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Transcriptional response of human enteroids/colonoids on transwells to infection

ABSTRACT: Transcriptional response of human enteroids/colonoids on transwells to infection

PROVIDER: PRJNA759635 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR15692500_1.fastq.gz	Fastqsanger.gz
	SRR15692500_2.fastq.gz	Fastqsanger.gz
	SRR15692501_1.fastq.gz	Fastqsanger.gz
	SRR15692501_2.fastq.gz	Fastqsanger.gz
	SRR15692502_1.fastq.gz	Fastqsanger.gz

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Transcriptional response of human enteroids/colonoids on transwells to infection

Project description:The goal of this study was to evaluate the transcriptional response of human enteroids/colonoids on transwells to infections (bacterial and rotavirus). Enteroids/colonoids lines C103, C109, D103, D109, I103, I109, J2 and J11 were plated on transwells coated with Matrigel, differentiated, and inoculated (rotavirus (Ito), bacteria or mock) for 6 or 24 hours. Subsequently, total RNA was isolated and paired-end sequencing was performed.

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Transcriptional response of NGN3 J2 enteroids

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Transcriptional response of NGN3 J2 enteroids

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Transcriptional response of NGN3 J2 enteroids.

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RNA-Sequencing of epithelium and colonoids from patients with pediatric inflammatory bowel disease

Project description:Objective: Children with very early onset inflammatory bowel disease (VEO IBD) present with more extensive, severe, and refractory disease than older children and adults with IBD. In the current study, we evaluated functional and transcriptomic differences in epithelial cells from patients with VEO and older onset IBD compared to controls. Design: We established enteroids and colonoid lines from patients with VEO and older onset IBD and control patients. We evaluated crypt conversion (initial growth efficiency) compared to histopathological and clinical parameters. We performed RNA-sequencing on colonoids followed by validation via qPCR and flow cytometry in additional patients and in colonoids after multiple passages. Results: Control enteroids and colonoids exhibited consistently high crypt conversion, whereas patients with VEO and older onset IBD exhibited decreased crypt conversion associated with higher inflammation scores. Transcriptomic analysis revealed increased expression of LYZ, reported previously in colonoids from adult patients with ulcerative colitis, as well as antigen presentation genes HLA-DRB1 and HLA-DRA, which persisted after prolonged passaging as verified by flow cytometry. Conclusion: We present the first functional comparison of enteroids and colonoids from patients with VEO and older onset IBD, a subset of which exhibit poor initial growth. Enhanced and persistent expression of epithelial antigen presentation genes in patient colonoids supports the notion that epithelial cell-intrinsic differences may result from or contribute to disease. Analyses of colonoids from pediatric patients with IBD will contribute to a greater understanding of epithelial cell-autonomous defects in patients with VEO and older onset IBD and will be an important tool for understanding novel disease variants in the future.

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Project description:Transcriptional responses of GII.4 human norovirus infection in jejunal human intestinal enteroids

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Transcriptional response to SARS-CoV-2 infection

Project description:Transcriptional response to SARS-CoV-2 infection

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Human norovirus efficiently replicates in differentiated 3D-human intestinal enteroids

Project description:To investigate the effect of human norovirus infection on the trascriptome of intestinal enteroids in the presence of a Jak kinase inhibitor, Ruxolitinib

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