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Isolation and in vitro expansion of human colonic stem cells [CGH]

ABSTRACT: Tissue for normal colonic stem cell isolation was obtained via colectomy from a colorectal cancer patient. It was shown that the resected tissue and the in vitro-cultured organoids grown from tissue-derived adult stem cells do not harbor chromosomal alterations. For that purpose, genomic DNA from resected mucosa or genomic DNA from adult stem cell-derived organoids grown in a 3-dimensional culture system was compared to white blood cell genomic DNA obtained from the same individual. Furthermore, in vitro organoids which were cultured and serially passaged for several weeks did not acquire chromosomal alterations.

ORGANISM(S): Homo sapiens

PROVIDER: GSE31256 | GEO | 2011/11/22

SECONDARY ACCESSION(S): PRJNA154103

REPOSITORIES: GEO

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Isolation and in vitro expansion of human colonic stem cells [CGH]

Project description:Tissue for normal colonic stem cell isolation was obtained via colectomy from a colorectal cancer patient. It was shown that the resected tissue and the in vitro-cultured organoids grown from tissue-derived adult stem cells do not harbor chromosomal alterations. For that purpose, genomic DNA from resected mucosa or genomic DNA from adult stem cell-derived organoids grown in a 3-dimensional culture system was compared to white blood cell genomic DNA obtained from the same individual. Furthermore, in vitro organoids which were cultured and serially passaged for several weeks did not acquire chromosomal alterations. Analysis of chromosomal stability of colonic tissue or in vitro-cultured organoids via comparison with blood cells derived from the same individual.

2011-11-22 | E-GEOD-31256 | biostudies-arrayexpress

Tissue extracellular matrix hydrogels as alternative to Matrigel for culturing gastrointestinal organoids

Project description:To determine the performance of the decellularized GI tissue ECM hydrogel, we analyzed differences in mRNA expression levels in native gastric tissues, gastric organoids cultured in Matrigel and those cultured in decellularized gastric ECM hydrogel. We also compared mRNA expression levels of native small intestinal tissues, small intestinal organoids grown in Matrigel and those grown in decellularized intestinal ECM hydrogel.

2022-01-30 | GSE165309 | GEO

Differential early pathogenic changes in human ileal gene expression in Crohn's disease and ulcerative colitis

Project description:The aim of this study is to identify early pathogenic changes in ileal gene expression that precede the development of macroscopic disease in inflammatory bowel diseases (IBDs). We focused on two IBD phenotypes that were unlikely to overlap: 1) ileal Crohn‚Äôs disease (CD) patients undergoing initial ileocolic resection of diseased ileum; and 2) ulcerative colitis (UC) patients undergoing total colectomy. The Control patients were those patients without IBD undergoing initial right hemicolectomy or total colectomy. In order to identify early pathogenic changes in the human ileum in inflammatory bowel diseases, we analyzed 99 two-color whole human genome expression profiles (Agilent 4410A) of a test human ileal cRNA probe vs. a common reference human ileal RNA from a Control patient (N17). A minimum of four biopsies were taken from the macroscopically disease-unaffected proximal ileal margin of freshly resected specimens from 47 ileal Crohn's disease patients undergoing initial ileocolic resection, 27 ulcerative colitis patients undergoing total colectomy and 25 Control patients undergoing either right hemicolectomy or total colectomy. The test and common reference probes were synthesized using the Agilent Low Input Linear Amplification Kit. Hybridization was carried out in DNA hybridization chambers, washed and scanned on an Axon GenePix 4000B scanner. The preprocessing, filtering and normalization of the array data was carried out using the R package LIMMA.

2010-09-26 | E-GEOD-24287 | biostudies-arrayexpress

Genomic profiling of EOC organoids: low-coverage whole-genome sequencing

Project description:Organoids were established from patients with ovarian cancer. DNA was extracted from organoids and primary tissue to investigate whether organoids retain the same genomic abnormalities and disease-associated features.

2020-12-01 | E-MTAB-8636 | biostudies-arrayexpress

Genomic profiling of EOC organoids: whole-exome sequencing

2020-12-01 | E-MTAB-8637 | biostudies-arrayexpress

Genomic profiling of EM organoids: low-coverage whole genome sequencing

Project description:Low-coverage whole genome of endometrium cancer derived organoids. Organoids were established from patients with endometrial diseases and DNA was extracted from low passage number and high passage number and compared with the primary tissue when available to investigate whether organoids retain the same genomic abnormalities and disease-associated features.

2019-06-04 | E-MTAB-7687 | biostudies-arrayexpress

Genomic profiling of EM organoids by whole-exome sequencing

Project description:Organoids were established from patients with endometrial diseases and DNA was extracted from low passage number and high passage number and compared with the primary tissue when available to investigate whether organoids retain the same genomic abnormalities and disease-associated features.

2019-06-04 | E-MTAB-7688 | biostudies-arrayexpress

Proteomics characterisation of induced pluripotent stem cells and cortical brain organoids.

Project description:A method was developed to reproducibly produce neural retina and cortical brain regions from confluent cultures of stem cells. The spontaneously generated cortical organoids were isolated and cultured in suspension conditions for maturation. Proteomic analysis of both the original induced pluripotent stem cells and the cortical organoids demonstrated the increased presence of synaptic components, indicating maturity.

2022-05-06 | PXD025933 | Pride

Array-based comparative genomic hybridization study of human embryonic stem cell lines

Project description:G-banding of human embryonic stem cells (hESC) has proved their predisposition to aneuploidy of chromosomes 12, 17 and X. Now, using array-based comparative genomic hybridization, we find that hESC also accumulate other recurrent chromosomal abnormalities, such as duplications of stemness genes, submicroscopic instability of 20q11.21 and the appearance of a derivative chromosome 18. Keywords: comparative genomic hybridization, genomic integrity of human embryonic stem cells Array-based comparative genomic hybridization was performed on 48 DNA samples from 17 human embryonic stem cell lines, all cultured in our laboratory under the same conditions. All lines were hybridized against DNA obtained from peripheral blood from donors with a known normal karyotype. No replicates were done from the same DNA sample, but, whenever possible the same stem cell line was analysed at later passages. All detected abnormalities were confirmed by FISH and/or G-banding.

2010-05-17 | E-GEOD-13422 | biostudies-arrayexpress

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.

2020-07-03 | GSE153715 | GEO

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