Similar studies for GEO DataSets (Select 200025106) - GEO DataSets

Links from GEO DataSets

Items: 20

Select item 2000251061.

Transcriptome of an intestine-adapted Escherichia coli K-12 mutant selected by animal passage for superior colonization

(Submitter supplied) Transcription profiling of wild type E. coli MG1655, intestine-adapted E. coli MG1655star, and E. coli MG1655 flhD mutant grown on glucose, mannose, and mucus. We previously isolated a spontaneous mutant of E. coli K-12, strain MG1655, following passage through the streptomycin-treated mouse intestine, which has colonization traits superior to the wild-type parent strain (Leatham, et. al., 2005, Infect Immun 73:8039-49) The intestine-adapted strain (E. more...

Organism:: Escherichia coli CFT073; Bacillus anthracis; Bacteroides thetaiotaomicron VPI-5482; Salmonella enterica subsp. enterica serovar Typhimurium str. LT2; Escherichia coli O157:H7 str. Sakai; Escherichia coli O157:H7 str. EDL933; Enterococcus faecalis V583; Escherichia coli str. K-12 substr. MG1655

Type:: Expression profiling by array

Platform:: GPL6702
13 Samples

Download data: CEL, TXT

Series

Accession:: GSE25106

ID:: 200025106

PubMed Full text in PMC Similar studies Analyze with GEO2R

Select item 2000112542.

Carbon nutrition of pathogenic and commensal E. coli

(Submitter supplied) Transcriptome profiling of E. coli MG1655, E. coli EDL933, E. coli ECOR26, and E. coli Nissle 1917 grown on mouse cecal mucus as carbon source The carbon sources that support growth of pathogenic E. coli O157:H7 in the mammalian intestine have not previously been investigated. In vivo, pathogenic E. coli EDL933 primarily grows as dispersed single cells within the mucus layer that overlies the mouse cecal epithelium. more...

Organism:: Salmonella enterica subsp. enterica serovar Typhimurium str. LT2; Bacillus anthracis; Escherichia coli CFT073; Bacteroides thetaiotaomicron VPI-5482; Escherichia coli O157:H7 str. Sakai; Escherichia coli str. K-12 substr. MG1655; Escherichia coli; Escherichia coli O157:H7 str. EDL933; Enterococcus faecalis V583

Type:: Expression profiling by array

Platform:: GPL6702
16 Samples

Download data: CEL, TXT

Series

Accession:: GSE11254

ID:: 200011254

PubMed Full text in PMC Similar studies Analyze with GEO2R

Select item 2001267103.

RNA-seq of Escherichia coli K-12 MG1655 and Stx2 phage lysogens

(Submitter supplied) Here, we investigated the impact of Stx2 phage carriage on Escherichia coli (E. coli) K-12 MG1655 host gene expression. Using quantitative RNA-seq analysis, we compared the transcriptome of naïve MG1655 and the lysogens carrying the Stx2 phage of the 2011 E. coli O104:H4 outbreak strain or of the E. coli O157:H7 strain PA8, which share high degree of sequence similarity.

Organism:: Escherichia coli K-12

Type:: Expression profiling by high throughput sequencing

Platform:: GPL26204
9 Samples

Download data: CSV

Series

Accession:: GSE126710

ID:: 200126710

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 2002416584.

Nitrogen nutrition of E. coli in the mammalian intestine

(Submitter supplied) Our focus of this study is to determine the differential expression of genes related to uptake and degradation of nitrogenous compounds in E. coli colonizing the mouse intestine as compared to E. coli grown in minimal medium in vitro. We colonized CD-1 male mice with E. coli MG1655 StrR wild type and extracted the total RNA from mouse cecal mucus (GSE217743). We also colonized CD-1 male mice with E. more...

Organism:: Escherichia coli str. K-12 substr. MG1655

Type:: Expression profiling by high throughput sequencing

Platform:: GPL26592
10 Samples

Download data: WIG

Series

Accession:: GSE241658

ID:: 200241658

PubMed Full text in PMC Similar studies

Select item 2002177435.

OmpC and bile tolerance are important for Escherichia coli colonization of the mammalian intestine

(Submitter supplied) Our focus of this study is to determine the gene expression changes in E. coli colonizing the mouse intestine as compared to E. coli grown in minimal medium in vitro. We colonized CD-1 male mice with E. coli MG1655 StrR wild type and extracted the total RNA from mouse cecal mucus. We also extracted E. coli MG1655 StrR RNA from in vitro culture and sequenced and compared to determine the genes important for E. more...

