From 8ae376060620bf207fc8bd5c602a8e22557ac392 Mon Sep 17 00:00:00 2001
From: Viktoria Petrova <vipet103@hhu.de>
Date: Sat, 2 Nov 2024 13:34:33 +0100
Subject: [PATCH] add community profiling assay and protocol

---
 .../README.md                                    |   0
 .../dataset/.gitkeep                             |   0
 .../isa.assay.xlsx                               | Bin 0 -> 6913 bytes
 .../protocols/.gitkeep                           |   0
 ...ture-independentCommunityProfilingProtocol.md |   3 +++
 5 files changed, 3 insertions(+)
 create mode 100644 assays/Culture-independentCommunityProfiling/README.md
 create mode 100644 assays/Culture-independentCommunityProfiling/dataset/.gitkeep
 create mode 100644 assays/Culture-independentCommunityProfiling/isa.assay.xlsx
 create mode 100644 assays/Culture-independentCommunityProfiling/protocols/.gitkeep
 create mode 100644 assays/Culture-independentCommunityProfiling/protocols/Culture-independentCommunityProfilingProtocol.md

diff --git a/assays/Culture-independentCommunityProfiling/README.md b/assays/Culture-independentCommunityProfiling/README.md
new file mode 100644
index 0000000..e69de29
diff --git a/assays/Culture-independentCommunityProfiling/dataset/.gitkeep b/assays/Culture-independentCommunityProfiling/dataset/.gitkeep
new file mode 100644
index 0000000..e69de29
diff --git a/assays/Culture-independentCommunityProfiling/isa.assay.xlsx b/assays/Culture-independentCommunityProfiling/isa.assay.xlsx
new file mode 100644
index 0000000000000000000000000000000000000000..264498e5c9b281fba58e4b4fb7dbab5204759eaa
GIT binary patch
literal 6913
zcmai3by(Ex(gvxeYlWp7=`NL$P*}RVS-QJLx?2QkM37XZ8!71y0Tl^pq?g8Tkr(yo
zd%pAhvDaR^bI&~2J+m|OyH`;L0TB%j4h{fEZECC)Kii6`1rG<eg9rzQ5BpR{+}_Rw
zV&`I@>gfP+)?@RqwJA-KvuoqP2|f~%Tw(=d=&7nnw&hm#5fmQ4jd_T%kk0O<w9LBW
zF%&UT78&9*r}A%mXLb-NR7Xosf~4-JMJn+DQD;UOZ3*j+(_8XmsdE78PaFxH%f;~$
z7wiP*JoAFmSik1RjEG1}L!vPimj$)URM~iNPWV{zLY+|2laAWw16eYnElh}Yu$7_;
zG~e}hEJ6BWj~?72#_QSF|M1oc{xgZ5*iyZ&&S7W*Ie^IBjku_)03JO^P}+id1wORd
zJyUiVEs-eb7#Xv8X|g*Sy^nn*c^Z<4&#0%ihWC_N1GC0-2_Ybtn3IowW3mL^7Ukkx
zUiPidLw+o$gY6#N6W_&4FW;cSd=x21^Ef*p=wM~6uDIwSE&@eV8p`pO?|h=3f%Ml)
zOMgt2LEEI46<-8*aWRj->s_Y5tG<6|6GXM%_d*D7`gFbA_&#&+I--u7NXY_;;y;;y
