From 0ec6760cf6e8a81406270867f025ed01227146c1 Mon Sep 17 00:00:00 2001
From: Viktoria Petrova <vipet103@hhu.de>
Date: Sun, 1 Dec 2024 16:59:29 +0100
Subject: [PATCH] create rna isolation and expression assay

---
 .../RNAIsolationAndExpressionAnalysis/README.md  |   0
 .../dataset/.gitkeep                             |   0
 .../isa.assay.xlsx                               | Bin 0 -> 6908 bytes
 .../protocols/.gitkeep                           |   0
 .../RNAIsolationAndExpressionAnalysisProtocol.md |   3 +++
 5 files changed, 3 insertions(+)
 create mode 100644 assays/RNAIsolationAndExpressionAnalysis/README.md
 create mode 100644 assays/RNAIsolationAndExpressionAnalysis/dataset/.gitkeep
 create mode 100644 assays/RNAIsolationAndExpressionAnalysis/isa.assay.xlsx
 create mode 100644 assays/RNAIsolationAndExpressionAnalysis/protocols/.gitkeep
 create mode 100644 assays/RNAIsolationAndExpressionAnalysis/protocols/RNAIsolationAndExpressionAnalysisProtocol.md

diff --git a/assays/RNAIsolationAndExpressionAnalysis/README.md b/assays/RNAIsolationAndExpressionAnalysis/README.md
new file mode 100644
index 0000000..e69de29
diff --git a/assays/RNAIsolationAndExpressionAnalysis/dataset/.gitkeep b/assays/RNAIsolationAndExpressionAnalysis/dataset/.gitkeep
new file mode 100644
index 0000000..e69de29
diff --git a/assays/RNAIsolationAndExpressionAnalysis/isa.assay.xlsx b/assays/RNAIsolationAndExpressionAnalysis/isa.assay.xlsx
new file mode 100644
index 0000000000000000000000000000000000000000..d55c9c09990662b1fdb2fe8a6cd56ef5d109a0f1
GIT binary patch
literal 6908
zcmai3by(AV_of*+n$eBaC@CccRJuC^l+iG{L8N;lM36>8T4^LiLg@|#73r3efrS2s
zyr_>p@9+Kmv1`|M?sGoZea_A~-+LO$=oq*tC@26F(fbb!6K2|Q3{g=~b}&#-NRgi!
z%R!yoAx`dQIzG-2H&b43M~CucRi}1-qOe2Bn~Pv2d{Z6Wo9%fueH6uCP{zDvd1z<$
zQeVz^k#Ll7F_xH<a;J%I`(<@fsn^9RPJ$G~(_=J6$Z)1dIUOk*k1}2s!kBXbdJkME
z+@8ykB+WZX%=+Yqrh}LA;zy(v6(Mm18p{$!6*{~^L|;XC@*`Yv@RAQZ=0bQf<81Cx
z8v`|Ciws`%b}mBtV23x*s7ZSE@4T&YMg2%)D!cf?#P}d0ksd(h<w;#qTZD=iDxqk@
zy@DFi>XoH3jGIIidW1z#x;WV#hu6oqlJX9cM9OKZyGHVmTc4obauGc^k6J*4ePgl=
z)e-ybR86JI_?9T4>zC~w;;#V<-+Ti?2Me(kT&&?vl8C_?n2DUs0Wms5Y&!PQR=`}6
zshQ%^H`^cr?Lo)ng6dBayTk-X-%Y<|ys8sFa0q2u?|ULi^6q&3`CW1DuyqV$PwBFG
