Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Single-cell transcriptomics reveals immune response of intestinal cell types to viral infection

ABSTRACT: In this work we have employed a single cell sequencing approach using 10x Genomics scRNAseq to study Astroviru infection of of ileum organoids

ORGANISM(S): Homo sapiens

PROVIDER: GSE171620 | GEO | 2021/06/01

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Single-cell transcriptomics of human intestinal organoids infected with SARS-CoV-2

Project description:In this work we have employed a single cell sequencing approach of both ileum and colon organoids using 10x Genomics scRNAseq and TAP-seq targeted single-cell RNA-seq.

2021-04-12 | GSE156760 | GEO

Single cell RNAseq of small intestinal stromal cells

Project description:We used scRNAseq approaches (Smartseq2 and 10X Genomics) to investigate the diversity of small intestinal stromal cells.

2022-05-31 | GSE154821 | GEO

Single-cell sequencing of developing human gut reveals transcriptional links to childhood Crohn’s disease

Project description:In this study, we performed single-cell transcriptional profiling of human embryonic and fetal gut samples obtained from 9 human embryos spanning ages 6-10 PCW and three regions (duo-jejunum, ileum and colon). Additionally, we profile mucosal biopsies from the terminal ileum of healthy children aged 4-12 years (n = 8) as well as a group of children newly diagnosed with Crohn’s disease (CD) (n = 7), a common form of IBD. Tissue samples were treated using an enzymatic dissociation protocol and single cell suspensions were then processed using the 3’v2 10x Genomics Chromium workflow. In a subset of samples, the intestinal epithelial cell fraction was enriched by performing magnetic bead sorting for EPCAM. In total, we generate single cell transcriptomes of ~90,000 primary human intestinal cells providing a rich resource and detailed roadmap. Using this data as well as scRNAseq profiles of human fetal gut derived organoids we describe embryonic and fetal epithelium composition, trace their differentiation dynamics and signaling partners, and provide links to regenerating Crohn’s disease epithelium.

2020-12-22 | E-MTAB-8901 | biostudies-arrayexpress

scRNAseq comparison of iPSC-derived retinal organoids from Control and LCA7 patients

Project description:To comprehensively capture changes in retinal transcriptome for the LCA7 organoids compared to control, we performed single cell RNA-sequencing (scRNAseq) using the 10X Genomics platform. Retinal organoids at D150 of differentiation were dissociated for scRNAseq analysis. scRNAseq data revealed significant dysregulation of specific photoreceptor genes between control and LCA7 organoids, as well as mutation-specific differences in various genes, including CRX, RCVRN, ARR3, and AIPL1.

2021-09-17 | GSE184080 | GEO

Spatially resolved transcriptomic profiling: an experimental comparison of GeoMx Digital Spatial Profiling and Visium CytAssist spatial transcriptomics in three cancer types (GeoMx)

Project description:We performed Visium CytAssist (10X), GeoMx DSP (Nanostring) and Chromium Flex (10X Genomics) full transcriptome profiling on Breast Cancer (BC), Lung Cancer (LC) and diffuse large B cell lymphoma (DLBCL) samples from archival FFPE blocks. We explore the data quality across blocks with different storage times and DV200 values for all the three methods. We compared the cell type signature purity between ST methods Visium and GeoMx by utilising pathology annotations and scRNAseq. For the Visium and Chromium methods with a large number of data points we explored the heterogeneity between tissues. Finally, we demonstrate the discovery of patient-specific tumor-TME interactions across all three methods.

2024-11-01 | E-MTAB-14566 | biostudies-arrayexpress

Spatially resolved transcriptomic profiling: an experimental comparison of GeoMx Digital Spatial Profiling and Visium CytAssist spatial transcriptomics in three cancer types (Chromium and Visium)

2024-11-01 | E-MTAB-14560 | biostudies-arrayexpress

Single-cell transcriptomics reveals immune response of intestinal cell types to viral infection.

Project description:Human intestinal epithelial cells form a primary barrier protecting us from pathogens, yet only limited knowledge is available about individual contribution of each cell type to mounting an immune response against infection. Here, we developed a framework combining single-cell RNA-Seq and highly multiplex RNA FISH and applied it to human intestinal organoids infected with human astrovirus, a model human enteric virus. We found that interferon controls the infection and that astrovirus infects all major cell types and lineages and induces expression of the cell proliferation marker MKI67. Intriguingly, each intestinal epithelial cell lineage exhibits a unique basal expression of interferon-stimulated genes and, upon astrovirus infection, undergoes an antiviral transcriptional reprogramming by upregulating distinct sets of interferon-stimulated genes. These findings suggest that in the human intestinal epithelium, each cell lineage plays a unique role in resolving virus infection. Our framework is applicable to other organoids and viruses, opening new avenues to unravel roles of individual cell types in viral pathogenesis.

| S-EPMC8311733 | biostudies-literature

10X Single cell RNAseq (scRNAseq) analysis of intestinal epithelial cells (IECs) from murine small intestinal organoids treated with vehicle (DMSO) or LXR agonist GW3965.

Project description:Intestinal organoids are a good model of in vitro tissue regeneration that faithfully recapitulates majority of cell types of the intestine. To analyze the impact of LXR activation in intestinal regeneration and overall cellular composition, organoids established from WT mice were treated with either vehicle (DMSO) or GW3965 and were analyzed using 10X scRNAseq platform.

2024-07-19 | GSE180079 | GEO

Single-cell RNAseq of the human normal and emphysema lung

Project description:To study emphysema, we conduct single-cell RNAseq of the human healthy and emphysema lung using 10X genomics scRNAseq technique.

2023-02-13 | GSE196638 | GEO

Transcriptional Responses of Human Intestinal Organoids to Interferon Types I, II, and III

Project description:RNAseq of intestinal epithelial cell (IEC) organoids derived from biopsy of ileum or colon from healthy subjects and treated with type I interferon (IFN beta), type II interferon (IFN gamma), or type III interferon (IFN lambda 2).

2021-12-21 | GSE190899 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data