From f1fca365f8d10417f210a229b48f6da82c37e523 Mon Sep 17 00:00:00 2001
From: Viktoria Petrova <vipet103@hhu.de>
Date: Sat, 9 Nov 2024 16:52:17 +0100
Subject: [PATCH] add microbiota profiling assay and protocol

---
 assays/MicrobiotaProfiling/README.md             |   0
 assays/MicrobiotaProfiling/dataset/.gitkeep      |   0
 assays/MicrobiotaProfiling/isa.assay.xlsx        | Bin 0 -> 6901 bytes
 assays/MicrobiotaProfiling/protocols/.gitkeep    |   0
 .../protocols/MicrobiotaProfilingProtocol.md     |   3 +++
 5 files changed, 3 insertions(+)
 create mode 100644 assays/MicrobiotaProfiling/README.md
 create mode 100644 assays/MicrobiotaProfiling/dataset/.gitkeep
 create mode 100644 assays/MicrobiotaProfiling/isa.assay.xlsx
 create mode 100644 assays/MicrobiotaProfiling/protocols/.gitkeep
 create mode 100644 assays/MicrobiotaProfiling/protocols/MicrobiotaProfilingProtocol.md

diff --git a/assays/MicrobiotaProfiling/README.md b/assays/MicrobiotaProfiling/README.md
new file mode 100644
index 0000000..e69de29
diff --git a/assays/MicrobiotaProfiling/dataset/.gitkeep b/assays/MicrobiotaProfiling/dataset/.gitkeep
new file mode 100644
index 0000000..e69de29
diff --git a/assays/MicrobiotaProfiling/isa.assay.xlsx b/assays/MicrobiotaProfiling/isa.assay.xlsx
new file mode 100644
index 0000000000000000000000000000000000000000..bb8b0147b40fc1c4676a77fee60739b402f00df5
GIT binary patch
literal 6901
zcmai3by(Ex(gs0Ta%on&rAtal0Tq_+E@5d{I%Gkln<YfLB&4Mqkx;rrKt)0tDG4dR
zMGoq#@A=O2$6kBw&OP&7_snl*_FiQ<6jV$kBqRWmwvUxg%uFkW4l)wbHYySlA>va#
zDX6^*#NNe7-O~Z$Y{2PZXIm1lVBf}#7kDUoZ;=CxZJ@4kuPwW(m!#k;(x`_dJH^ay
z;;R{V0_H+innGhjwj{wVuk?-^N;Q$P6CfGklyDURB8=$~7CX}VqtsV<(R5h=%_oi|
z&gD`Bar5>fvz|EtDIA}(qlU$0Wg(F`%1a`;rRtn~c;5urbAp{Pu;LHf=lt2zA}vkH
z^nfZ6`P#30Iu;?l(T8`hkr8z78NRD<LjFi@Ai3C}ueTo@O9i;$?nYKvosWzaAR=qY
zwu~Iy;+`%)gc)}u;0O(;XmO$|604VMIbjMCN62EJu}biiO$(>iY!SsTn~X<*X?>y?