z8jb&C0_8_0kmUb7Sjcx~t`G+|zDt{nZ0%($POl-qQ$|BU!TV{$du~~t_)4vVA75tM
z|K{S!V<!bbZb1`c{s(p;sWw(8n%cN0ogtsMqu?_5akkj;E}JXXeH#N3aqDqf2wHre
zQfe~HzQKsWw!Uw+E<i3ktOyotLFat@^ku6v6&9u9o)(xPxk5LVZ^BWIN1dc<DtA0t
zuX>-YEa%YpTBK)N{Fjo7ZTI7zpyklwx<Q%g7i>?@1V)7&oQ$Ds30oF<jMhe{y&RS*
zbWsm{#<w%V^_O$GG=^79^`@FmC5y5YhI4c3GHi&oi`C})j9z-s&Y0q?48<zT)_-rL
zeH<3d;$?_)?^JN~is-OE$|WOzvxbgj#M|K~Wq%vsTp0Wtv!Sfd_0E}XL^4bLyO|f%
z)&4FNYJdJqxFp)HgP%x#`waK_p^>MN5@&)N=K~YtL-f#^Iu!>+8&SuzLtPpLT0ky#
zc4yh!v^NSH1BYUf>MG;dl{s8WM60ULTDHmjg=S8yi8`l^B{5*Q?5uCcy*5N?g;wZX
z16UJOB{-e?cW){Q65dw58M(TzN;CTOTHkoj(}6o)9Qu&2tYh!d*YVV!SL2Qj>M=g%
zoWI{JH-o@33%M4%`c)~EH7mTIk2>?ZCFX5YO9uGVg1+)=w~t+J$Jr8urN;Qc7`;#K
zvL}O_(mTyjUymsI7ZUl+n6`SD_NW$xj&BaUDW>w-U07%M??e+`5OhwBn+*iw{%4ui
zM{B+aMH1PLBpmdY?GK2+IiC+xG@<GIL_xEM-0)c%F;P|~v=UFvTE%oB$4tZ~h_npt
zR$Wrv$w8Bt@?u5K1TaC2MvCyHHDf=0r6P_{mZtbPxQ&M?VYRWu@+EioP{c_oc~mSU
zpv!0?Cb$_O=hO@QnluV4ByPV2SXI42Z6D!5OY<=@J}r$}9(J{Ml&%`IZt8#qHdvxx
zpH5}(Vg8)D*%S3_a@*qRixd+FvRSXZ`YVwX;Of*?+eP!in)sL4QvzoV3>6LQSn>`K
z?yZ=R#HR}zLrr&V>l}Bhvn>XX(zb#{kJMbtV@tO1UG9?xoD3LdbSZG{E6r2V>PwF1
z@pgmDwmIMp{T~Jnd3&JOOXLR-<!2RHQaFwFJfAg{m}~3HH@hfZh`?&(tUi(m&042^
z$cu_QBJIv5mBIOIOXM_GhH3T(WOKdfpZD70PXP8HAKtVPvZUoVe$ZVkT0sy)FDncP
zp?5oFT5o^CB(c70p5aB;-h}XW&kzO94M=`G5aT15E1-u;4H}2;P|)+yt$^jcm0|Uu
zm2z2cZdg6-3WOf^4fe>Vc_M6O`SWR`!>K78gWPXke?`7gE>*f!hF^1+D4(d=)h2J1
zshfF6I5_G>1Y<&*C=R<4L$C>&8GGu}K)@)Df3~?S3P2Fozreg56_AMQUurJ=pg$Pi
zD#337B&dowMhq8Q5nBQewsOBullrwdnv3r~T+7^49gm)V;LP%+81}-x6w512w?=oe
z<TI`C+qy8RTTgG4Cre`QMxDsLJtN`-3*7KJ=IG9;nNTtE2few^ona#y(rG1E?Netk
zir?rxUX=(_0nw7Zk-lQ`+-Ms6Kv}QOCG%a_BgFlF##Y*wz0#Lee$im5OEG)wkmFDu
zIS$D#D%Z`%!WCkv?e1#pWbO8&YLnH~Lu81$wgaOFK0@q)uR%FXSc&X)B0<<NZk0av
z6KpRE?ba4Nfm>m4M0fu-7-~%)nqHl_NXmozgvFP#j04p)&1h9y-mGsE@qonLWXgn^
zfOrdajlC6zm~K}qj@U87o`I^P1hq?mA8a#wjk>g9ABO0BR@-LpfRd5u&|>uAYFAic
zzF?*&v1ujeTFuewr?n!Y2#)#TE=5gND3hB@cX+!Oal)Y`Hmx`wZVd}$wjDyo`HCx1
zhy0VXZPoU;_*?s$ur&uvR`qHhT^!vfaY99buO_8esr9QzxmD;`y*hlCU#TcC`c<&E
zejUD*vYiB`z8_kjwt8LiWGOz2bN~WFOOv6Gb#_ki&T57ja9qpxK_qUEHm7>I>?C}-
z=e;at?Pm2&BkkEEb8*e2atbx)s2KD0F;2=TxrLYE5Osgw{n@kpiik$=)i+PzcQd{)
zKcd0uyAszaOqIUAjQ08z%J>cKGB^LVle^nM93ej&{zVEC2ZgW1A_r(E<HbgUoCp_Y
