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Sample GSM1386752 Query DataSets for GSM1386752
Status Public on Feb 19, 2015
Title SMS_Bi
Sample type RNA
 
Channel 1
Source name SMS_Bi
Organism Citrobacter rodentium
Characteristics genotype: EColiSMS complemented RegA mutant
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 0.363128541962869
2 0.0220737311256569
3 0.0720391937975355
4 -0.00505010544624435
5 0.10760976158101
6 0.0995991671478272
7 -0.100857009259439
8 -0.142617177186935
9 0.145340974331771
10 -0.0925268218261032
11 -0.537105197565976
12 0.131683881546953
13 -0.144077086324517
14 0.269508891066423
15 0.196398982848534
16 0.253366175696483
17 -0.249656766431486
18 -0.197637722309175
19 0.10976099676313
20 0.210823366105875

Total number of rows: 15744

Table truncated, full table size 371 Kbytes.




Supplementary file Size Download File type/resource
GSM1386752_US83403541_251966710007_S01_GE2_105_Dec08_1_2.txt.gz 3.9 Mb (ftp)(http) TXT
Processed data included within Sample table
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