkr(nprSGH%|@myTfsr_WS%M)nR3#u<#ut{cap{roT5FFgTI9j_umC_ST=q;|00+F
zy5OHJ^GesfK382a9G2l5E%NV9|I~SJP;hW1KQTYV$p7W+N)Ej~SI$~srSwA_z47$V
z=&qisug?`=?i%p#0sbkM-T+~LE5O{s{9MC+FWUbb@0F@}eXiUy!4w$SJ%7^}Z$iIr
zS%0dGH)uFG^?zW0X^y`b`*+3X*DY8mKO*>t{`2dG|3_f~;KvO&GR5D+|5K>=<#_ma
z*e}`Qm*4Bi|6CS-T@VfH88Gggf3A+dp#Lvq4&2|S^)J|8L*kFI{>!7r@36my{6Elt
xjF?|&08DE8xgy*QoIl}z_QYTCM1r5Ca--Bgl0*9OTf>H}ADys@q$IjB{}1|%P+9;0

literal 0
HcmV?d00001

diff --git a/assays/DifferentialExpressionAnalysis/protocols/.gitkeep b/assays/DifferentialExpressionAnalysis/protocols/.gitkeep
new file mode 100644
index 0000000..e69de29
diff --git a/assays/DifferentialExpressionAnalysis/protocols/DifferentialGeneExpressionAnalysis.md b/assays/DifferentialExpressionAnalysis/protocols/DifferentialGeneExpressionAnalysis.md
new file mode 100644
index 0000000..95a52ac
--- /dev/null
+++ b/assays/DifferentialExpressionAnalysis/protocols/DifferentialGeneExpressionAnalysis.md
@@ -0,0 +1,3 @@
+## Differential expression analysis
+
+Differentially expressed genes between microbe treatments and mock treatments were identified using Sleuth (Pimentel et al., 2017; Figure S2). The p-values were adjusted using the Benjamini-Hochberg correction (FDR ≤ 0.05; Benjamini and Hochberg, 1995). Since Sleuth relies on replicates within treatments, BioProjects without replicates were removed from this part of analysis. We evaluated differences between i) *R*-genes and all genes, ii) proportion of up- versus down-regulation iii) average absolute fold changes
\ No newline at end of file
-- 
GitLab