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Sample GSM1386765 Query DataSets for GSM1386765
Status Public on Feb 19, 2015
Title WT_Bi replicate 2
Sample type RNA
 
Channel 1
Source name WT_Bi
Organism Citrobacter rodentium
Characteristics genotype: wild type
agent: bicarbonate
Treatment protocol Bicarbonate was added to a final concentration of 45mM
Growth protocol overnight cultures of Citrobacter rodentium were inoculated into LB medium to obtain an OD600 of 0.1 and grown until the OD600 was 0.8-0.9
Extracted molecule total RNA
Extraction protocol 10mL of a culture was incubated with 20mL of RNAprotect solution (Qiagen) at room temperature for 15min. Cells were pelleted and RNA was purified using a FastRNA Pro Blue kit (Qbiogene). RNA samples were Dnase treated (Qiagen) and further purified using an RNeasy MiniElute kit (Qiagen).
Label Cy3
Label protocol 5microg of total RNA was labeled with Cy3-ULS or Cy5-ULS (Kreatech) as per manufacturers instructions
 
Channel 2
Source name Reference
Organism Citrobacter rodentium
Characteristics sample: common reference
Treatment protocol Bicarbonate was added to a final concentration of 45mM
Growth protocol overnight cultures of Citrobacter rodentium were inoculated into LB medium to obtain an OD600 of 0.1 and grown until the OD600 was 0.8-0.9
Extracted molecule total RNA
Extraction protocol 10mL of a culture was incubated with 20mL of RNAprotect solution (Qiagen) at room temperature for 15min. Cells were pelleted and RNA was purified using a FastRNA Pro Blue kit (Qbiogene). RNA samples were Dnase treated (Qiagen) and further purified using an RNeasy MiniElute kit (Qiagen).
Label Cy5
Label protocol 5microg of total RNA was labeled with Cy3-ULS or Cy5-ULS (Kreatech) as per manufacturers instructions
 
 
Hybridization protocol Hybridization was conducted as per Agilent 2 color microarray-based gene expression analysis manual (version 5.7) with the modification 4 microg of labeled total RNA was used per hybridization.
Scan protocol Images were quantified using Agilent Feature Extraction Software.
Data processing Data was normalised within arrays using loess normalisation, and between arrays with quantile normalisation in limma. DE was analyzed in limma with:
design<-cbind(array=c(0,0,0,0,0,0,0,0,1,1,1,1,1,1,1,1),
citr=c(0,0,0,-1,0,0,0,0,0,0,0,0,0,-1,0,0),
citr_bi=c(0,0,0,0,0,-1,0,0,0,0,0,-1,0,0,0,0),
mut=c(0,0,0,0,-1,0,0,0,0,0,-1,0,0,0,0,0),
mut_bi=c(0,0,0,0,0,0,-1,0,0,0,0,0,-1,0,0,0),
sms=c(0,0,0,0,0,0,0,-1,0,-1,0,0,0,0,0,0),
sms_bi=c(0,-1,0,0,0,0,0,0,0,0,0,0,0,0,0,-1),
wt=c(0,0,-1,0,0,0,0,0,-1,0,0,0,0,0,0,0),
wt_bi=c(-1,0,0,0,0,0,0,0,0,0,0,0,0,0,-1,0))
contrast.matrix<-cbind(mu_wt=c(0,0,0,1,0,0,0,-1,0),
citr_wt=c(0,1,0,0,0,0,0,-1,0),
sms_wt=c(0,0,0,0,0,1,0,-1,0),
mu_bi_wt_bi=c(0,0,0,0,1,0,0,0,-1),
citr_bi_wt_bi=c(0,0,1,0,0,0,0,0,-1),
sms_bi_wt_bi=c(0,0,0,0,0,0,1,0,-1),
wt_bi_wt=c(0,0,0,0,0,0,0,-1,1),
mu_bi_mu=c(0,0,0,-1,1,0,0,0,0),
citr_bi_citr=c(0,-1,1,0,0,0,0,0,0),
sms_bi_sms=c(0,0,0,0,0,-1,1,0,0),
sms_citr=c(0,-1,0,0,0,1,0,0,0),
sms_citr_bi=c(0,0,-1,0,0,0,1,0,0),
citr_mu=c(0,1,0,-1,0,0,0,0,0),
citr_mu_bi=c(0,0,1,0,-1,0,0,0,0),
sms_mu=c(0,0,0,-1,0,1,0,0,0),
sms_mu_bi=c(0,0,0,0,-1,0,1,0,0))
 
Submission date May 15, 2014
Last update date Feb 19, 2015
Contact name Matthew J Wakefield
E-mail(s) [email protected]
Organization name Walter and Eliza Hall Institute
Department Bioinformatics
Street address 1G Royal Parade
City Parkville
State/province VIC
ZIP/Postal code 3050
Country Australia
 
Platform ID GPL7345
Series (1)
GSE57689 Analysis of the evolutionary adaptation of an AraC-like global regulatory protein in the murine enteric pathogen Citrobacter rodentium

Data table header descriptions
ID_REF
VALUE normalized log2 ratio (Cy5/Cy3)

Data table
ID_REF VALUE
1 0.890117931138019
2 0.067764484486261
3 0.0449006365437177
4 0.0306860114884662
5 0.139364784351218
6 0.0385362038653756
7 -0.252543519137219
8 0.76605862159163
9 -0.243043771690862
10 -0.136801114593101
11 0.332408722514648
12 -0.241608736920084
13 0.289150569061196
14 0.229681372971323
15 0.0220036011004896
16 -0.0940555960365588
17 -0.0121695015792893
18 -0.359449250424843
19 -0.126163257288968
20 0.184148709922939

Total number of rows: 15744

Table truncated, full table size 371 Kbytes.




Supplementary file Size Download File type/resource
GSM1386765_US83403541_251966710005_S01_GE2_105_Dec08_2_3.txt.gz 4.1 Mb (ftp)(http) TXT
Processed data included within Sample table
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