zKVE<Ioh?Ik=!^*2cdp>i6_&<(**Q)YeV$_?w!yErhFMs~DDEi<DR4z;l7Xhjc+s)k
zJ9yDOXDmQ^=9qe$RY205uE~H%NyTq0(>m#Owj&lUDCzlu+q-WL=^4yAOQ+Q3>}c=t
z0%DA;zD7Gzi|xIG%P*w(K!^E+Rpb=N2#6uXPH9(p`ZuO3^1xJ|h-et;qQK*V=$u8y
zDQy0rTl2W-^MI^45HKN>m%&&rUQNbcp*-4gs*EV1TZow~c(i3C^5`vym2042k3OtY
zA=<L7=(J7Ux?ef}?OcAwX=K_ChiE*pV;cVuJQIJXSco7xG!z>=rY2qJu~kw_mRBVs
za%D<g+O4s%%~?xv>FCIrb5*QD+n(=0U+^rw;ZBSG#ze}o7Rp|Lfvw?_>N~p`*F>;;
zA5(w$;9GB`w{z`mg1~=9^&6SLN0^t$&RJ`Hl?7q4@CSnC8C%a6C4pXHm5!e_JexMg
z$^CJ0IilEUY-Y-JTe|EX!HJ*D7<rF*93S-3w#phduJ$gn7?RmDUBBB53>t4#NbH7J
zbJ8<0IMe4X!b$H%#G(V5Iipj9ESl~fZgKfvxvw^@BpF@D->YaX*ZLNubOdT&vE(vd
z1`pdUGxC`=i}{_NZtiYdt7m0Me)EtzEPO8#{o1E-N;+VF2xvxq|2tw~qiA-0ml<~d
zpijT@+tI%2dV%allXYd5wBOgWsrzTAI_OY0_tXfWLS&c=b~eb%5P&zX5(NC(q==6u
zPliK=qJ_TMBZK-ejj5!=<C$Ii39Volp*M?^Rs%hTM2b9mGhHaI^CN+23zMddnI4m`
zOPwPI($`@74NU;Ljb+3n?faM_qCNSdQM_leZrQ>0BcR&`)IC>4UKy|;f{3~*nmSih
zo+Sv;6FmuuoMc6J<v5U?Va0ga?~d_mBHGb&n}+U|$9mI|!OiwM8J!{$?XFl+4Ia&>
zkXYHrw?8vdtt!y>H&lX56n4IVw5`5`8vru<>9aZAp>p9PO#zPvWyyQk(pKT(k<TTn
z`q=LTwHK#cjS7}P6sF2VGT+Nq1mhHbhUWtVWi)e}wn=$r9gSy0@biK2Ma6y(W3;Ot
z(u1o2i_AR{;KR-7WqBI9Oz*N#1mSD4%p9iIuUpcuOQZ`*t{J0RK6EUr9suXRwi|^#
z3liikwik+Llf`+5E@6e~?`drxWgVVJw97o;#ctRA<x}!l;i%-gda{m^ca`k{D?&bU
zu)srFM#+FJAQv`81^eg$d(c1P*Zs*W<w0kl(+oaQ*KrUPBL~0x8ioAb7KN%zt>*^Z
zqFSO`y#$j+Eu@L7<y}KY?-l|dSFJoDm!LFTCo4!kKq~?qGVs{H;D|>EWUxNc9f0WW
z-!HR^M(jbrZiam(lY-f0DTWXE^uB@BOW1h)m##7=(|1#Ki8F)!F*eUE7_i3FxN7`6
zga~r3Wvji4yQVaQWxa>T91?<}YVp|hdWS*3E-Xv{f~It(TEol8w`-1<#_Gw^-h2T&
zfU%J}V$@!MFzj*vE&GFsnWlo{8c_-#G^dg;r>w3?#jGXNBnRtX6_U4N?v9K<vq_%q
zZ145KB)o#o2JJAtat~t;i%C-DG`WYb*>5h3SFrHKX0(-$>PovrIlMb8U5S}89F>-S
zql0pD!%BO5Jv!x9%dUXGqvJ9bb+P0E2Et?lQ&{S8T|e>Z7{-7z?y-DgF%jKu@Yo|a
zxtHozX|7C73K&#80m<dktR!wBi9~lLx3Q?p8y<3dob0nr)ksVC8E&Y(enO0Zyy`B&
z8xmxjE@A+vUFX3X#eTKZDV8trGNw(#sU-vCtPpBq<fh=w+n}#!qO8AP{?w$dtd1jZ
z3}rw)*<WzzldYfPmHPPPwc`?=OdQ~wvluatS>BoyAv{93uLZ@4cZ7euuI^Cp#PSQP
zj=+7+-8pR8cq2LW@{%GwcTW@Z8}RfBJ@a~{Tv6#AAp@8Zx4wR1OPsNzr#D8zY?z&J
zp_V1z8@1e11jS*3A-lqD%6CgT)B;z)`?*_nbd~eIY)x|rCAEp?$^`YM;9ApqqtA_y
zrkP?1v?tw+JWcQ32OL>v4=z7KtR21X3TWV{tvuqXF)+e5E_U{HF{>amdryPGv;RzQ
zO|*1Ct$e(!?u4yq#y0u!opSB<$!6dB*@O4Ds=s#&#cMwstMFATpW>M4&C++Z^OSu#
