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Single cell RNA sequencing for the paired TNF-free and -treated intestinal organoids

ABSTRACT: Organoids grown from intestinal crypts of controls and patients with Crohn's disease were sub-cultured at least 6 passages. Single cell RNA sequencing was performed for the paired TNF-free and -treated control and Crohn's organoids.

ORGANISM(S): Homo sapiens

PROVIDER: GSE153802 | GEO | 2020/07/05

REPOSITORIES: GEO

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RNA sequencing for the paired TNF-free and -treated intestinal organoids

Project description:Organoids grown from intestinal crypts of controls and patients with Crohn's disease were sub-cultured at least 6 passages. RNA sequencing was performed for the 12 paired TNF-free and -treated control and Crohn's organoids.

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RNA sequencing for the paired TNF-free and -treated intestinal enteroids

Project description:RNA sequencing was performed for the TNF-free and -treated enteroids derived from control (n=8 pairs) and Crohn's disease patients (n=8 pairs).

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RNA sequencing for the paired TNF-free and -treated intestinal organoids

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RNA-seq of wildtype mouse small intestinal organoids grown in Matrigel or in/on collagen.

Project description:We aimed to analyse the effect of different extra-cellular matrices on the growth of small intestinal organoids. Small intestinal crypts of wildtype mice were harvested and grown under standard Matrigel organoid conditions. After establishment of organoids (passaged 1-2), organoids were grown in Matrigel, on collagen or in a drop of collagen. Growth in a droplet of collagen requires addition of Wnt3a, therefore all samples are either provided with standard culture conditions (ENR) or with ENR+50%Wnt3a-CM (WENR). Samples were grown in specified matrix for at least 1-2 passages before RNA was purified.

2021-04-01 | E-MTAB-10082 | biostudies-arrayexpress

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Project description:RNA sequencing was performed for the TNF- or vehicle-treated organoids derived from the large intestine of healthy male C57BL/6J mice (n = 3 per group).

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RNA sequencing for endoscopic biopsy tissue samples from controls and Crohn's disease patients, and organoids derived from these specimens.

Project description:RNA sequencing for endoscopic biopsy tissue samples from controls (jejunum [S170], n=1; ileum [SN2], n=1) and patients with Crohn's disease (jejunum [non-inflamed area, A2/L2+L4/B2, infliximab maintenance therapy, S93], n=1; ileum, [non-inflamed area, A2/L2/B2, infliximab maintenance therapy, S95], n=1). Organoid culture was performed using intestinal crypts derived from these specimens, as described previously (Sato et al. Nature 2009; 459: 262–265]. Organoids were sub-cultured at least 6 passages. RNA sequencing was conducted for organoids on day 3, day 6, and day 9 [S170 and S93], and organoids treated with TNFɑ 30 ng/ml on day 3, day 6, and day 9 [S170 and S93]. RNA sequencing was conducted for organoids on day 6 and day 9 [N2 and S95], and organoids treated with TNFɑ 30 ng/ml on day 6 and day 9.

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Multiomic (Joint snRNA/snATAC) sequencing data of intestinal crypts and epithelial only organoids derived from human fetal duodenum

Project description:Here, we used joint single-nuclei RNA-sequencing (snRNA-seq) and single-nuclei ATAC sequencing (scATAC) to profile freshly isolated crypts from the human fetal intestine and matched intestinal epithelial only organoids (also known as enteroids) derived from these crypts after one passage of in vitro growth. Organoids were grown in the standard 25% LWRN media with either 100 ng/ml of EGF or 1 ng/ml of EREG added. Fresh crypts were not placed in culture but rather immediately frozen for multiomic processing.

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