Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcriptomic profiles of intestinal stem cells cultured in natural and synthetic three-dimensional matrices

ABSTRACT: We used RNA-seq to define the gene expression profiles of intestinal stem cells (ISCs) expanded in Matrigel, degradable poly(ethylene) glycol (PEG) and non-degradable PEG matrices. Comparison of mRNA profiles between ISCs grown in Matrigel and non-degradable PEG show no major differences in expression of gene related to stemness, proliferation and signaling via the Wnt and Notch pathways. These results also show that ISC cultured in degradable PEG matrices upregulate stress- and inflammation-related genes compared with cells expanded in non-degradable PEG matrices.

ORGANISM(S): Mus musculus

PROVIDER: GSE85391 | GEO | 2016/11/01

SECONDARY ACCESSION(S): PRJNA338315

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Intestinal subepithelial myofibroblasts support the growth of intestinal epithelial stem cells

Project description:Intestinal epithelial stem cells (ISCs) are the focus of recent intense study. Current in vitro models rely on supplementation with the Wnt agonist R-spondin1 to support robust growth, ISC self-renewal, and differentiation. Intestinal subepithelial myofibroblasts (ISEMFs) are important supportive cells within the ISC niche. We hypothesized that co-culture with ISEMF enhances the growth of ISCs in vitro and allows for their successful in vivo implantation and engraftment. ISC-containing small intestinal crypts, FACS-sorted single ISCs, and ISEMFs were procured from C57BL/6 mice. Crypts and single ISCs were grown in vitro into enteroids, in the presence or absence of ISEMFs. ISEMFs enhanced the growth of intestinal epithelium in vitro in a proximity-dependent fashion, with co-cultures giving rise to larger enteroids than monocultures. Co-culture of ISCs with supportive ISEMFs relinquished the requirement of exogenous R-spondin1 to sustain long-term growth and differentiation of ISCs. Mono- and co-cultures were implanted subcutaneously in syngeneic mice. Co-culture with ISEMFs proved necessary for successful in vivo engraftment and proliferation of enteroids; implants without ISEMFs did not survive. ISEMF whole transcriptome sequencing and qPCR demonstrated high expression of specific R-spondins, well-described Wnt agonists that supports ISC growth. Specific non-supportive ISEMF populations had reduced expression of R-spondins. The addition of ISEMFs in intestinal epithelial culture therefore recapitulates a critical element of the intestinal stem cell niche and allows for its experimental interrogation and biodesign-driven manipulation. Two samples of intestinal subepithelial myofibroblasts were used in this study.

2013-12-20 | E-GEOD-52402 | biostudies-arrayexpress

circular RNA (circRNA) expression profile in intestinal stem cells

Project description:Purpose: circRNAs emerge as critical modulators in various biogical processes, but their roles in intestinal stem cells (ISC) reamin unclear. Here we want to identify a functional circRNA in ISCs, and firstly, we explore the expression profile of circRNA in ISCs. Methods: We isolated Lgr5+ ISCs and Lgr5- non-ISCs from the intestine tissue, followed by circRNA seq. Results: Many circRNAs are differently expressed in ISCs and non-ISCs, and we selected circRNAs highly expressed in ISCs for further investigation. Conclusions: circRNAs may play a critical role in ISC self-renewal.

2018-11-29 | GSE123051 | GEO

Xenogeneic-free culture of human intestinal stem cells on functional polymer-coated substrates for scalable, clinical-grade stem cell therapy

Project description:Inevitable need for basement membrane extract (BME) with undefined constituents, such as Matrigel, for intestinal stem cell (ISC) culture in traditional system poses a significant barrier that must be overcome for the development of clinical-grade, scalable, ready-to-use ISCs. Here, we propose a functional polymer-based xenogeneic-free dish for the culture of intestinal stem cells (XF-DISC), ensuring substantially prolonged maintenance of ISCs derived from 3-dimensional human intestinal organoid (ISCs3D-hIO). XF-DISC enables remarkable expandability, exhibiting a 24-fold amplification in cell number within 30 days, with long-term maintenance of ISCs3D-hIO through consecutive passaging more than 30 times (> 210 days), and is fully compatible with a cell banking system. Notably, the ISCs3D-hIO cultured on XF-DISC are successfully transplanted into the intestinal injury and inflammation models, leading to full regeneration of damaged intestinal epithelium. XF-DISC, an extraordinary reliable and scalable xenogeneic-free ISC3D-hIO culture method exhibits significant promise in the development of regenerative ISC therapy for human intestinal diseases.