z`;iG4`9BXb?45xV#KxKZ#^yR(ds)&mYq0NRZo$E!|FmJdvMfz_C*RJ2A-e4&xpem2
zP709ovVk)16FrY`E3F+#RrHIFz;D~(aiSQ}mMAffn=9sh8v}yT>(R<kQVf=2VjxoA
zVCZ0L-=(D^HWNB>C=CjiLmo!jve|_!4Y;tUDOT&YR5!9${BgExwUAs2a}2Ooq0dr`
zacF!k%&j%%pr~xy<+R6tIjFFDP;{oA?$rh7D6fs3j{REvmQgOHx%PQ4gQ+Z8_!H0Z
z?eq|h<s2r(;T1jgsfKf*f=sF5ob2j!3tW{#`Gr317FW_)J=B$<C>gPu?{%clg9B*X
zwNOpYxkm5s5BtE~F!DER2rx!GY<^Pqw*l(4!M`yZL|d+Y#cUmnS>oT#-0hvLjqUBN
zuYL(PL|e6U;7Dv=pp_qKyJ>?N<DD6w=;|CH1XWhc+DKdQ+g=>0kw}pOa!|55N<O5%
zm)aOO5(ra}9Y=Yc%>>3-m3z~)4fNreJu}DYn9&hJj76iT{V?vn!B5JwLgwU48!sow
z=+M6_3Fg9jBqtfRx-UmE`s!}qc+aZ=eRl>8$O-M(M}&2Bh4Kot(Lr^}=Zp)F8^vd#
z$OeITqgGGALA046{p`dU_e_x<>6uc*O)YB3bUA<SbUw`z#46Uoz>ZY^;v#l7$SAVY
z7=Ch0(7%|#VL-LjL$yb=#B(Y+@V=19b9Zr_;=dD(bxqI}HO>|gh|8a4S`(pE9|R+^
z4MsTVFWVmw&MQ8jCM(&eap3sR9WlqvkqGe9Qr#+YQ>v0q<FU<vZi4VjZau6{tUfzz
z5Rh3a%bviF7a$SFI%`hfPg^OA#u6hbJPl}Np^9IvD>7|i?j8y~E502b1@Z0Fo`?)+
z1c=-9VxJ_A#^&R;Jp`=EJs`FYbtNVF92S$BN-Pn}T{TKp0b19yL1xwbO1?gmLf=FE
zEoHMO{LSRH(X0AoT^rz>dv490Fap+!lxE8%!@<g!7L+N@i&~1Z+I3_J8wm4OWMIOp
z#f_l`eamXw-HI%u!Q<4e0RCfnr_!jREeyxU_`YWYTIroqO#9#kLQ)N((OkA}){<?8
zxZ3_t14nE<_V<b;2B4)EWtqaLb=EB3l)%(gHKm)KgpN3@^0#R{g`i4RcKwk0GJU=_
z2i?~Jd23&9lbC6xS|0-EdlA0vwZ@zQtU;b^sUyI|<@et9yU3(mAc|hvSZoNn^EuUe
z+Y2he^<Besce1tysE12BKlc29(C0$|cFg&g<o3dYIzc-G<m_ZCtl}Oru{EHTQZWza
z*c#Fm2zl&f>@&~CiQtvxZ|8M3=X!C7x4joMRwU}gQ$(6YIh1yB@^BiREOJ+=x~X?~
z1H$V=DdSuDQR%@H0lK#g=u=+#0Y*`MvJA!G09<H3FAdw^0SRb6#fH33`UB#c1v!kc
zG2e!sLWc{@a80ofw{pJE;CnaO8s6W1x|XpiHy$zb#DV6ZFt*;h7}-5otx|2W=o=~T
zhw5PAhp!%#CJCYJhM$RlxWHj#<$U0N%Fvx%IU%d<1A70MIo*Oku)|Ee!n0a)6r;{#
z{B1(4EQl2NUgVB$x%Ldop^SR9W5#swGw9=f%4X7*UXhzBzizNXG>V1}uyH5_8;8K_
z%5}Cda)OwuxHwtbnLGce+9U;qKvA5|ZNG?t&$FdMAQS%(p170`U<)A+T_bJ2X_4BB
zl)Wu7Vv}(^<JkUl^2Q8LnaX=a1H!E@ocNY&_L0mDnKhWbqfYvSvpzY8Jebk8GN)P=
zqBNl6$2B&jtpe@S2SFbIN{Bh|R?3iMG6MG>B6}S?dQys_WrBbcMbOu|AP*{JF@L&Y
z6L#X%qh&tfjk2*VhL;1*jmvA$J0%W}lQ3rRxs3}M;-f6zH*7_&-qty$=!Aa3lqp7Y
z5a5}0TgE)+oypknK`QCrbDSVA>bkcTa}iW3GR#}{@TEoyQzb^bSJyjTOG6z?HlMzn
zXyZ?7qTH#BItZop`O_sCoRuxZgrCWh@;3p&PJRUa3d9P82E@s|5heXueRAsGx-x)3
z8RE{wypm|5Q^~Kr-%(~?Jr_z)qvMqiAfi)Mz>^f`H=aps6g(O7)1JzN3Js8kg!hW(
zq%468j85gu7oMl<t#^shuWH2k+`7rof9>Zk77$y=&$fS^$b>=OJ5jJP+Ch1}*TCk&
zwb_r?AKhn5OTm7Y5BQxa;9Hrg&R$lwol&3L7@uW8*VZr%%@~0Rm`92!TnPx88Dm30
zc4=oraGNy(sT(4xZ@$IG&+eS`4HJ^Sq?u7otF|05a)e9E^V{Bie?(4U&`~_4AZ|r!
