GEO DataSets

(Submitter supplied) The fitness landscape is a concept commonly used to describe evolution towards optimal phenotypes. It can be reduced to mechanistic detail using genome-scale models (GEMs) from systems biology. We use recently developed GEMs of Metabolism and protein Expression (ME-models) to study the distribution of Escherichia coli phenotypes on the rate-yield plane. We found that the measured phenotypes distribute non-uniformly to form a highly stratified fitness landscape. more...

Organism:

Escherichia coli str. K-12 substr. MG1655

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL24659 GPL17024

18 Samples

Download data: CSV

(Submitter supplied) We compared the exposure of E. coli MG1655 to ten commonly used antiseptics and disinfectants for short (30min) and long (7-12h) term, looking for common and unique stress response elements.

Organism:

Escherichia coli str. K-12 substr. MG1655

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17024

45 Samples

Download data: CSV, XLSX

(Submitter supplied) Previously unpublished expression data from E. coli K-12 MG1655 involved in the creation of a large RNAseq database.

Organism:

Escherichia coli str. K-12 substr. MG1655; Escherichia coli BW25113

Type:

Expression profiling by high throughput sequencing

4 related Platforms

12 Samples

Download data: CSV

(Submitter supplied) We report binding of Topoisomerase IV on the E. coli genome. We report the cleavage sites of Topoisomerase IV on the E. coli genome

Organism:

Escherichia coli str. K-12 substr. MG1655

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL17024

20 Samples

Download data: WIG

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Escherichia coli str. K-12 substr. MG1655

Type:

Expression profiling by genome tiling array; Genome binding/occupancy profiling by genome tiling array

Platforms:

GPL17024 GPL8708 GPL15010

24 Samples

Download data: PAIR, TXT, WIG

(Submitter supplied) As descirbed in the manuscript "The impact of anaerobiosis on expression of the iron-responsive Fur and RyhB Regulons" we mapped the locations of Fur DNA binding in E. coli K12 under aerobic or anaerobic growth conditions and anerobic iron deficient growth conditions.

Organism:

Escherichia coli str. K-12 substr. MG1655

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL17024 GPL15010

9 Samples

Download data: WIG

(Submitter supplied) In this study transcriptional start sites (TSS) of E. coli were determined for several growth conditions

Organism:

Escherichia coli str. K-12 substr. MG1655

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL17024 GPL15010

22 Samples

Download data: WIG

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Escherichia coli; Escherichia coli O157:H7; Escherichia coli str. K-12 substr. MG1655; Escherichia coli O157:H7 str. Sakai

Type:

Expression profiling by array; Expression profiling by high throughput sequencing

4 related Platforms

12 Samples

Download data: GPR, GTF, TXT

(Submitter supplied) UV-crosslinking and high througput sequencing of cDNAs (CRAC) was used to map the binding sites Hfq in enterohaemorhaggic E. coli (EHEC). Hfq was tagged with a His-FLAG dual affintiy tag and UV crosslinked after growth in the MEM-HEPES media essentailly as per Granneman et al (2009) PNAS. We additionally crosslinked Hfq in non-pathogenic E. coli K12 str. MG1655 grown in LE media. Hfq-RNA complexes were purified and trimmed using RNase A/T1. more...

Organism:

Escherichia coli O157:H7 str. Sakai; Escherichia coli str. K-12 substr. MG1655

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL17026 GPL17024 GPL17025

11 Samples

Download data: GTF

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Escherichia coli K-12; Escherichia coli str. K-12 substr. MG1655

Type:

Expression profiling by array; Genome binding/occupancy profiling by genome tiling array; Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL17024 GPL8708 GPL14649

13 Samples

Download data: GFF, PAIR, TXT, WIG

(Submitter supplied) We found many binding sites for ArcA under glucose fermentative anaerobic growth conditions. Descirbed in the manuscript "The response regulator ArcA uses a diverse binding site architechture to globally regulate carbon oxidation in E. coli"

Organism:

Escherichia coli str. K-12 substr. MG1655

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL17024

2 Samples

Download data: WIG