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E-GEOD-16399 - Gene expression profiling in Salmonella Typhimurium encountered with heterophils

Status
Released on 1 January 2011, last updated on 1 May 2014
Organism
Salmonella enterica subsp. enterica serovar Typhimurium
Samples (32)
Array (1)
Protocols (14)
Description
To study the pathogenicity of Salmonella Typhimurium (ST) in heterophils, a whole Salmonella genome array was used to analyze RNA isolated from Salmonella in vitro encountered with heterophils (30 min, 1 h, 2 h, and 3 h) or medium control (NS). Dual-color, direct comparisons were carried out between heterophils-encountered ST and non-encountered controls (30 min vs. NS (30M/NS), 1 h vs. NS (1HR/NS), 2 h vs. NS (2HR/NS) and 3 h vs. NS (3HR/NS)). Each comparison includes four biological replicates. Out of 4588 genes on an array, there were 605, 758, 944 and 945 genes differentially expressed in the comparisons of 30M/NS, 1HR/NS, 2HR/NS and 3HR/NS, respectively (P < 0.001, fold-change > 2). Most of the Salmonella genes associated with invasion function were found differentially expressed at 2HR/NS and 3HR/NS comparisons. These candidate genes include TypeIII-secreted protein effector sopE2, Invasion proteins (e.g. invA, invE, invG, invH), and Invasion genes tranction activator hilA. The results of continuous transcriptional changes provide important information to elucidate the pathogenicity of ST in heterophils. Dual-color, common reference comparisons were carried out between heterophils-encountered ST and non-encountered controls (30 min vs. NS (30M/NS), 1 h vs. NS (1HR/NS), 2 h vs. NS (2HR/NS) and 3 h vs. NS (3HR/NS)). Four biological replicates, with dye swap labeling, were included in each of comparisons. Background subtracted signal intensity were collected from 16 arrays and normalized before data analysis.
Experiment type
transcription profiling by array 
Contacts
Huaijun Zhou <geo@ncbi.nlm.nih.gov>, Christina L Swaggerty, Hsin-I Chiang, Michael H Kogut, Scot E Dowd
MIAME
PlatformsProtocolsVariablesProcessedRaw
Files
Investigation descriptionE-GEOD-16399.idf.txt
Sample and data relationshipE-GEOD-16399.sdrf.txt
Raw data (1)E-GEOD-16399.raw.1.zip
Processed data (1)E-GEOD-16399.processed.1.zip
Array designA-GEOD-8140.adf.txt
R ExpressionSetE-GEOD-16399.eSet.r
Links