Organism:: Escherichia coli str. K-12 substr. MG1655

Type:: Expression profiling by high throughput sequencing

Platform:: GPL26592
5 Samples

Download data: WIG

Series

Accession:: GSE217743

ID:: 200217743

PubMed Full text in PMC Similar studies

Select item 2000218396.

Transcriptome analysis of wild type E. coli (K-12 MG1655) comparing to mutant E. coli strain (ECOM4) under aerobic and anaerobic conditions

(Submitter supplied) Cytochrome oxydases and quinol monooxygenase were removed from the E. coli genome resulting in oxygen-independent physiology We used microarray profiling to identify perturbed metabolic or regulatory functionality resulting in the inability to undergo aerobic-anaerobic shift.

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

Type:: Expression profiling by array

Platform:: GPL3154
12 Samples

Download data: CEL

Series

Accession:: GSE21839

ID:: 200021839

PubMed Full text in PMC Similar studies Analyze with GEO2R

Select item 2000613277.

Expression Profiling E. Coli Evolved on Glucose Minimal Media

(Submitter supplied) mRNA sequencing was performed on E. coli evolved at 37C on M9 Minimal Media with Glucose

Organism:: Escherichia coli str. K-12 substr. MG1655

Type:: Expression profiling by high throughput sequencing

Platform:: GPL17439
11 Samples

Download data: CSV

Series

Accession:: GSE61327

ID:: 200061327

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 2000406488.

Effect of simulated microgravity on E. coli K12 MG1655 growth and gene expression

(Submitter supplied) This study demonstrates simulated microgravity effects on E. coli K 12 MG1655 when grown on LB medium supplemented with glycerol. The results imply that E. coli readily reprograms itself to combat the multiple stresses imposed due to microgravity. Under these conditions it survives by upregulating oxidative stress protecting genes and simultaneously down regulating the membrane transporters and synthases to maintain cell homeostasis.

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

Type:: Expression profiling by array

Platform:: GPL3154
8 Samples

Download data: CEL, CHP

Series

Accession:: GSE40648

ID:: 200040648

PubMed Full text in PMC Similar studies Analyze with GEO2R

Select item 2000076959.

Caveat Mutator

(Submitter supplied) The use of whole genome microarrays for monitoring mutagenised or otherwise engineered genetic derivatives is a potentially powerful tool for checking genomic integrity. Using comparative genomic hybridization of a number of unrelated, directed deletion mutants in Escherichia coli K-12 MG1655 we identified unintended secondary genomic deletions in the flhDC region in deltafnr, deltacrp, and deltacreB mutants. more...

Organism:: Escherichia coli

Type:: Expression profiling by array; Genome variation profiling by array

Platform:: GPL3051
5 Samples

Download data

Series

Accession:: GSE7695

ID:: 200007695

PubMed Full text in PMC Similar studies Analyze with GEO2R

Select item 20000359110.

A reassesment of the FNR regulon and the effects of nitrate,nitrite, narXL and narQP

(Submitter supplied) The fumarate and nitrate reductase regulator protein, FNR, is a global transcription factor that regulates major biochemical changes as Escherichia coli adapts from aerobic to anaerobic growth. The ability of an fnr mutant to grow anaerobically in the presence of trimethylamine-N-oxide (TMAO) as the terminal electron acceptor was exploited in microarray experiments designed to determine a minimum number of Escherichia coli K-12 MG1655 operons that are regulated directly by FNR. more...

Organism:: Escherichia coli

Type:: Expression profiling by array

Platforms:: GPL3051 GPL1246
55 Samples

Download data

Series

Accession:: GSE3591

ID:: 200003591

PubMed Full text in PMC Similar studies Analyze with GEO2R

Select item 20002659111.

Genome-scale reconstruction of the PurR regulon reveals its role in the adenine stimulon of Escherichia coli K-12 MG1655

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

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

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

Platforms:: GPL3154 GPL8387
12 Samples

Download data: CEL, PAIR

Series

Accession:: GSE26591

ID:: 200026591

PubMed Full text in PMC Similar studies Analyze with GEO2R

Select item 20002658912.

ChIP-chip of E. coli K-12 MG1655 with antibody against PurR-8myc under various conditions.

(Submitter supplied) We integrated transcription factor binding regions and mRNA transcript abundance to elucidate the PurR regulon experimentally. To measure transcription factor binding at a genome scale, we employed a ChIP-chip method to derivative strains of E. coli K-12 MG1655 harboring PurR-8myc under various conditions.

Organism:: Escherichia coli str. K-12 substr. MG1655

Type:: Genome binding/occupancy profiling by genome tiling array

Platform:: GPL8387
4 Samples

Download data: PAIR

Series

Accession:: GSE26589

ID:: 200026589

PubMed Full text in PMC Similar studies Analyze with GEO2R

Select item 20002658813.