z!ZVSnRIoKZ6PGm>C{!<8=D*v-5AEHUet9|LE`}GTc+eeB<mQZy9AE_h*+1NU93Vdy
zkAh@V<ho22zJ18eGpmhGz!Mc@XB(|koX#bj<hc=~Says~HI|@yvMr89LgF!9i0FM&
z3CrF;zS_8!FT>X_WKv3otuJ*;h5W^$-J|)+^!Mra#tll8xN7clN<G7xwPZ+qO^@L>
zebtJXNGEB&rS>2ZUikK^Vmi0!RZNzLB8f(;kLhgfI&9uGC~Con5AQK^>U%TtKz5~x
z6bIal{lZd&YyJB$>m#zl5_nP$#R~{N;5tuZUNy?$ja2n68&<B2R=5NDu-bbEHF>pU
z9@B5j;|4`21u4!mC<`X>ZimI3p_VO#MrT#e@NGbjctoFd!OPP31lL@;dlO~x9N}SF
z{XH1&T#aHmlw4Z0*K<YNv2M7&jlOd#0JtH2d*og_nB3pKfwV^>7fSufl}W8aRsvv%
zM&p#GdCh$o1SJ$s)pQodQprAqZD!_1FvbqDe<2wEV5i-#n}Jy1fJB);48sZEMpV?k
zV0Riedb`TQdF_Mk%`iE7>sVBCJoe6{rpnn8JWqY5iC&ZG6TvR$-4E+9CJ=Q8>Q#5z
z?-?S`X5(&}dh|%=p2$*uNs4~2Sa=lUM{`#;$FVPLX&o5;z|b>kDscS88&^Y25L>AY
z_vW%t>OAMSex;ASJIM##W;Jxxg-5S4b%>g%%c_BKTgKzmS@YRmrLdR-Q+i*w`@)A-
zQ#^YVBX(Oit7j&BGx<)3U!Hj&>}GeZ-b7%*AuNo2u`zT5(yB($L)Syj0>8H*8V_%R
zPO|gb4)^S(cdP_5{q~Qp@9l8_rgj}XD3?ak4p-w|hN=gf3o?Mgk5rtyc(<T~x?-%W
z-yp<`-XxaCt<|%a1^Vwxm?iX{hAY(h&nLj1r4C3aa*t+5K9dt6>-eXcg|qYd4xO2J
z13JTxAGUo$9{xEl!-*qYMo%E0#@FCEisH;dTaP=BP6|eXaN^l<58?dv4Yel8MBq?1
zXUUA*N;Ey`yHDKDO_K9upt6o<tt7A}sDAd%8~CkQloERLk*rP!*tLpGckjmNEMllX
zv`Je~QW6Av%EU+@d`3gZQC9@FAU4$YJG`k=gpz$5Rm}<B=3j&-^<8kuiaK?NzS9_C
zU)>oQ`wVi+(lfj3K8doDJr11Am&u)*-*}ay?JA{n%_e49*idR+tH-Cf4vV(J?U_>>
zG1u2gjYB}kpolrC?Zke`?G7e#%lj+krZMxBM1*1wSD6fVc+~2&1?(uJk^%|W!i?nE
z*@~7qRz5b?Wq)xMvUIUcCRLbx6e-?ExOThxLFaeIJA+ZTu>|hbU`Rgz#BUP~F`RG*
z(!BskZEL8lqe^VL?5M3b9q@etdCd`mhLl?!N*wWUHcolRSX2l+vTc)SPB$n{={KrZ
z&dkN4ipJh;EDhwH8l)_+W%wzznl^kxzf9~!=YgjKJ<O09TR?Un;@>lN59$i}kut5m
za~ZJtkehingp|G@S{6PXt)0L{K3*a^b*GK(IoQv(dv?l)NM>n#W^i!Rn?Y^m4KpyX
z?RxP<Y-dO$Mot5TmZP<0i%}?$)ww&_yit#zg<MQ<=(Cm+Nd>ss$gwRCgVLL2iNwju
zGQx&LiEj4BtM_f($yY?DDext0jO{?P)!<<ZvJYcuaGdbi$?)7YIz?+vZ>TMy2oxWq
z2rh?;OBaVNAZbtRFy}-e)E`y_H=t_ZluT$jUbW=o>2uYHr!L->E@bF?RBtt|QR1sh
ztB``5<&1}4J1}Wi>0Yemn^5YLoGLe&-!y#t^UeVQ?TkCnpQp`*o8VZyc2T!I`yNoY
zxZF9bMfRWo)UG#EQZU#Zl5x%C*bT}W`DXq7h8fqE=gc4q^NzUUG(lGC;mFv&-Hj>>
zA=-#t{@8h42}SlXONp~Gzt$3I8j24r-#sO$-1kk-`Zg*5nGGwjT%ZXu8}7(#059gi
z??O~uqN+Ml><iyMjpjHk2Zx|eOe+H5o;PTNxc9WYVp90J)(pN&I^9knqU3ei?1Y(#
z8<wk2MzY)*{is`&x}ue%-8$l=-%~$T^sbyNxlP!-xkCw|;A(1CCKVvz&>{^O^wQ}G
zP|EEW)bgv5abp<XRor+I*6H*fLdGmB=htbe>Y29E*B|V;r^2ytAJpnt+m2m%J%%@v
