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Dynamic changes in chromatin states during specification and differentiation of adult intestinal stem cells [rnaseq]

ABSTRACT: To follow the changes in the transcriptional programs accompanying the specification, maintenance and differentiation of the adult ISCs we sequenced whole transcriptomes of embryonic intestinal epithelium progenitors (at E12.5 and E14.5), adult ISCs and their differentiated progenies, the majority of which are absorptive enterocytes. EpCAM positive embryonic gut epithelium was isolated from dissected small intestines using fluorescence activated cell sorting (FACS). Adult ISCs were purified on the basis of GFP fluorescence from crypts of Lgr5GFP-Cre-ERT mice (Barker et al. 2007), whereas enterocytes (EpCAM+ CD45- CD31-) were isolated from villi.

ORGANISM(S): Mus musculus

PROVIDER: GSE89683 | GEO | 2017/03/29

SECONDARY ACCESSION(S): PRJNA352951

REPOSITORIES: GEO

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Id2 controls specification of Lgr5+ intestinal stem cell progenitors during gut development

Project description:To follow the changes in the transcriptional programs accompanying the specification of the adult ISCs we sequenced whole transcriptomes of embryonic intestinal epithelium progenitors (at E11.5 and E12.5) and adult ISCs. EpCAM positive embryonic gut epithelium was isolated from dissected small intestines using fluorescence activated cell sorting (FACS). Adult ISCs were purified on the basis of GFP fluorescence from crypts of Lgr5GFP-Cre-ERT mice (Barker et al. 2007) Double positive adlut ISCs were isolated by FACS based on GFP and tdTomato fluorescence.

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Distinct populations of embryonic epithelial progenitors generate Lgr5+ intestinal stem cells

Project description:To follow the changes in the transcriptional programs accompanying the specification of the embryonic Lgr5+ cells we sequenced whole transcriptomes of embryonic intestinal epithelium progenitors (at E13.5 and E15.5). EpCAM positive embryonic gut epithelium was isolated from dissected small intestines using fluorescence activated cell sorting (FACS). Lgr5+ progenitors were purified on the basis of GFP fluorescence from Lgr5GFP-Cre-ERT mice (Barker et al. 2007). Double positive embryonic progenitors were isolated by FACS based on GFP and tdTomato fluorescence.

2019-09-24 | GSE104727 | GEO

Role of polycomb repressive complex 1 in the intestinal homeostasis [RNA-Seq]

Project description:These data include RNA Seq data generated from wild type and Ring1a Ring1b dKO ISCs from Lgr5Gfp-CreERT2, Lgr5Gfp-CreERT2 Ring1a-/- Ring1bf/f, Lgr5Gfp-CreERT2-Ctnnb1-ex3 and Lgr5Gfp-CreERT2 Ring1a-/- Ring1bf/f-Ctnnb1-ex3 mice. Total RNA extracted from sorted wild type and Ring1a Ring1b dKO ISCs.

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Transcriptomics informs design of a planar human enterocyte culture system that reveals metformin enhances fatty acid flux

Project description:Background & Aims: Absorption, metabolism, and secretion of lipids occurs in the small intestinal epithelium. Caco-2 and organoids have been used to study these processes but are limited in physiological relevance or preclude simultaneous apical and basal access. Here, we develop a dynamic and flexible planar absorptive enterocyte (AE) monolayer system, investigate how fatty acid oxidation (FAO) regulates FA mobilization mechanisms and probe a role for metformin in FA mobilization. Methods: Single-cell RNA-sequencing (scRNAseq) was performed on primary human jejunum. Transcriptomic signatures and trajectory analysis defined in vivo AE maturational signatures, which informed culture methods to differentiate ISCs and mimic in vivo AEs. The system was scaled for high-throughput drug screening and FAO was pharmacologically modulated. BODIPY (B)-labelled fatty acids (FAs) were used to easily and sensitively evaluate FA handling via fluorescence, and thin layer chromatography (TLC). Results: scRNAseq shows increasing expression of lipid-handling genes as AEs mature. In vitro, ISCs differentiate into AEs that mimic the in vivo maturational program, exhibit strong barrier function and express FA-handling genes. FA synthase inhibitor, C75, increased apical to basolateral mobilization of B-C16. Short-chain FA (B-C5) was unaffected and diffused freely through AEs. FAO inhibitor, etomoxir, decreased apical to basolateral mobilization of medium and long chain FAs (B-C12, B-C16) whereas anti-diabetic drug, metformin, augmented this mobilization. Conclusions: Primary human ISCs in culture undergo programmed maturation in vitro to generate a sensitive culture system of absorptive epithelium to investigate FA-handling. Modulating FAO impacts mobilization of FAs across absorptive epithelium and FAO enhanced by metformin increases basolateral mobilization pointing to an intestine-specific role.

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Dynamic changes in chromatin states during specification and differentiation of adult intestinal stem cells [k27m3]

Project description:To determine chromatin changes associated with ISCs specification we performed chromatin immunoprecipitation followed by sequencing (ChIP-seq) using 2x105 FACS purified E12.5 or E14.5 embryonic intestinal epithelial cells, Lgr5+ adult ISCs and enterocytes.

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Dynamic changes in chromatin states during specification and differentiation of adult intestinal stem cells [k27ac]

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Dynamic changes in chromatin states during specification and differentiation of adult intestinal stem cells [k4m3]

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2017-03-29 | GSE89679 | GEO

Dynamic changes in chromatin states during specification and differentiation of adult intestinal stem cells [h2az]

Project description:To determine chromatin changes associated with ISCs specification we performed chromatin immunoprecipitation followed by sequencing (ChIP-seq) using 2x10e5 FACS purified E12.5 or E14.5 embryonic intestinal epithelial cells, Lgr5+ adult ISCs and enterocytes.

2017-03-29 | GSE89678 | GEO

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