z*$(~eR8hV{@4g_e)7PzT{BPb1=a0Mt2J+Bl94+AXq6Y(2(fU#n`}io-5h>_Lo8EJA
z21c@<&#ioM)CTP0b1OfI?BL@ZeK$ByeO)8GZyP|n*85zPVCs0S{Gl*g;2Nr)n|Sd&
zx$=K9f%GF22=ad(G{ie2Cy1>x*Okp>wstdQr&kf*$z4N2!un~$d0|-+`&zM`8(U%v
zc5m?{*<J>amD@;@^MQ#^td+r@ygKrEhyRzYP`Ctkq!oIU<HoW@?|Q#T<XWWa0R=XD
z5gF0--htqO*4}d~M<6Q}S};92uR{)Y%98n+JUzIeyE$5iSf&f@QOr@MYmKNvB3l$u
zk5aFdB+KB~YKU8F)Yrn&EtlhN-=%<pngNOF2F4d>JR|(J_Il9Om`#&x8VlXi9%eIn
z%FrjCV_T^~T1#21%0tTrnv;#EqWS4ELs^+Msh0R^1&Z^%y02U*W(+Wv2P5PpYrof1
zBnSG@yX#<>p7M^|6dZyfT`}@EYbXdtJZyhb_O}7XrNO^38^BPmdBJQwf?2ZP&D^0*
zHV>gtn~NvmifHS0ZanF&GtBZsT{m4YON=wi6Melylz^%ld0SaaLA$d<4RRR@Ko)vN
zNAbI)w=(Pfhe9Dr@?+>_nXF*E6@{10TSPFvnG*}Vj%htn)M!j5hIeD`>w*+~%al&u
z3^58KEDn7;_rSck4;1c&tn4X}kG#0uJJ$W8-_V^|3-XO&^gYTNmQr~o=E#61O)|^;
z<0h$@12iN5+Yu|@zyS>DL490gX?M)7KQJ((hEFbN$-Qy@*y((nA%a_^hYbwZ{Ny5e
zGQc9f-4y!mh@@{JmfMJSvzvDJ#v<SGz5cfaH#~P1)~NqG(YTicT~Om}34yr$S*EpN
zDh&Y$BHIvzgZ{Gp0pYpe^J#(#G=&?_clMACK1(hn$Uu9o&`qUUHigeF?O+2$SbXh%
zO<c{%exs1wVrk|$Fh+=64ELlZbuVSPG!j>myx`ccm7O+brM}SY6<gO}@JSJIXavN&
zQ+GVvuL&S!-vj&>HxiwP-*z9cqHveYCfJpN{9{N|QWBYT^sVX<%1Y3hfh`(`_GhZK
z=|rY(x-W?v-JvfhwoG0$B<R}`&AMmT-V7n(s7!3JS~MQ0ih6}U$#YgmU0Sz>CT$C0
z+YI-QeX+1U*l1`~W4BY8VKQ)(wCN{!r07%<QMifi_?Xc9q+chsQ-*a9JWooYB|4JL
z*~L-3#SE|O`_O;L*$ur@DBXWha#oryhEZ?B{zU~$S6y4O(Mjrv$Dv5f;3;~bQf=P{
zX(%-mXmijn^UGQNOiXUBlVr0`G}nXjWw$lz1YiU5<V+eSid%Z?1>HfT;000lFhm0(
zRL-ZgYi-YIMb>tVQ{5@s8V@{NQU!r?{h}ZDg}89$a;czV19}15Bvf3K%N$Z3a?!P*
z<q}B`w&+@lWe8RDdGs^Srt!e#r7x%Twx<SgRAR4rt!3$YsYLM>32v1gyd1nHC(G;=
z+Ag|ne!tL$V49d#K@27^wV(bqBc{X`K7bJnScb7A5`Y&ImTTOG42Z>q6&dqC>GOlP
zh;W+#aVmn34~7cN@y&qyn_1td3B8)_jD>feuBL4$jD<}<aiITN5Zz!?gytToQKd0a
z_=ST1T}`0a{TFvj;ziMSLQkaLo#C-?@Z5DjX70+Y8kg6Ff!;o5OSKgA?=Y9D^sLby
