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Sample GSM789201 Query DataSets for GSM789201
Status Public on Mar 01, 2012
Title LB + bile salts, OD600=0.2, biological rep2
Sample type RNA
 
Source name E24377A grown in LB + bile salts (3% w/v) at OD600=0.2
Organism Escherichia coli O139:H28 str. E24377A
Characteristics treatment: grown in LB + bile salts (3% w/v) at OD600=0.2
Growth protocol Single colonies were grown overnight at 37C and 225 rpm in 5 ml LB. The next day, cultures were diluted 1:100 in 25 ml LB, grown at 37C at 225 rpm
Extracted molecule total RNA
Extraction protocol Cultures were either extracted using the RiboPure RNA kit from ambion, or a acid phenol/lithium chloride method
Label biotin
Label protocol Digested cDNA was end-labeled with Biotin-11-ddATP (Perkin Elmer, P/N NEL548001EA) using Terminal Deoxynucleotidyl Transferase, and verified by gel shift assay, according to Affymetrix standard protocols
 
Hybridization protocol A hybridization mixture was prepared that contained labeled cDNA, 7.8% DMSO and OligoB2 mixture (Affymetrix, P/N 900301) according to the manufacturers protocols. GeneChips were prepared by pre-hybridization for 10 minutes at 45ºC with the kit pre-hybridization solution; samples were denatured at 95ºC for 1 minute, equilibrated to 45ºC, centrifuged, and transferred to prepared arrays. Hybridization was continued in a rotating incubator for 16h at 60 rpm and 45ºC. Post-hybridization, the hybridization cocktail was recovered and the arrays washed and stained using the standard Affymetrix ProkGE-WS2v3_450 fluidics protocol and GeneChip Hybridization, Wash and Stain Kit reagents (Affymetrix, P/N 900720).
Scan protocol Chips were scanned with the Affymetrix GCOS software
Description Expression in bile salts at low growth density
Data processing Array data was processed with the Simpleaffy bioconductor package in R
 
Submission date Aug 31, 2011
Last update date Mar 01, 2012
Contact name Jason Sahl
E-mail(s) jasonsahl@gmail.com
Organization name University of Maryland
Department School of Medicine
Lab Institute for Genome Sciences
Street address 801 West Baltimore St.
City Baltimore
State/province MD
ZIP/Postal code 21201
Country USA
 
Platform ID GPL13175
Series (2)
GSE31804 Expression data of enterotoxigenic (ETEC) isolate E24377A
GSE31806 E. coli strain E24377A

Data table header descriptions
ID_REF
VALUE GC-RMA signal

Data table
ID_REF VALUE
A0001_at 8.547209752
A0003_at 7.705555139
A0004_at 8.495611771
A0009_s_at 10.66919078
A0011_s_at 12.41013881
A0014_s_at 6.296683397
A0015_s_at 6.329504794
A0019_s_at 9.118708379
A0020_s_at 8.522187058
A0022_s_at 5.302305137
A0023_s_at 7.13772565
A0024_s_at 9.005068285
A0025_s_at 7.256173702
A0026_s_at 7.081764746
A0027_s_at 6.879023695
A0028_at 7.302511416
A0029_at 6.861966807
A0030_s_at 7.894886026
A0031_s_at 8.690065493
A0032_s_at 7.340742596

Total number of rows: 23163

Table truncated, full table size 536 Kbytes.




Supplementary file Size Download File type/resource
GSM789201_ETECIKS_LBB-OD02-B.CEL.gz 2.1 Mb (ftp)(http) CEL
Processed data included within Sample table

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