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Series GSE20397 Query DataSets for GSE20397
Status Public on Jul 22, 2010
Title Transcriptomes of genetically distinct E. coli O157:H7 strains
Organism Escherichia coli
Experiment type Expression profiling by array
Summary Transcriptomes of 24 clinical strains of E. coli O157:H7 that differ phylogenetically and by Shiga toxin profiles were compared after 30 min co-incubation with epithelial cells.
 
Overall design Total RNA was harvested from the 24 O157:H7 strains exposed to, but not attached to, MAC-T epithelial cell monolayers for 30 min, using a previously described in vitro model of O157:H7 exposure to MAC-T cells. The microarray platform (Operon E. coli oligo set version 1.0.2) probes for 5978 ORFs from E. coli O157:H7 Sakai, O157:H7 EDL 933, and K12 MG1655, and for 110 ORFs from the pO157 plasmid. Thirty-six dye-swap hybridizations were performed between four groups with six strains per group, according to a balanced double loop design. Strains were grouped based on cladestx profiles and each strain was considered an independent biological replicate of its group (n=6). The six strains from each group were randomly hybridized with six strains from every other group; each hybridization compared a pair of strains that differed in either clade or stx profile, or both.
 
Contributor(s) Abu-Ali GS, Ouellette LM, Henderson ST, Lacher DW, Riordan JT, Whittam TS, Manning SD
Citation(s) 20422047
Submission date Feb 17, 2010
Last update date Mar 22, 2012
Contact name galeb abu-ali
E-mail(s) abualiga@msu.edu
Organization name michigan state university
Department NFSTC
Lab Microbial Evolution
Street address NFSTC
City East Lansing
State/province MI
ZIP/Postal code 48824
Country USA
 
Platforms (1)
GPL7445 MSU E. coli 6.1.K Ver. 1.0.2
Samples (36)
GSM510507 strains TW07961 vs TW11029 epithelial exposure
GSM510508 strains TW14279 vs TW10045 epithelial exposure
GSM510562 strains TW04863 vs TW14279 epithelial exposure
Relations
BioProject PRJNA125527

Download family Format
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Supplementary file Size Download File type/resource
GSE20397_RAW.tar 47.0 Mb (http)(custom) TAR (of GPR)
Processed data included within Sample table
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