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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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ESC Exposed to Butyrate

ABSTRACT: This SuperSeries is composed of the following subset Series: GSE15107: R1 mESC Exposed to Butyrate GSE15109: BG02 hESC Exposed to Butyrate GSE15110: H1 hESC Exposed to Butyrate Refer to individual Series

ORGANISM(S): Mus musculus

SUBMITTER: Brig Mecham

PROVIDER: E-GEOD-15112 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Histone deacetylase inhibition elicits an evolutionarily conserved self-renewal program in embryonic stem cells.

Ware Carol B CB Wang Linlin L Mecham Brigham H BH Shen Lanlan L Nelson Angelique M AM Bar Merav M Lamba Deepak A DA Dauphin Derek S DS Buckingham Brian B Askari Bardia B Lim Raymond R Tewari Muneesh M Gartler Stanley M SM Issa Jean-Pierre JP Pavlidis Paul P Duan Zhijun Z Blau C Anthony CA

Cell stem cell 20090401 4

Recent evidence indicates that mouse and human embryonic stem cells (ESCs) are fixed at different developmental stages, with the former positioned earlier. We show that a narrow concentration of the naturally occurring short-chain fatty acid, sodium butyrate, supports the extensive self-renewal of mouse and human ESCs, while promoting their convergence toward an intermediate stem cell state. In response to butyrate, human ESCs regress to an earlier developmental stage characterized by a gene exp ...[more]

PMID: 19341625

Similar Datasets

BG02 hESC Exposed to Butyrate

Project description:To assess the effect of sodium butyrate exposure on human ESC grown without culture support for self-renewal (I.e. without conditioned medium and added bFGF) in support of data generated on H1 hESC - two groups were compared - BG02 culture in feeder conditioned versus on sodium butyrate - in triplicate and compared on Agilent whole human genome array BG02 hESC were grown under two conitions - A. for 31 passages on Matrigel in feeder conditioned medium and B. for 29 passages on Matrigel in feeder conditioned medium followed by 20 passages in 0.2 mM sodium butyrate without conditioned medium and in human ES cell medium containing no added bFGF

2009-03-04 | E-GEOD-15109 | biostudies-arrayexpress

Transcription profiling of human H1 hESC exposed to butyrate

Project description:To assess the effect of sodium butyrate exposure on human ESC grown without culture support for self-renewal (I.e. without conditioned medium and added bFGF) - three groups were compared - H1 culture in feeder conditioned medium vs without conditioned medium in 0.2 mM sodium butyrate vs. grown in sodium butyrate for 4 passages followed by return to conditioned medium conditions for 3 passages. The three groups were grown in triplicate and compared on Agilent whole human genome array Experiment Overall Design: H1 hESC were grown under 3 conditions: A. 48 passages total, the last 9 passages off of feeders on Matrigel in feeder conditioned medium B. 48 passages total, within the last 9 passges, #39-41 were in conditioned medium and #42-48 were without conditioned medium and added bFGF but with 0.2 mM sodium butyrate on Matrigel C. 49 passages total, within the last 10 passages #39-41 were in conditioned medium, #42-46 in 0.2 mM sodium butyrate (without feeder of bFGF support) and #47-49 back to conditioned medium + bFGF. The RNA from these cells were compared via Agilent whole human genome array.

2009-03-15 | E-GEOD-15110 | biostudies-arrayexpress

Transcription profiling of mouse R1 mESC exposed to butyrate

Project description:To assess the effect of sodium butyrate exposure on mouse ESC grown without self-renewal support (I.e. without feeders or LIF) - these cells were compared to cells grown without sodium buytrate, but with added mouse LIF via Agilent whole mouse genome array Experiment Overall Design: R1 mESC were grown under 2 conditions, with mLIF on gelatin or without LIF on gelatin for 15 passages to compare change in the RNA profile

2009-03-15 | E-GEOD-15107 | biostudies-arrayexpress

Effect of butyrate and DZNep on hESC HSF-6

Project description:In order to recover nuclei with two active X chromosomes (class I), we developed a reprogramming strategy by supplementing hESC media with the small molecules sodium butyrate, and 3-deazaneplanocin A (DZNep). In order to determine how B+D affects global gene expression, we performed microarray analysis in triplicate in the HSF-6 (8) C and HSF-6 (8) B+D treated cultures. We also evaluated HSF-6 (S9) B+D in triplicate and identified no statistically significant changes in gene expression in HSF-6 (S9) B+D compared to HSF-6 (8) B+D treated cultures. This suggests that global transcriptional differences are more strongly modulated by presence or absence of B+D and not the percentage of class I, II or III nuclei. We performed gene expression profiling on hESC HSF-6 (8, S9) in absent (control) and presence of butyrate and DZNep. All cell were collected after 11 passages in absent and presence of butyrate and DZNep.