z!LIihtB8%32T>5c6~C!pt~-ssFQ-}Km^Kyo?BH=9O$)`V9`UOxzihDR#Jg})#5fc{
zj6<T!%5}Chae|nsxj0$bTR8uy+BhY-b_u-BEuS#RmYWTbE;fhAO5!Cy!_FtiWcif9
zGc|XC5tx_YJ!u8NCeN)`wI}AwjJoMn4>ML|bP4wwr&4e6JuS(--EmqX52Y5O2j-zc
zaNaaY&G#-c(e1L!;B+?aoF6fxYT#IBCW&Taq&2&e!H!(e?>-1tR`Xw}CJ6s_YG?@$
zs_dzG^A=YAshEHFd1roxBteWkT}E-(!+k1@4C!nx7-?vxDLJY&r8Qsr(+~Ju&$UAp
zD>XD|_oXWBiriO9he>K&i7Q}fQAOZlGSjD`E`&AbcPHz}o*J64s(m`ykMJ*0@2bf}
zZ^?qjz3b|kN~@ycwK!A_%mK)93)foQyqEvF{tQ#6W?*y@Ryh#9<5h{*#(jhpU>0fc
zJs6zZh&t1iEK0u0$efHiNgHh)+m#IeZl%PXdg}gIW0KR>J$dSo3sX$mIJUQ>Z8dJ7
zgTH`m?F}7cTXY5t`6?;@wS~J_LhK+vJN;$uVh8wdMj$3<2hHUwgBS&uW<OqkG@MNx
zCFqO*(RWtAFQsOByBV4GCcSQ>0#<%+HizixM@dY<d@`(|Dny{^QBD*zmv&ARw;2<V
zrtx*njS3)PX6J-=h^Xv2{j_>Yjn%M;BT`C^&(_Y{Ln>;cj-p8=DQgN-PC&S>`L{4T
zGNIimxb#ATCv=F5UtUUv2nQd6Z=ZCFy>ET8G@IkbCp>Z*%219mUKEymy#z)W=>9xr
z$~+)F5(JD1;H1`*ic*xYktqqYn=HnQ>Efd!@*8O$4mo-UVqoph-K7dFlL<3x%|C5b
zvgnh`c{i7ndK!|n%`6y&Z<oY92v5V_F5trn3kX2x7*!O{bKNYgCd#gm5V$$1B<@^a
z-|C<$`}yd|fn`OgRLzEKUyJuFrOvQfYkfT7SQTm4TiZ(Kd8Oe_>TLn^o@BBQA0E}}
zYHr^?8^?joD4Y|)Tm#(&w$EB>D@<_X`9I(^%~-iL6#BRamf3w;cWYc9BZgsOGKVse
zTh5edG<RA*gX2G+(e)U0J>Ku3Xpz*ZU+Gz-*CDc@z4NdM=sQ*~6Wax^WTB#^cA&~$
zgcF(uN1y<jSi%y0O&T8_ZnDB|K31Fti-y&3_sCjEwY&p?k3en9W~_Qk97EPiG+aha
zLSCn*8#`MTO6jSh=dNOhdG7_n-gwqeihJ)30*%NXe?M4Q&!1h}p^JXJ->X%2ezd2s
zmMgj5Xi=6f?)B|#^6}ZJIttX;B{3K%6B6i%o&j>#0bq^E`vSi;%3@!WCc+>>QbpP5
zmO%cPL|fSI`qH}Xgn~B^*MnY6wT=o^BtaUbi827w;Tg}giGE}1Ot=2G&mF_s;<uys
z>KXx*>q`d{6z{|H@ph&2N3dQ>I%oLR4uc+OlXc$`c&$x;;EUH;+Ssuy|1yS;3h%jp
z$OHq56Z5|03<K(`J{Q#2<6(AgTjZ4YUDq0qwC}amNT}x%sC7mNDzmG+fJ8_pKlnm(
zV?~CludWQFFSGp>q-Op#NE?vWN0q_i0+k9HZuEXOAW7WKn6v^H4k;I@=w&kWZ7WE)