Transcriptome analysis of E. coli MG1655

(Submitter supplied) Expression profiling of wild type and purR deletion strains of E. coli K-12 MG1655 under both M9 minimal media and addition of adenine.

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

Type:: Expression profiling by array

Platform:: GPL3154
8 Samples

Download data: CEL

Series

Accession:: GSE26588

ID:: 200026588

PubMed Full text in PMC Similar studies Analyze with GEO2R

Select item 20002598214.

Effect of the global regulators RpoS and cyclic-AMP/CRP on the transcriptome of Escherichia coli K12 during carbon- and energy-limited growth

(Submitter supplied) The faecal indicator bacterium Escherichia coli K12 was used to study the effects of the global regulators RpoS and cAMP at the transcription level using microarray technology during short-term (physiological) adaptation to slow growth under limited nutrient supply. Effects due to the absence of one global regulator were assessed by comparing the mRNA levels isolated from rpoS or cya mutants under glucose-limited continuous culture at a dilution rate of 0.3 h-1 for the rpoS mutant or 0.16 h-1 for the cya mutant with those from wt E. more...

Organism:: Escherichia coli K-12

Type:: Expression profiling by array

Platform:: GPL534
6 Samples

Download data

Series

Accession:: GSE25982

ID:: 200025982

PubMed Full text in PMC Similar studies Analyze with GEO2R

Select item 20000178015.

The expression profile of Escherichia coli K-12 in response to minimal, optimal and excess copper concentrations

(Submitter supplied) The gene expression profile of E. coli K-12 MG1655 grown in minimal medium supplemented with elevated copper concentrations (as copper-glycine) has been analysed using whole genome oligonucleotide microarrays. “Pool” RNA was isolated from five independently grown 50ml DMA cultures of E. coli K-12 MG1655. “Test” RNA was isolated from three independently grown 50ml DMA cultures of E. coli K-12 MG1655, for each growth condition (no added CuSO4, or supplemented with either 0.75mM or 2mM copper glycine). more...

Organism:: Escherichia coli

Type:: Expression profiling by array

Platform:: GPL1246
9 Samples

Download data

Series

Accession:: GSE1780

ID:: 200001780

Select item 20000958716.

luxS-Dependent Gene Regulation in Escherichia coli K-12 Revealed by Genomic Expression Profiling (II)

(Submitter supplied) The bacterial quorum-sensing autoinducer 2 (AI-2) has received intense interest because the gene for its synthase, luxS, is common among a large number of bacterial species. We have identified luxS-controlled genes in Escherichia coli under two different growth conditions using DNA microarrays. Twenty-three genes were affected by luxS deletion in the presence of glucose, and 63 genes were influenced by luxS deletion in the absence of glucose. more...

Organism:: Escherichia coli; Escherichia coli K-12

Type:: Expression profiling by array

Platform:: GPL199
4 Samples

Download data: CEL, CHP

Series

Accession:: GSE9587

ID:: 200009587

PubMed Full text in PMC Similar studies Analyze with GEO2R

Select item 20000958217.

luxS-Dependent Gene Regulation in Escherichia coli K-12 Revealed by Genomic Expression Profiling

Organism:: Escherichia coli; Escherichia coli K-12

Type:: Expression profiling by array

Platform:: GPL199
4 Samples

Download data: CEL, CHP

Series

Accession:: GSE9582

ID:: 200009582

PubMed Full text in PMC Similar studies Analyze with GEO2R

Select item 20008898118.

Revealing the genome-scale transcriptional regulatory landscape of OmpR highlights its expanded regulatory roles and unexpected importance of narU under osmotic stress in Escherichia coli K-12 MG1655

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

Organism:: Escherichia coli str. K-12 substr. MG1655

Type:: Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing

Platform:: GPL17439
6 Samples

Download data: GFF

Series

Accession:: GSE88981

ID:: 200088981

PubMed Full text in PMC Similar studies

Select item 20008898019.

Revealing the genome-scale transcriptional regulatory landscape of OmpR highlights its expanded regulatory roles and unexpected importance of narU under osmotic stress in Escherichia coli K-12 MG1655 [RNA-seq]

(Submitter supplied) A transcription factor (TF), OmpR, plays a critical role in transcriptional regulation of the defense system for osmotic stress in bacteria. However, its full genome-wide regulatory potential is unknown. Here, we perform a genome-scale reconstruction of the OmpR regulon in Escherichia coli K-12 MG1655. Integrative data analysis reveals that a total of 37 genes in 24 transcription units (TUs) belong to OmpR regulon. more...