2011-11-22 | E-GEOD-33864 | biostudies-arrayexpress

Gene expression profile of butyrate mediated prevention of coloractal cancer in a mouse model

Project description:To further elucidate the mechanism of butyrate mediated chemoprevention of colorectal cancer,we have employed whole genome microarray expression profiling as a discovery platform to identify genes that differentially expressed in mice from Butyrate group compared those from DMH group. The mice of DMH group were received normal diet (calcium concentration,1.24%) and subcutaneous injection of 1,2-Dimethylhydrazine at a dose of 20 mg/kg once weekly for 20 weeks; the mice of Butyrate group were received high calcium diet (calcium concentration,3%) with 1.5% Butyrate and subcutaneous injection of 1,2-Dimethylhydrazine at a dose of 20 mg/kg once weekly for 20 weeks. The mice were sarcrificed at 24 week. Nine normal colonic mucosa (3 from DMH group, 3 from Butyrate group mice with tumors, and 3 from Butyrate group mice without tumors) were used for the microarray analysis. The differentially expressed genes were identified between butyrate group and DMH group,as long as differentially expressed pathways and gene ontology terms.

2011-12-31 | E-GEOD-25858 | biostudies-arrayexpress

Clostridium acetobutylicum ATCC 824 (pRDNA7) butyrate stress (0.6%)

Project description:An intergenic region found to be enriched from a genomic library under butyrate stress was overexpressed and challenged with butyrate (0.6%). The overexpression strain was compared to the plasmid control to determine the transcriptional changes due to overexpression and butyrate stress. RNA samples were taken from both the overexpression strain (pRDNA7) and the plasmid control strain (pSOS95del) at 0, 15, 40, 120, 240, and 360 min post a 0.6% butyrate (pH 6.7) stress. Two slides per timepoint were hybridized on a dye swap configuration.

2009-01-28 | E-GEOD-14433 | biostudies-arrayexpress

Butyrate Induced Changes in Wnt Signaling-Specific Gene Expression in Colorectal Cancer Cells

Project description:To identify Wnt target genes whose expression is differentially modulated by butyrate Doxycycline inducible DN-Tcf4 expression was used to repress Wnt signaling, cells were treated with butyrate or mock treated. Genes differentially regulated by butyrate in the absence of doxycycline but not in its presence (> 2 -fold, P < 0.01) were evaluated.

2014-01-16 | E-GEOD-54127 | biostudies-arrayexpress

The Warburg effect alters histone acetylation in cancer cells by influencing the utilization of HDAC and HAT mechanisms.

Project description:Microarray transcriptome analysis of siMock and siACL HCT116 cells treated with 0, 0.5, 2.0, and 5.0 mM butyrate over three days. Gene expression is measured at control cells (siMock) and ACL-depleted (siACL) cells with 4 dosages (0, 0.5, 2.0, and 5.0 mM) of butyrate treatments

2012-12-01 | E-GEOD-41113 | biostudies-arrayexpress

Genome-wide measurement of acetylated histone H3 in naÃ¯ve cells under Treg-inducing conditon

Project description:To investigate the molecular mechanism how butyrate promoter differentiation of naÃ¯ve T cells into regulatory T cells Examination of acetylated histone H3 during the differentiation of regulatory T cells in the presence or absence of butyrate

2013-11-20 | E-GEOD-49653 | biostudies-arrayexpress

BUTYRATE ENEMAS ON PATIENTS WITH ENTEROSTOMY

Project description:The aim of this study was to evaluate the effects of sodium butyrate enemas on the mucosal genes expression profiles of patients with an enterostomy.

2015-09-01 | E-MTAB-2436 | biostudies-arrayexpress

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