z!Ul-cHam&1B^KD5j+0nS_Ou^n=am(g0%GDqaP3mLS^77o%5qtWzTl8hl7+L5b0IJm
z=p@tmfF3TOr7Zw5qe0m5L2MK{;xY1~)>5Srwo@fI@!dSsz<|-Fk+9<rAX=t@mwV*F
zucabPTMN!x70ml(@;=PxrJskT?lADj;M%5g48>(&>=g1~Mg#?+u#U-#<hyPaRRMF~
zit^o=QV?;jt7~;omi~Ht?7+AxP^MzdeyG89kyfkUq_HuPe5wq$=c{R{^`b(5H~lUj
zO7C;xPoKPMwAFX+UQA&6%*tH?eO!ax`F1XvYu*}RCGmd3Y@D@pt1t3%4}NX?Wy7su
zWBj%c8X7}5J&DC^sajK~)w4L<7qi+PW3H!%y`;@zT6L?vOEg+QYpQ$3joAL<by5l4
zaTSc@R1^;6xl3{QCZSOXfJVlM6n~=z<D)GmpF5A`XTU-c)f~Oj=HksCK;UCg+lncZ
z&NAz;)iNc!L8E~8`T6GVwz)!Py3nPo@KOFpzKAZ*x+xLg{UK}v;>X{iiyH-V>$}vk
zj}QAaUSA&X%dNi@+h{O<ohjmdaxwMz;#?KM-q|H36k94R*byZQ<gNukAD8vVK53A~
zxFrEZ1;QyKZ1#x4e@>+;YIl8O)pkb86^!LUBdlCYjwqNcfzU`6gy!&!bH+%wA$_(-
z_vCBGh^ENh*!|iD0NKVebdvOAWC6~eM8PQf8!_jsfSM7|BTeESZoYS#G*Ew>&a#G%
z71=lOJmfep0>dV05u6wf#b#*{Tl!rP-%Ui=x^0t?J#<}fIM$SGs}@x)z*Fgr;#Xu*
zdIgCRd;aJfCDE!Bd4KI|kgn9u0Z7H{AVd?8(NCVm=wdG(GScAtY*6fW4_)eN-2Jd}
z!MA<%`u=T&$=u-qg3$aF(J*S0ENNEM{BLo2*nXl)ISt$REOWLxbAcFn*l|nJ{jNH<
zxLrjCR{=&DdwkeWH)ob5NXRlgN`jzRUBHZNs;;i4w0nYSTtaI)@TN~~ODYCf^SZ1?
zW8e65F&0|$#L$VMP9q4KA^EtOTZfy6<l^j754h7?bsv058p|IQT31L?1$(@;Jfww6
zgbluQ6%hq%()s4ZP7%d^c8z_~KjPi}#Xb2+ho9Xn22SUxKM^GZhszp)gmIJ9+YIG$
zO=f;&{;gijN$n>5gw@i{A?@i!zvpjPUfdQWG*}0|Ogg+(063yxv94!`fpVtPK2sZj
zsO>*4v5J81L0Fx&`gA9`vPzP*p0cZ7vMLnOvG{!DrcNU7ChELT&FX`=d0|9>JSNXn
z>C?`GnSD1){$2E4@GP?V9y)bkAe@}hbEkXln*D0A!JLp=;5!wH?%H0R^K2w$FTU<A
zyrc(E))9w}T61CrKkt8NeK;}O@ba{hpTP5$UD3fgty5wlZ4oiv;rfYG(pIGL$oLzJ
zq`8i^UQZ;fI|y|4?Rs}i5a*Gpgk;Z?de|Gi=QG*3^6NJv%sk~*+5}7Ex`Wfe)Py1M
zq~sgzgqs^?D%<N3$q$=$IelzxmywAJg%%N^x)Vse!q2PwanHvP2OQ8&B@zm8$R4qd
zJ#!XsQ7}t&qH2&rBx3PRDixu{a}G?vF&5fJCN8ag%Itc!Pd8O5BGRX|A>Z`^7YcdT
zU4%ZwMK@DG0g%7Pf;@`yZl^;akFzDRRne{~9poStq^s>L<-t~~p{^^Vv0wU1x4NX7
zA$JUJKq1M8Yv_xmxAdKwn54DSB9;tP?DrRu0<LpxmB~ElSaDuP1ZN(hJ~3))L%kEr
z^=9pU`;5EuC}J_%;tHij1?nztx`q$p(#q5gYrr}DB0D^qvD(ZU8u?ApI<{^ei1Bm5
zR=oMjrtI(KbIzdzNAX(pQjZ9yzp4^*-eKL(*{UXcz2HUHFb@UGPn64G*66WT>D6d|
ztAjMm77E^a(M`$HF#XZ@*gR`+`5AQWxU18*mZ9qPF-xVUHi}N6gO{U08PMP(2_nn>
z8}&8*;sN>6@sjE@x`J8Dr04pjD(jPtUNv)vA0JkH@8*e7c{5h#C0{zlFwvW-;bi3|
z)-u8}kpX_WH9i}iIp)Vx!&~CB+rVMpyD`&pGvls@7t(!yeK*+ti~t*8nEz}cE}k}!
