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Genome-wide Expression Differences in Colonocytes Isolated From Conventionally Raised or Germfree Mice

ABSTRACT: Microarray transcriptome analysis of colonocytes from conventionally raised and germfree mice.

ORGANISM(S): Mus musculus

PROVIDER: GSE27950 | GEO | 2011/03/15

SECONDARY ACCESSION(S): PRJNA137821

REPOSITORIES: GEO

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Genome-wide Expression Differences in Colonocytes Isolated From Conventionally Raised or Germfree Mice

Project description:Microarray transcriptome analysis of colonocytes from conventionally raised and germfree mice. 12 samples were analyzed, with 6 germfree (GF) samples vs. 6 conventionally raised (CONV) samples.

2011-03-15 | E-GEOD-27950 | biostudies-arrayexpress

Transcriptional profiling of 77 tissue samples from germ-free and conventionally raised mice.

2011-12-08 | GSE17438 | GEO

Transcriptional profiling of 53 tissue samples from germ-free and conventionally raised mice

2014-01-31 | GSE31115 | GEO

Mus musculus

Project description:Genome-wide Expression Differences in Colonocytes Isolated From Conventionally Raised or Germfree Mice

| PRJNA137821 | ENA

Transcriptional profiling of 53 tissue samples from germ-free and conventionally raised mice

Project description:Whole-transcriptome survey of gene expression differences between germ-free (GF) and conventionally raised (CONV-R) mice. To assess the role of toll-like receptor signalling, both wild-type and Myd88 -/- mice were used. Three different tissues were harvested from 20 mice (5 WT CONV-R, 5 Myd88 -/- CONV-R, 4 WT GF, 6 Myd88 -/- GF) and expression profiles were determines using the Affymetrix Mouse Gene 1.0ST platform.

2014-01-31 | E-GEOD-31115 | biostudies-arrayexpress

Transcriptional profiling of intestinal tissue samples from germ-free and conventionally raised mice which are either wild-type or Myd88-/-

Project description:Whole-transcriptome survey of gene expression differences between germ-free (GF) and conventionally raised (CONV-R) mice. To assess the role of toll-like receptor signalling, both wild-type and Myd88 -/- mice were used. Four different tissues were harvested from 20 mice (5 WT CONV-R, 5 Myd88 -/- CONV-R, 4 WT GF, 6 Myd88 -/- GF) and expression profiles were determines using the Affymetrix Mouse Gene 1.0ST platform. 77 samples remained after quality control.

2011-12-08 | E-GEOD-17438 | biostudies-arrayexpress

Temporal profile of germ-free and conventionally raised male mice (DUODENUM and ILEUM)

Project description:Temporal profile of germ-free and conventionally raised male mice (DUODENUM and ILEUM)

| PRJNA471298 | ENA

Temporal profiles of germ-free and conventionally raised female and male mice (LIVER)

Project description:Temporal profiles of germ-free and conventionally raised female and male mice (LIVER)

| PRJNA471297 | ENA

Genome-wide gene expression analysis of mucosal colonic biopsies and isolated colonocytes...

Project description:Background & Aims: Genome-wide gene expression (GWGE) profiles of mucosal colonic biopsies have suggested the existence of a continuous inflammatory state in quiescent ulcerative colitis (UC). The aim of this study was to use DNA microarray-based GWGE profiling of mucosal colonic biopsies and isolated colonocytes from UC patients and controls in order to identify the cell types responsible for the continuous inflammatory state. Methods: Adjacent mucosal colonic biopsies were obtained endoscopically from the descending colon in patients with active UC (n=8), quiescent UC (n=9), and with irritable bowel syndrome (controls, n=10). After isolation of colonocytes and subsequent extraction of total RNA, GWGE data were acquired using Human Genome U133 Plus 2.0 GeneChip Array (Affymetrix, Santa Clara, CA). Data analysis was carried out by principal component analysis and projection to latent structure-discriminant analysis using the SIMCA-P11 software (Umetrics, Umeå, Sweden). Results: A clear separation between active UC, quiescent UC and control biopsies were found, whereas the model for the colonocytes was unable to distinguish between quiescent UC and controls. The differentiation between quiescent UC and control biopsies was governed by unique profiles containing gene expressions with significant fold changes. These primarily belonged to the family of homeostatic chemokines revealing a plausible explanation to the abnormal regulated innate immune response seen in patients with UC. Conclusion: This study has demonstrated the presence of a continuous inflammatory state in quiescent UC, which seems to reflect an altered gene expression profile of lamina propria cells. Keywords: Colonocytes, continuous inflammation, mucosal colonic biopsies, gene expression profiles

2009-09-16 | GSE13367 | GEO

RNA-seq analysis of conventionally raised zebrafish larvae compared to germ-free zebrafish larvae and germ-free larvae treated with zebrafish metabolites.

Project description:Here, we explore the impact of rearing zebrafish embryos in the absence of microbes on early neural development as well as investigate whether any potential changes can be rescued with treatment of metabolites derived from the zebrafish gut microbiota. RNA was extracted from a pool of five heads for each treatment at long-pec stage (2 days post fertilization) and sequenced at a depth of 80-100 million reads per sample. We identified 361 genes significantly down regulated in GF embryos compared to conventionally raised embryos via RNA-Seq analysis. Of these, 42 were rescued with the treatment of zebrafish gut-derived metabolites to GF embryos. Gene ontology analysis revealed that these genes are involved in prominent neurodevelopmental pathways including transcriptional regulation and Wnt signalling.

2022-01-01 | GSE182725 | GEO

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