E-MTAB-8484 - SS2_1: Single-cell RNA sequencing of human steady-state immune cells from the lamina propria of colon and matching mesenteric lymph nodes

Status
Submitted on 15 August 2018, last updated on 30 October 2019, released on 1 January 2020
Organism
Homo sapiens
Samples (768)
Protocols (4)
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.
Experiment types
RNA-seq of coding RNA from single cells, organism part comparison design
Contact
Citation
Distinct microbial and immune niches of the human colon. James KR, Gomes T, Elmentaite R, Kumar N, Stares MD, Gulliver EL, King HW, Bareham BR, Ferdinand JR, Petrova VN, Polanski K, Forster SC, Jarvis LB, Suchanek O, Howlett S, James LK, Jones JL, Meyer KB, Clatworthy MR, Saeb-Parsy K, Lawley TD, Teichmann SA.
MINSEQE
Exp. designProtocolsVariablesProcessedSeq. reads
Files
Investigation descriptionE-MTAB-8484.idf.txt
Sample and data relationshipE-MTAB-8484.sdrf.txt
Links