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GenomicsDecoding genome-wide GadEWX transcriptional regulatory networks reveals a multifaceted cellular response to acid stress in Escherichia coli
This SuperSeries is composed of the SubSeries listed below. Refer to individual Series
ORGANISM(S): Escherichia coli str. K-12 substr. MG1655 
2015-08-11 | E-GEOD-66482 | biostudies-arrayexpress
TranscriptomicsRNA polymerase
This SuperSeries is composed of the SubSeries listed below. Refer to individual Series
ORGANISM(S): Escherichia coli str. K-12 substr. MG1655 
2014-02-05 | E-GEOD-46740 | biostudies-arrayexpress
GenomicsDecoding genome-wide GadEWX transcriptional regulatory networks reveals a multifaceted cellular response to acid stress in Escherichia coli [ChIP-seq]
The response to acid stress is a fundamental process in bacteria. Three transcription factors, GadE, GadW, and GadX (GadEWX) are known to play a critical role in the transcriptional regulation of glutamate-dependent acid resistance (GDAR) system in Escherichia coli K-12 MG1655. However, the regulato...
ORGANISM(S): Escherichia coli str. K-12 substr. MG1655 
2015-08-11 | E-GEOD-66441 | biostudies-arrayexpress
TranscriptomicsDecoding genome-wide GadEWX transcriptional regulatory networks reveals a multifaceted cellular response to acid stress in Escherichia coli [RNA-seq]
The response to acid stress is a fundamental process in bacteria. Three transcription factors, GadE, GadW, and GadX (GadEWX) are known to play a critical role in the transcriptional regulation of glutamate-dependent acid resistance (GDAR) system in Escherichia coli K-12 MG1655. However, the regulato...
ORGANISM(S): Escherichia coli 
2015-08-11 | E-GEOD-66481 | biostudies-arrayexpress
TranscriptomicsExpression profiling of E. coli rpoS knock-out strain during stationary phase in M9 minimal media with 0.2% glucose
Investigation of whole genome gene expression level in E. coli rpoS knock-out strain grown up to stationary phase in M9 minimal media supplemented with 0.2% glucose E. coli rpoS deletion mutant grown up to OD600nm 1.5 (stationary phase) in M9 minimal media supplemented with 0.2% glucose. The high-de...
ORGANISM(S): Escherichia coli str. K-12 substr. MG1655 
2014-02-05 | E-GEOD-46543 | biostudies-arrayexpress
TranscriptomicsStructural systems biology evaluation of metabolic thermotolerance in Escherichia coli
Investigation of whole genome gene expression level in E. coli K-12 MG1655 in glucose M9 minimal media with/without heatshock A six chip study using total RNA recovered from E. coli K-12 MG1655 grown up to OD600nm 0.6 (mid-exponential phase) in M9 minimal media supplemented with 0.2% glucose with/wi...
ORGANISM(S): Escherichia coli str. K-12 substr. MG1655 
2013-06-20 | E-GEOD-42675 | biostudies-arrayexpress
TranscriptomicsGenome-scale reconstruction of the sigma factor network in E. coli
We report the application of single-molecule-based sequencing technology for high-throughput profiling of transcription start sites for Escherichia coli under different conditions. By obtaining sequence from 5' RACE (rapid amplification of cDNA ends) followed by deep sequencing, we generated genome-...
ORGANISM(S): Escherichia coli str. K-12 substr. MG1655 
2014-02-05 | E-GEOD-46737 | biostudies-arrayexpress
TranscriptomicsChIP-chip of E. coli K-12 MG1655 with antibody against RNA polymerase subunits, RpoB, RpoD, RpoS,RpoH, RpoN, FliA, and FecI
We investigate sigma factor binding regions for each sigma factor under various enviromental and/or genetic conditions. To measure sigma factor binding at a genome scale, we employed a ChIP-chip method to derivative strains of E. coli K-12 MG1655 wild type and its isogenic rpoS and rpoN knock-out s...
ORGANISM(S): Escherichia coli str. K-12 substr. MG1655 
2014-02-05 | E-GEOD-46541 | biostudies-arrayexpress
TranscriptomicsComparative analysis of regulatory elements between Escherichia coli and Klebsiella pneumoniae by genome-wide transcription start site profiling [TSS-Seq]
We report the application of single-molecule-based sequencing technology for high-throughput profiling of transcription start sites for two enterobacteria: Escherichia coli and Klebsiella pneumoniae.By obtaining over fourteen billion bases of sequence from 5' RACE (rapid amplification of cDNA ends) ...
ORGANISM(S): Escherichia coli K-12 
2012-07-30 | E-GEOD-35821 | biostudies-arrayexpress
TranscriptomicsDeciphering the Fur transcriptional regulatory network highlights its complex role beyond iron metabolism in Escherichia coli
This SuperSeries is composed of the SubSeries listed below. Refer to individual Series
ORGANISM(S): Escherichia coli str. K-12 substr. MG1655 
2014-09-09 | E-GEOD-54901 | biostudies-arrayexpress
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