z73wE)ke4VCLT8#G%Yl*i1)c-+kx<EM+#+P3wbPsR$Ib!57iIfg^{(A=6(3jun569r
z0H1D5FG-VArg;<x9N@koO3S2u^QJlFjz|ix=&ByF*;BjX%6^WVH`XK3FMWAg3T*hI
z7$q^LP(;kH!`v)vLM?)_@pkC?-I=VrzJ7`y%^MM2Q;JsydsJBMGaN{V4CK0sOMtZ*
zy|bbxZ$y7|jegQM?A7(jJ>f}*kNpfbUgxpz4H{-{msJw!hs`n-X{zPgY=WwSn>{!a
zy3K^KD<z$Sx>E~2$ra1biA6|_)`)WB_pjvx4yoB~8knOFcv2ajY4k%h_8u2ohaK!f
zIGlBQ^(S~UiW796a%rA(C>1iY!#>}li>K<k(J4&F0Ylw5GoeNsRb;J#we#U*-p){b
z9eEo(gJ!XdMd$C2q+pWlbf;arPa`^z2XYO3vr^ez_fh8@C%O6a&%5)vOaPjCvfvRL
z9^Am>zWX-&<1>x9$5nzPp4aRPzn(HU#T76Vk`e5$eUpjb41YL0_R=zbwxg}b^E&QL
z6h>&f!A(=tIW$^P`P2Art|qU!bWYy9hK(?DPle?+krH@UU<#OyGzgi3YQ3FwW8GYB
zYb`9{e)A3w%+78JjjTX)0rfzC{5ro_a!nup=_qQy1Lm=GYylqS1CG&W&Qh<G%#)mG
z8)Z;$uzSash%*p4`^Vxv6x~82E2(?R=6bTnI9Vkw-m9~&_~tqO0pxX8A=V%-<8(eX
zK=BSc+6emV?GB+Fo>$?m%J$8vAP1QMeO+f656(I*O?^47y^<IDHN`c|*`rAPO7Sq>
z!B19RvNvm^;#ZFg+0!t9Z_mPoTxU6}68Nxi;g3v6PCSBPQ5qV9J>yFa=IuUvEIV`P
zl2N)+N+pH)nl5ho#&_W<rJBaI;4DG$Z9eU2T{bPPyyi$fJ2wy1nAt#U{ybGPuD6O=
zrw1g5F*-~#4@jpztCR8E<k-vFtf4HMf5g~0cK}u#FPFoqHQ=Z=sMY;a4{4k!5V`ie
zi-x^%>b>`oMaIC=vxC*6H=W*f%++N_>{Z&j=z0YXj~tCkiHzQpqq6V4)La!T>Q^io
zE3P?V%%8D}Pc|%3TbpQlR6D!>{(j~6F1{$Wm!qYR6iX(V$9vMXoUGj>Uk$U5r-5@f
z$7UkaM}7Ee`HNvYjoi?l_32kvGwyPDT^IH>bVIDnD2M@u^Pk1T#nTq@W8=t;H$d#k
zL_u4JZ0xgYC^+n)zSdS@>IEsR{BdsUzOu!~C^tr96i&8;(Fh1!r}GYa-j+pY>>b~#
zU(J!=>f_TdB0|>^yDv}NuxR~kzAWW^is_hkA(*x5A&b~cv{^Ii*f&(DUemYC@$uB-
z=9{bcW8r!4Zpo&w8Qi)~|5PAWcO{w9%DUZhs!moFK6GeG$D-vy!w%UI$CK@M*7FKX
z;ID@DUat*K4~$_?I26vs`GDy#ef^ehCTEC(NAZwcS(uC==)+2nA#(gm;rw;4P1n05
z0VISNFQN3;@psxy=5$o8Amr*RnmX^iGlheDEplHKy~nxj*wqs&iDd^5RPF0Vbz!X+
z$|Pk~rMQzN*oJo3>0OxNDG%VT_=927HV$H#O&wvkau$^AlM}6CsiX)%=Nh?vlFDtD
zArKUoKT*YjA5A{vFnS{`E0`u?faxpF*avI1HjUJS1!hR7@zX$zpsj<_>INqJA>DT?