2024-10-22 | PXD050747 | Pride

A genome-wide analysis of human pluripotent stem cell-derived endothelial cells cultured in synthetic hydrogels compared to standard 2D or 3D cell culture platforms

Project description:The influence of 2D and 3D cell culture platforms on vascular function was investigated by comparing gene expression for human pluripotent stem cell-derived endothelial cells (H1-ECs), primary human brain vascular pericytes (pericytes), and human umbilical vein endothelial cells (HUVECs) cultured on tissue culture polystyrene (TCP, “2D”), on or in poly(ethylene glycol) (PEG) hydrogels formed via “thiol-ene” photopolymerization, and on or in gelled Matrigel. ECs cocultured with pericytes in PEG formed vascular networks with global gene expression that was highly correlated to a standard 3D Matrigel assay (Spearman’s coefficients ≥ 0.98). H1-ECs, HUVECs, and pericytes were characterized gene expression signatures associated with the cell cycle and mitosis when cultured on TCP surfaces compared to cells cultured on top of or encapsulated in PEG hydrogels or Matrigel. The proliferative signature was not necessarily a function of the 2D format, since endothelial cells cultured on PEG hydrogels were not characterized by increased proliferation or a proliferative gene signature compared to cells encapsulated in PEG hydrogels. The proliferative phenotype for H1-ECs on TCP was regulated by FAK-ERK activity, and inhibition or knockdown of ERK pathway signaling decreased proliferation and cell cycle genes while increasing expression of “3D-like” vasculature development genes. Our results suggest that cells in 2D culture adopt a highly proliferative state that interferes with normal vascular function and provides unique insight into the importance of cellular and extracellular context for in vitro tissue modeling.

2017-02-22 | GSE93511 | GEO

Next generation seuquencing of 3D breast cancer cell culture in synthetic hydrogels presenting either a collagen mimic or laminin mimic with low and high mechanical properties

Project description:MDA-MB-231 (ER-) and T47D (ER+) breast cancer cells were encapsualted in synthetic hydrogels, formed with a multi-arm bioinert polymer poly(ethylene glycol), cell-degradable peptide crosslinks, and receptor-binding pendant peptides, and cultured for 3 days and up to 40 days to assess initial cell responses to different matrix compositions. The synthetic matrices had a Young's modulus (E) ~ 0.6 kPa (low wt%) and # ~ 5 kPa (high wt%), in the range of bone marrow or healthy mammary tissue and lung tissue, respectively, and Biochemcial cues to mimic binding sites found in collagen (GFOGER peptide) or laminin (IKVAV peptide). After 3 days and 40 days in culture, mRNA was collected and RNA-seq performed to compare cell responses between the collagen and laminin mimetic cultures overtime in both low wt% and high wt% matrices.

2022-03-01 | GSE145696 | GEO

Postnatal epigenetic development of mouse intestinal stem cells

Project description:We used unbiased whole genome bisulfite sequencing (WGBS) to identify DNA methylation changes in the intestinal stem cells (ISCs) or their progeny during the suckling period of mouse colon development. Lgr5-EGFP mice were used to identify ISC populations in the colons. WGBS were performed using EGFP labeled Lgr5+ ISCs and epithelial cell adhesion molecule (EpCAM) labeled epithelial cells isolated at the beginning and end of the suckling period (postnatal day 0-P0 and P21).

2015-08-25 | E-GEOD-58532 | biostudies-arrayexpress

Postnatal epigenetic development of mouse intestinal stem cells (RNA-seq)

Project description:We used RNA sequencing to quantify the gene expression levels in the intestinal stem cells (ISCs) or their progeny during the suckling period of mouse colon development. Lgr5-EGFP mice were used to identify ISC populations in the colons. RNA sequencing was performed using EGFP labeled Lgr5+ ISCs and epithelial cell adhesion molecule (EpCAM) labeled epithelial cells isolated at the beginning and end of the suckling period (postnatal day 0-P0 and P21).

2015-08-25 | E-GEOD-64054 | biostudies-arrayexpress

Next generation seuquencing of 3D breast cancer cell culture in synthetic hydrogels presenting either a collagen mimic or laminin mimic

Project description:MDA-MB-231 (ER-) and T47D (ER+) breast cancer cells were encapsulated in synthetic hydrogels, formed with a multi-arm bioinert polymer poly(ethylene glycol), cell-degradable peptide crosslinks, and receptor-binding pendant peptides, and cultured for 3 days to assess initial cell responses to different matrix compositions. The synthetic matrices had a Young's modulus (E) ~ 0.6 kPa, in the range of bone marrow and healthy mammary tissue, and biochemcial cues to mimic binding sites found in collagen (GFOGER peptide) or laminin (IKVAV peptide). After 3 days in culture, mRNA was collected and RNA-seq performed to compare cell responses between the collagen and laminin mimetic cultures.

2020-02-20 | GSE121179 | GEO

Yki- and Ras-induced intestinal stem cells (ISCs) overproliferation affects gene expression in the midgut of adult flies

Project description:Purpose: Activation of yki or Ras signaling pathways in ISCs causes overproliferation and ISC reprogramming. To gain insight into yki- and Ras-induced ISC reprogramming and gene expression, we performed a transcriptomic analysis of adult midgut with overexpression of yki-3SA or Ras1A in the ISCs.

2018-04-27 | GSE113728 | GEO

Intestinal subepithelial myofibroblasts support the growth of intestinal epithelial stem cells

2013-12-20 | GSE52402 | GEO