zAM3}<Bt6*D3=G*mVrH3BLBM1Q_qVc)P%TVj;!Skh@Ru$*MIaiBmpj|OkBo=sI+G9W
zeg8T(YyXtHZY@ugy`M+77>J@F{809G{gTzQh1Y2x(@e%Si@;2k#*D&mkmpP(61vC{
zy=S=1aB)-<7n-UL6XNnea7(8#>v1E|JmpK!UVTnxY1M8qT`R2|H+*D5&8Xo)$pYCG
z!I2(t*6|Kb=B@JSL#heQ431|>KDz%B^AnoG3=+3?Hd~mSN6E0v>j)`*(5Ka2efXr+
zq6H-HE!PJGK?L}yZ|rH1aCh5{=Czb9Atb7+>RKOsv+sxYnZIl){)l<kvAZ`x4Ba*^
zSh>Fk(S@l_Ae)d$ne<)`e;e`xrw<YO=bV5CB9BH)+E{P<Sl8nBDCXD`e{rIcFB204
zXx$>QOI5n-G7PfE;!RO<;6;|rI*Q%Q$O)y48l*qK9RFmc(x#RUU1WfS8$Jz24cUg4
zRn^nm4Qqc`WnsMg$x<>{oZLJL-VmL>BeCK2ToJmP2GvBb?#vlir^D{2^;jwpaXUP>
z3+eZCzBhBxl6tN^A~|Pbga?TcAEon;BfUwC#j<Vtg1@d~hdj}8OPul>uYd2Pg#@B2
zwqV{|=1Ey#yzB>m?%hc`>^7(*tH?iom!XQ&KwMIR9lfP9PMo=r<z5^cd8kM3<@}iU
z$ZU#bk6^@VOR{2i!YhOQe7NPp6>2rNYxX`AISxWY*%uW_HXtIW9Wit-@WStVE41!N
z5_Fc8+j_KTEwW?Anc=;Ed~a`$0Wh^|<4X8-B=u-Dx+O><z>tfAmGzmdLnqso{h*ov
z?dl~2cgX|K^t8ER?xsNheF-zQH&Jx5clh%;u;*(#BnY-m)5D(3abR`))6B@h;cAo4
zNO)jB%YhNReRezKTXeb|Lx`w4XC8@{W;vYn>|$$=3yW$pVmxoc#c2=L!o3ao2B8G(
zp)AItS@D$!a{TEp%;maCxuW)BwinHKu?_YbS&|Phnvn?w)fd8O?G90@q^XRJBUP6W
z6`oq8E`q^atZt%_f>6)VpmF#Wt}TcKvGopH$`qDR-^Sa<cn`w^-boEdG+;r8+R%3r
zZ4~aEk+E+e=S+12W0y&|m8@~>$vn}V`Gt*l*(y%Ls&_3SmwB~>*Ohxb3#*Yy%befX
zwc;|JOe!7$+6Vaz@hvCziypO8-8Ox^QmPlZK!}4S@N|_*YllU?T7}b!Fg(!@Yb{t?