z>@2rGSltVhqOyoUHpXJ=h-)mHEyQxuq8;zipFZL3blCZ@7EKExYe&B2Lh(IS;N@)O
zJp<Qn@vIX`(ywu0?`89j!oA2JN@m*i27X=x20hVni<|TrYk2FVa~;H3WXZO%#FseF
za^462*s~qK-(^%qS($hAI!zs~k*v597`dr8MwULG;a(ISzHdPF$oVn<q4^~HF3GU<
z=Do_9@keP~r$evKTo0^gcg)`gqroBcG`$hwl>Oogx?zKN{Lg&8w;t3V-UFRvWVasf
z+K6wP^Q3w09o^a8Wd=;{*t(K_9!@%3iF_5H<Y&xF&B5_Z-l3Co6FQ(F#ISM>!C&+s
zFgtFkoV_a0e_z7Ppr*=BP=`N%`gMP9hXf!NXePvuaXdsF|1>jkaJX2W(_-&JXSlHg
zw@!$IzC@<lGY3g%^5l>|(k@4mompt@c41dfK#k##Jv;8koxiiL*eDtc9L!)ToRL}%
zqavL8#8$2!pDh8Ev^#4dh;D>xW!$@q-GW9cqB$SJV84%EEld0GVYvDts?t--qy;dT
zm%~jWT;#xWBw!4AnRgRnNoKRnnK+3n+PhxS6yst1m48CZ5tAstLu2qexi0#x?cvcc
zAm?;VqlYdNNXr>xz=<4*thxF1*O_WgV(Pao!<YDV#MV^1Jqv2kC`z4Q+PC7few$D}
z1hfwb7!z8J?-f31rzJLfyj)@sK2M5=EA(`QR%e@Cu||!@nlv=d2X{44SDJ}2e~Eed
zV|`7=S0_F*N2_>3nTcm1!o9ew4=SH@e5WxS2z`LYV_JnO{sa)Ug*Qlj!sbKS01(?!
zR$N0C*>K!eTx;Ct`U-NN!vzh>wb&NgVPUMFa*oo=<G5y6#gU(`lblkmS1z9!3x(#7
zPOX3L&py>oSYS-`0=F2{ougbO_OkOx_m^cFAu_gr=sx(rXUr7p1o@FN)!qyJuj!DD
zZq}cWN+VPfJ{_hO!%93>C^%`@%2>|fWz{u1>4_)td2D82V8er2arrGB(5LlI!FWW6
ze+X)39f_))g;}$10Fc3<E8e(XlbfDch<EUdsy#s|N0Y8yYc?vW2mNOPdvmj3O9C+E
z?A_PzTiN1o3Qm(?i&p7bgJvr^hD?Y)j9!Cd1Vu~)Wvx=mTCjLPt#AdP*r@q%DP&B_
zNOT@i8+_Y2dlJ6BzzVqbjXD<5nC9aZGcNXCC*>%zf-Uhp>fUFy=3~l*k2EM`5-`&p
zu&}H9C#=g{3REA(6nVxcN=@W64n6p?y^ljN;{t@Sw>q-n91B-3YP4mT0yPRs9MYR5
z_j5sQnlpvD16}^9xAl*mp$s8!*WRxiv2MD}3?R{M3(HR9q$eH@kM3FDtuW!E2zI2n
zKdK=j%cR1a?lU23G@gMI{w3zIa5{Fwx6*US0oFgWVa_4tqmRgj3nCl9%Q^770u>pn
zpoCEQg0@b>m=8-h{E^3}WdU%vyA-}`yQ=Qt30$44+TTU(AH?91ayo8wL>md~lqgMv
z(BB{Vs8Nx)teUCTGHkEaT|1dSRYDZs%5U7%4nB}^GB7F@^A@pf76%Ntt9N^Yv-)^d
zy{aUfsfTuC*PjP=*uRGm(Md{qb(kr*B`x>%`MK@NGcP;_wb)g+p_knW=S-u;$6?S^
z@}jiN*4d{{4fI%PllLSCm5<-g_Xz--Xw*;LrZ%yuTUT=wjqyA|x2q0Ihovk<9Fu&@
zpQRfNn}6@rY+e2OaBu8-z&5tqi-$Sf607CI7%5;Ug$3~)EgHAEmeHWJ#(OProwGdx
zE)~9ak`^OuMae6tdA&tV%sHQ8F&5;;9w>_j2ftUL^w#4kO)(cDv{%o;5c35b?+`LX
zQSe()VPLWF&qkyyStCIRWuK@Nn{m^x=5=vF-;l=*93v8ee2oa{zf0qYZ2WfqMJWH}
z;O~}sq3B+oi>?@k$ncd4`Olz#D!f-HB&5=xm>)9a{}=2+2)#TP!CDce^g|ZCiuCvG
zE`-s`a{-vU1pNC2{}f8EfQUa75MdE<E@8hH?f<;*g`RkMF2b`Qv=@Y*f2fOBSHEmo
zf9i`@Xe1<!zp%g5#$SwGdihi9`Q-(O{^JIJDL=nF{4WY~06#oj$rS&*{+~j{ufV;(
z!+yyYzvBM;viQqE2%={oxO4uwI{t$GuPd_<{5GwB!7d~IIo5wgRQ?_IpCSJz`p*&b
u3ypZ-eys>s1LsfppFQyx98UbRRIW67Wx4A=o;5tg`tb%)kvB*$%>NIS-&tb-

literal 0
HcmV?d00001

