Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

DNA methylation profiling of intestinal epithelial cells from paediatric biopsies including Inflammatory Bowel disease and healthy controls

ABSTRACT: We purified the intestinal epithelial cells from biopsies taken from the ileum and colon of a paediatric cohort of IBD patients and healthy controls

ORGANISM(S): Homo sapiens

SUBMITTER: Kate Howell

PROVIDER: E-MTAB-5463 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

DNA Methylation and Transcription Patterns in Intestinal Epithelial Cells From Pediatric Patients With Inflammatory Bowel Diseases Differentiate Disease Subtypes and Associate With Outcome.

Howell Kate Joanne KJ Kraiczy Judith J Nayak Komal M KM Gasparetto Marco M Ross Alexander A Lee Claire C Mak Tim N TN Koo Bon-Kyoung BK Kumar Nitin N Lawley Trevor T Sinha Anupam A Rosenstiel Philip P Heuschkel Robert R Stegle Oliver O Zilbauer Matthias M

Gastroenterology 20171012 3

<h4>Background & aims</h4>We analyzed DNA methylation patterns and transcriptomes of primary intestinal epithelial cells (IEC) of children newly diagnosed with inflammatory bowel diseases (IBD) to learn more about pathogenesis.<h4>Methods</h4>We obtained mucosal biopsies (N = 236) collected from terminal ileum and ascending and sigmoid colons of children (median age 13 years) newly diagnosed with IBD (43 with Crohn's disease [CD], 23 with ulcerative colitis [UC]), and 30 children without IBD (co ...[more]

PMID: 29031501

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Project description:Human intestinal epithelial organoids (IEO) culture models are rapidly emerging as novel experimental tools to investigate fundamental aspects of intestinal epithelial (patho)physiology. Cellular source and culture protocols vary between different IEO models and reliable markers for their characterization/validation are currently limited. DNA methylation has been demonstrated to play a key role in regulating gene expression and cellular function. This epigenetic mark is comparably stable and has been shown to reflect cellular identity such as tissue origin, developmental stage and age. Our genome wide DNA methylation datasets of purified human epithelium represent a unique resource, which can be used by other researchers to validate their model systems We provide the following datasets of genome-wide DNA methylation profiling by Infinium HumanMethylation450 BeadChip: Purified intestinal epithelial cells (EpCAM+) from paediatric ileum and colon, Non-epithelial mucosal cells (EpCAM-), Whole colonic mucosal biopsies, Intestinal organoid cultures from paediatric ileum and colon, Purified intestinal epithelial cells (EpCAM+) from foetal small intestine and foetal large intestine, Intestinal organoid cultures from foetal small intestine and foetal large intestine, Intestinal organoid cultures derived from induced pluripotent stem cells.<br>Note:</br><br>Some samples in this data set were previously submitted to ArrayExpress under accession number E-MTAB-3709. They're clearly marked in the âDescriptionâ field in sample annotations. </br><br>Information about batch effect during sample handling is included in the experimental variable âblockâ. Batch effect is not massive but present, so it is recommended that batch correction is carried out in data analysis.</br><br>Complementary RNA-seq data on the purified cells and organoids can be found in ArrayExpress at E-MTAB-5015 ( https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-5015/ ). </br>

Dataset Information

DNA methylation profiling of intestinal epithelial cells from paediatric biopsies including Inflammatory Bowel disease and healthy controls

Publications

DNA Methylation and Transcription Patterns in Intestinal Epithelial Cells From Pediatric Patients With Inflammatory Bowel Diseases Differentiate Disease Subtypes and Associate With Outcome.

Similar Datasets

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