GEO DataSets

(Submitter supplied) Our aim was to identify candidate transcripts that distinguish AIEC from non-invasive E. coli (NIEC) strains and might be useful for rapid and accurate identification of AIEC by culture-independent technology. We performed comparative RNA-Sequence (RNASeq) analysis using AIEC strain LF82 and NIEC strain HS during exponential and stationary growth.

Organism:

Escherichia coli LF82; Escherichia coli HS

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL20214 GPL20215

12 Samples

Download data: TXT

(Submitter supplied) We used next generation sequencing to sequence the transcriptome of AIEC str. NRG857c and identify the genes that are differentially regulated in the gut.

Organism:

Escherichia coli

Type:

Expression profiling by high throughput sequencing

Platform:

GPL14548

6 Samples

Download data: TXT

(Submitter supplied) RNA-seq was performed to interogate the transcriptional changes in response to infection with Adherent Invasive E. coli and a control, non-invasive E. coli

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

12 Samples

Download data: CSV

(Submitter supplied) RNA-seq was performed to interogate the transcriptional changes in response to infection with Adherent Invasive E. coli and a control, non-invasive E. coli

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

12 Samples

Download data: CSV

(Submitter supplied) Imbalance in beneficial and harmful bacteria underlies gastrointestinal diseases, such as inflammatory bowel disease. Here, we demonstrated that certain E. coli strains, specifically adherent-invasive E. coli (AIEC), utilize a serine metabolism pathway to outcompete other E. coli strains in the inflamed gut. In contrast, amino acid metabolism has a minimal effect on their competitive fitness in the healthy gut. more...

Organism:

Escherichia coli LF82

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20215

8 Samples

Download data: TXT

(Submitter supplied) Pyschological stress produces unique transcriptomic changes, many of which can be reversed by IL-22fc pre-treatment

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

9 Samples

Download data: CSV, TXT

(Submitter supplied) In the present study, the transcriptional analysis of CD biopsies reveals profound alterations in the ileum transportome profile. More than 60 SLC transporters showed different expression pattern compared with the healthy donors, being mostly decreased. Changes were confirmed in almost all the eighteen altered SLCs analyzed by RT-PCR. The results obtained display alterations in amino acid transporters, purinome members, Zn transporters and metallothioneins. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL10558

11 Samples

Download data: TXT

(Submitter supplied) To investigate the architecture of the E. coli K-12 transcriptome, we used two RNA-Seq technologies to analyze strand-specific transcription at single-nucleotide resolution. We analyzed the data by using an organizational schema to annotate the promoters and terminators that define transcription units across the genome. Our results showed that most (ca. two-thirds) operons have a single promoter and terminator, whereas one-third of operons contain multiple transcription units. more...

Organism:

Escherichia coli K-12

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17884

26 Samples

Download data: TXT, WIG

(Submitter supplied) Purpose: To investigave how a unique rpoD variant of LF82 contributes to its biology by seeing how it affects phenotype and global gene expression Method: Isogenic E. coli MG1655 and D445V mutant were grown to a cell density of OD600 ~0.5-0.6 in LB broth at either 37oC or 23oC. RNA was isolated at 5 post-infection using method II of (Hinton 1989). rRNA subtraction was performed with the bacterial RiboMinus Kit (Ambion) according to manufacturer instructions. more...

Organism:

Escherichia coli str. K-12 substr. MG1655

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17439

12 Samples

Download data: CSV

(Submitter supplied) We develop a method SMRT-Cappable-seq that combines the isolation of unfragmented bacterial primary transcripts with the longread sequencing using PacBio. This method allows the identification and phasing of the transcrription start sites and the termination sites, thereby revealing the operon structure and the regulation of gene experession in bacteria. Applied to E.coli, our method results in an unprecedented definition of the transcriptome with 34% of the known operons from RegulonDB database being extended by at least one gene, and identifies a total of 2300 operons from which around 900 are novel.

Organism:

Escherichia coli

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL25343 GPL24462

6 Samples

Download data: TXT

(Submitter supplied) Escherichia coli spans a genetic continuum from enteric strains to several phylogenetically distinct, atypical lineages that are rare in humans, but more common in extra-intestinal environments. To investigate the link between gene regulation, phylogeny and diversification in this species, we analyzed global gene expression profiles of four strains representing distinct evolutionary lineages, including a well-studied laboratory strain, a typical commensal (enteric) strain and two environmental strains. more...

Organism:

Escherichia coli

Type:

Expression profiling by high throughput sequencing

Platform:

GPL14548

24 Samples

Download data: TXT

(Submitter supplied) Using a highly efficient and strand-specific RNA-seq method combined with a highly accurate and robust algorithm and tool we developed, TruHMM for assembling full-length transcriptomes, to profile the transcriptome of E.coli K12 under different culture conditions and growth phases, we showed that the dynamic transcriptome structures appears to be culture condition and growth phases dependent.

Organism:

Escherichia coli

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL14548 GPL10328

15 Samples

Download data: BIGWIG