zf}XBmnPKH~U3J!h6OXB*WfH#B<g>8*eOPOcDxP$Fr_>(|e}v3wQi&+?1Q4^0GemL5
z>_=7)5Z+dlUxydmblj0&Z#ZN>0J+a&frez7ZHjEsQ8&)n#%N?QU9&6`NzOM2&dE0_
zRxS($!VAWxH@*(!o@*vA(xrQYoAqih5pEKD-FfD5h5hwm8C!&PAKc$FW@7II`H?c^
zzAG`X@rapvE-=x*hzae16|=l#k*Z?xXI*bpws6~N8S%^J!9X~sg3oSlX7A4&ss+>`
zI|!4~rOULL60~rgRdGcri346l!f~xsDgjTm-=*_>>85V!tCg;+-m$8JkHpjc5}hPd
zmzqeHE6wQYgL2y$|FvS~M=Kr9gJFVkj%IVDVcLjqmPp-*;tzG&hofRl-vE6oc~ErR
zkONd0a&863bS0)_RspJ=_|fkzi)l&QV0=u<>{jx1aRN@d3KbS)j2}^q#ZL6;@LMsc
zH85e(4k0SkA%)B=lT>Ncs}nVKR|$eysJ2JNS83djPmyDMy%2>7zSKTNzR2*}W11f-
z56z!c7Z}pdfhuF<3|Frea_?oEVrg7{)InV+zk780tT*Hnl-nP0E<frQcxT!7^q^5c
zK`=Z)3-sP7sbrBhLw?KxIt}$vd(2l7^5}BQgA26WaQf`zk7pP&R&hUFSTbB-$-urI
z1HY?L(Ft-2FvTxq`#gf-sFXDjequ%%5a;%Q)Sr1z**!9uy>m_TyO7<ZcpO4D$IXsd
zgZo;g3X@?p4@W<%y-itB&Q@t2vD4_OnJSnr1tzuf8aB3rp;AtI1|`D2f;LSefI)ZF
z9$#=yKbNw1rKmH-@UHa6i{K8sj}RcWn7DU`shnHtN?(6~+ny}L;$u*=ZB-k}>wA%G
z8C1BKwCW1pWEQzvhZO0-9;<D#o+P01iH8M#L0}`by6L+VM%J|(Dvm<&o@XewRS}s!
zY0FWk1SbV^)I$*qADx=4s@@&#k0S-`V7R?9&f^eWD<45k13SqritK7oy3IF_g=92H
zHpgjQ?BlU3@q7?7A7w6nzIvYDSKP>u_ay;!QD*#+qEKk)M<p^}9nP{eGXZ=%)jU*T
zf57Q3K5YysuO&GuIwS8~RNAr?90XtbiBgFv2hCc3H@kfoN#fusx}psHEg;-~m&sw-
z`0f0QX#UH=-yQQx-Mv0nO)&zN;TuKrKZE|M_THf2;L3hten^u4U$84t^!i){YlW54
z4~g_9(%-kc5=pPm6=41v@b4G=Q#8E+!v0)<g@whrhW%c&|MR|A+T!)O3eO1BVPJm#
zLutIZ`gO<pQ)|3I!@;Tjh5e;G{$lLf%b&W>FE7|AKW^}s3iQjv|Dv!Q@WaE6O7Wl9
z|5K;<75KyNuwSahuekrdEB<ou6xK6f+&TZ;9DhOo*OmG3ejC=mVAm1<oa(<K>irJ;
zXU6}D{&T|oLSw@Ox1Srr&Aj;&{%2481y8^Ivs7;MdPNzeAHOvm*!Ix{t4KP+EA#&Y
DTWDAU

literal 0
HcmV?d00001

diff --git a/assays/Culture-independentCommunityProfiling/protocols/.gitkeep b/assays/Culture-independentCommunityProfiling/protocols/.gitkeep
new file mode 100644
index 0000000..e69de29
diff --git a/assays/Culture-independentCommunityProfiling/protocols/Culture-independentCommunityProfilingProtocol.md b/assays/Culture-independentCommunityProfiling/protocols/Culture-independentCommunityProfilingProtocol.md
new file mode 100644
index 0000000..090b4a9
--- /dev/null
+++ b/assays/Culture-independentCommunityProfiling/protocols/Culture-independentCommunityProfilingProtocol.md
@@ -0,0 +1,3 @@
+## Culture-independent community profiling
+
+Bacterial communities were profiled by amplicon sequencing of the variable v5-v7 regions of the bacterial 16S rRNA gene. Library preparation for Illumina MiSeq sequencing was performed as described previously (Duran, P. et al., 2018). In all experiments, multiplexing of samples was performed by double-indexing (barcoded forward and reverse oligonucleotides for 16S rRNA gene amplification).
\ No newline at end of file
-- 
GitLab