Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

The human gastrointestinal tract through space and time- Fetal VDJ

ABSTRACT: Using single-cell RNAseq (scRNAseq) and paired VDJ analysis, we create the first comprehensive cell atlas of the healthy developing, paediatric and adult human gut, including 347,980 cells from up to 10 distinct anatomical sites. We use this data to trace the cellular composition of the gut throughout life, define novel cell markers and cell-cell interactions. We find four neuronal cell populations in the developing enteric nervous system, with expression patterns indicative of irritable bowel syndrome and Hirschsprung’s disease, and identify key cell players and communication networks initiating lymphoid structure formation in early human development.

INSTRUMENT(S): Single cells were captured using the 10x Genomics Chromium Controller., Illumina HiSeq 4000

ORGANISM(S): Homo sapiens

SUBMITTER: Kylie James

PROVIDER: E-MTAB-9533 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

The human gastrointestinal tract through space and time- Fetal GEX

Project description:Using single-cell RNAseq (scRNAseq) and paired VDJ analysis, we create the first comprehensive cell atlas of the healthy developing, paediatric and adult human gut, including 347,980 cells from up to 10 distinct anatomical sites. We use this data to trace the cellular composition of the gut throughout life, define novel cell markers and cell-cell interactions. We find four neuronal cell populations in the developing enteric nervous system, with expression patterns indicative of irritable bowel syndrome and Hirschsprung’s disease, and identify key cell players and communication networks initiating lymphoid structure formation in early human development.

2021-05-24 | E-MTAB-9536 | biostudies-arrayexpress

The human gastrointestinal tract through space and time- Adult VDJ

2021-09-13 | E-MTAB-9532 | biostudies-arrayexpress

The human gastrointestinal tract through space and time- Adult GEX

2022-07-11 | E-MTAB-9543 | biostudies-arrayexpress

scRNA-seq of first and second trimester human gonads - 10x dataset

Project description:scRNA-seq of first and second trimester human gonads

2022-06-30 | E-MTAB-10551 | biostudies-arrayexpress

VDJ: Single-cell RNA sequencing of human steady-state immune cells from the lamina propria of colon and matching mesenteric lymph nodes

Project description:The human colon contains an extensively diverse microbial ecosystem and one of the most numerous communities of immune cells. Studies have highlighted dynamic crosstalk between immune cells and commensals. While studies have demonstrated increasing diversity of microbiota from stomach to stool, whether and how immune cell heterogeneity and microbiota diversity change across the colon is undefined. Furthermore, whether these changes are co-depended in the healthy colon is unknown. Here, tissue samples are collected from caecum, transverse colon, sigmoid colon and mLN of cadaveric donors by the Cambridge Biorepository of Translational Medicine (CBTM). We use single cell RNA sequencing (10X genomics) to assess the dynamics of immune cell populations across the colon and in matching lymph nodes. Associated microbiome 16S sequencing data is available.

2020-01-01 | E-MTAB-8476 | biostudies-arrayexpress

GEX: Single-cell RNA sequencing of human steady-state immune cells from the lamina propria of colon and matching mesenteric lymph nodes

2020-01-01 | E-MTAB-8474 | biostudies-arrayexpress

sc/snRNAseq of human endometrium from controls and endometriosis patients

Project description:The study profiles endometrial samples from donors in reproductive age with and without endometriosis collected either during natural cycles or under exogenous hormonal treatment. Samples where profiled either with single-cell RNA sequencing (scRNA-seq) or single-nuclei RNA sequencing (snRNA-seq) using 10x technology.

2024-05-22 | E-MTAB-14039 | biostudies-arrayexpress

Spatial transcriptomics of human implantation sites, placenta and decidua

Project description:These samples are part of a study to provide a spatially resolved single-cell multiomics map of human trophoblast differentiation in early pregnancy. Here we profiled with 10x Visium Spatial transcriptomics of the entire maternal-fetal interface including the myometrium, allowing us to resolve the full trajectory of trophoblast differentiation.

2023-02-03 | E-MTAB-12698 | biostudies-arrayexpress

multiomic snRNAseq/snATACseq of first and second-trimester human gonads

Project description:Comprehensive map of first- and second-trimester gonadal development in humans using a combination of single-cell and spatial transcriptomics, chromatin accessibility assays, and imaging.

2022-05-12 | E-MTAB-11708 | biostudies-arrayexpress

Human uterine Natural Killer cells regulate differentiation of extravillous trophoblast early in pregnancy - scRNA-seq data

Project description:We used trophoblast organoids differentiating to extravillous trophoblast (EVT) to study the effects of key cytokines secreted by uterine Natural Killer (uNK) cells on EVT behaviour. Specifically, we exposed the organoids to four uNK-derived cytokines (CSF1, CSF2, XCL1, CCL5) and collected cells at different time points along the EVT differentiation pathway for scRNA-seq. We observe enhanced EVT differentiation in cytokine-treated organoids demonstrated by the increased proportion of late EVT subtypes and regulation of related pathways such as epithelial-mesenchymal transition. Moreover, uNK cytokines affect other processes important during early pregnancy including dampening of inflammatory and adaptive immune responses, regulation of blood flow, and placental access to nutrients.

2024-01-10 | E-MTAB-13382 | biostudies-arrayexpress

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