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Single cell analysis of innate lymphoid cells and T lymphocytes in the small intestinal resection of Crohn’s disease patient versus those of adjacent non-inflamed tissue.

ABSTRACT: Single cell analysis of innate lymphoid cells and T lymphocytes in the small intestinal resection of Crohn’s disease patient versus those of adjacent non-inflamed tissue.

PROVIDER: PRJNA763904 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR15915324_1.fastq.gz	Fastqsanger.gz
	SRR15915324_2.fastq.gz	Fastqsanger.gz
	SRR15915325_1.fastq.gz	Fastqsanger.gz
	SRR15915325_2.fastq.gz	Fastqsanger.gz
	SRR15915326_1.fastq.gz	Fastqsanger.gz

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Single cell analysis of innate lymphoid cells and T lymphocytes in the small intestinal resection of Crohn’s disease patient versus those of adjacent non-inflamed tissue.

Project description:The focus of this study is to define the full spectrum of T cells and innate lymphocytes in the context in human inflammatory bowel disease. Results from this study may yield novel findings on the heterogeneity of these lymphocytes and determine how they change in the inflamed human intestine.

2022-06-27 | GSE184291 | GEO

Microbiota and ileocecal resection in Crohn’s disease

Project description:Impact of ileocecal resection on gut microbiota in ileal Crohn’s disease patients

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Microarray of formalin-fixed, paraffin-embedded uninvolved terminal ileal tissue obtained from ileo-colic resection surgeries of Crohn’s disease and control patients

Project description:The interpretation of transcriptional profiling studies of intestinal tissue from Crohn’s disease patients and control patients can be confounded by differing proportions of cell subsets (e.g. immune cells) present in these samples. In this study, we aimed to control for cellular composition using standard, archival formalin-fixed, paraffin-embedded (FFPE) tissue specimens from Crohn’s patients (n=36) and controls (n=32) who underwent intestinal resection surgery. This approach allowed us to use the same tissue specimens for histological screening to select study samples with similar cellular composition and for RNA extraction for RNA-seq transcriptional profiling. We hypothesized that this approach would allow us to more clearly identify molecular signatures in ileal tissue that were associated with Crohn’s disease-associated pathological mechanisms.

2018-05-22 | E-MTAB-5790 | biostudies-arrayexpress

Agilent Microarray of formalin-fixed, paraffin-embedded mesenteric adipose tissue associated with different amount of fibrosis from ileocolonic resection specimens of Crohn’s disease patients

Project description:In Crohn’s disease (CD) pathology, we observed that: 1) a continuous process of fibrosis includes all the layers of the intestine as well as the surrounding mesenteric adipose tissue (MAT); 2) the amount of fibrosis in the MAT varies between samples even within a single case. To further investigate the molecular features of this fibrosis pattern, we did a paired study using formalin-fixed, paraffin-embedded blocks from ileocolonic resection specimens of seven CD patients. Specifically, one block contained ≥10% fibrosis amount while the other block contained <10% fibrosis amount within the MAT from the same case. MAT was selectively collected from serial histologic sections and total RNA was extracted for the Agilent Microarray analysis.

2021-07-16 | E-MTAB-8570 | biostudies-arrayexpress

A distinct epigenetic profile distinguishes stenotic from non-inflamed fibroblasts in the ileal mucosa of Crohn's disease patients [RNA-seq]

Project description:The Illumina NextSeq500 was used to sequence the gene expression profiles of 21 ileal fibroblast samples. Samples included 6 control samples and 15 Crohn’s disease samples. The Crohn’s disease samples can be further subdivided into inflamed (4), non-inflamed (6) and stenotic (5) samples. This experiment together was performed in conjunction with a DNA methylation experiment (GSE99788). Use Supplemental Table 2 of the manuscript to quickly find the samples that were present in both experiments.

2018-12-19 | GSE99816 | GEO

A distinct epigenetic profile distinguishes stenotic from non-inflamed fibroblasts in the ileal mucosa of Crohn's disease patients [methylation]

Project description:The Illumina Infinium EPIC Human DNA methylation Beadchip was used to obtain DNA methylation profiles across approximately 867,000 CpGs in ileal fibroblast samples. Samples included 5 control samples and 13 Crohn’s disease samples. The Crohn’s disease samples can be further subdivided into inflamed (2), non-inflamed (7) and stenotic (4) samples. This experiment together was performed in conjunction with a gene expression experiment (GSE99816). Use Supplemental Table 2 of the manuscript to quickly find the samples that were present in both experiments.

2018-12-19 | GSE99788 | GEO

A Multicenter Trial Comparing REMICADE (Infliximab) and Placebo in the Prevention of Recurrence in Crohn’s Disease (CD) Patients Undergoing Surgical Resection Who Are at an Increased Risk of Recurrence

Project description:REMICADE (infliximab) is a drug used to treat active Crohn’s disease and is being tested in an experiment to see if it may be useful in preventing relapse of Crohn’s disease after surgical resection. This study will compare the effects (both good and bad) of REMICADE (infliximab) to those of placebo. Placebo looks like the drug being studied but has no active ingredients.

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2025-12-17 | GSE264073 | GEO

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Project description:The DNA double-strand breaks that initiate homologous recombination during meiosis are subject to extensive 5ʹ→3′ exonucleolytic processing. This resection is a central and conserved feature of recombination, yet its mechanism is poorly understood. Using a purpose-made deep-sequencing method, namely S1Seq, we mapped meiotic resection endpoints genome-wide at high spatial resolution in Saccharomyces cerevisiae. Generating full-length resection tracts requires Exo1 exonuclease activity and the DNA-damage responsive kinase Tel1, but not the helicase Sgs1. Tel1 is also required for efficient and timely initiation of resection. We find that distributions of resection endpoints at individual genomic loci display pronounced heterogeneity that reflects a tendency for nucleosomes to block Exo1 in vivo, yet modeling experiments indicate that Exo1 digests chromatin with high apparent processivity and at rates approaching those for naked DNA in vitro. This paradox points to nucleosome destabilization or eviction as a determining feature of the meiotic resection landscape.

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2020-10-08 | E-MTAB-7860 | biostudies-arrayexpress

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