diff --git a/assays/MicrobiotaProfiling/protocols/.gitkeep b/assays/MicrobiotaProfiling/protocols/.gitkeep
new file mode 100644
index 0000000..e69de29
diff --git a/assays/MicrobiotaProfiling/protocols/MicrobiotaProfilingProtocol.md b/assays/MicrobiotaProfiling/protocols/MicrobiotaProfilingProtocol.md
new file mode 100644
index 0000000..02284f8
--- /dev/null
+++ b/assays/MicrobiotaProfiling/protocols/MicrobiotaProfilingProtocol.md
@@ -0,0 +1,3 @@
+## Microbiota profiling
+
+Roots of 3-weeks-old plants grown via the CD-Rhizotrons were cut into 2-cm segments as described in “Root metabolite profiling” (Figures S1E and S1F). Each root segment was manually separated from the surrounding soil leaving only tightly adhered soil particles. The roots were then placed in 15 mL centrifuge tubes filled with 10 mL of deionized sterile water and inverted ten times to further displace residual soil from the roots. To harvest the root (endospheric) fraction, the roots were transferred to clean centrifuge tubes filled with 10 mL of detergent (0.1% Triton X-100 diluted in 1x TE) and shaken for two minutes. The roots were then transferred into clean centrifuge tubes filled with 10 mL of 80% ethanol and shaken for 30 seconds. The same step was repeated but replacing 80% ethanol with 2% bleach. Finally, roots were rinsed three times with deionized sterile water before they were dried on sterile filter papers and flash-frozen in liquid nitrogen and stored at -80 °C until further processing. To harvest the rhizospheric fraction, the soil wash-offs were centrifuged at 3000 × g for 10 min. The supernatants were discarded and the pellets were resuspended and transferred to clean 2 mL screwcap tubes. The tubes were centrifuged at 3000 × g for 10 min, after which the supernatant was discarded, and the pellets were flash-frozen in liquid nitrogen and stored in -80 °C for further processing. The similar protocol was applied for harvesting the root fraction of plants grown on ArtSoil. For rhizospheric fraction of plants grown on ArtSoil, a clean scalpel was used to scrape approximately 0.5 cm (wide) of agar along the surface where the roots grew. The agar scraps in clean microcentrifuge tubes were flash-frozen and stored at -80 °C for further processing.
\ No newline at end of file
-- 
GitLab