ziI{*@Pu-8sCeQGIAtTItwOz%B2K0R5R#9N6l7(*LyK4*<_6-}_E|Lj8C)kd)(OLfK
z%dy84UyEj$hoa}-ySCWXzB=3=#|+)U_k4OcpI>I}`3O$BlB?>1^sYXm=UnSpcxKbh
zR=DBWJ_(<u&|6vSQSQ>mtEYv1rOh1qpAvBvl*eytNJd1w*Q5(D7N|(K5+ile$;Xij
z0vzv>vc}U2+tTCUaSG4IrZ3x}Ku8rIXqH*>v#b?%^Fd$JBn=+pX(*$jk)ix|g&diU
z-_F12<-Z*K-7?RG-HUVH6{C?Ez7!+>8T3z~_Y#GIQt=b>Lyi3Zf}QK37w0@!8?uys
zsH2yW{=VJ0K6-J^0dp6Cf4|_Ldg&z)`M&}(EHcgo?DwMmpZ7hN6)(<tcuu4QgY@$c
zk@52C7cJ{gneh^hf};Bu_Lu1Ri?ItYe@Z^Tya2I(+~6+(=$D88MPVu6hlfj<;-A<5
zQ>geAc=UJJFWKT(+<#vde>s35dj^s_x1X!yFX;ceGC#?0)A|?eBI2K8{Z~Z&-(mk5
z@_(ZL95KJp$S3PxE5hZ#`4j$UPy7XcME<i>E~R=6Wy~MHH6rBt@ful?jFji*{|6(^
BRyzOy

literal 0
HcmV?d00001

diff --git a/assays/RNAIsolationAndExpressionAnalysis/protocols/.gitkeep b/assays/RNAIsolationAndExpressionAnalysis/protocols/.gitkeep
new file mode 100644
index 0000000..e69de29
diff --git a/assays/RNAIsolationAndExpressionAnalysis/protocols/RNAIsolationAndExpressionAnalysisProtocol.md b/assays/RNAIsolationAndExpressionAnalysis/protocols/RNAIsolationAndExpressionAnalysisProtocol.md
new file mode 100644
index 0000000..004ba30
--- /dev/null
+++ b/assays/RNAIsolationAndExpressionAnalysis/protocols/RNAIsolationAndExpressionAnalysisProtocol.md
@@ -0,0 +1,3 @@
+## RNA isolation and expression analysis
+
+Total RNA was extracted from the roots of 18-day-old plants by standard phenol/chloroform extraction and LiCl precipitation. Thereafter, DNase treatment was performed and cDNA was synthesized from 600 ng of total RNA using the QuantiTect Reverse Transcription kit (QIAGEN) according to the manufacturer’s protocol. The product was diluted with autoclaved water to a final volume of 200 μl. Using quantitative real-time PCR (qPCR), 11 genes were examined using the gene-specific primers indicated in Supplementary Table S2. The qPCR was performed using the SYBR green as per the manufacturer’s instructions using a CFX96 Touch Real-Time PCR Detection System (Bio-Rad). All quantifications were normalized to the *TIP41* (AT4G34270) and *UBC21* (AT5G25760) genes using the 2−ΔΔCt method. The RT-PCRs were performed in duplicate for each of the four independent samples.
\ No newline at end of file
-- 
GitLab