Transcriptomics

Dataset Information

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SS2_2: Single-cell RNA sequencing of human steady-state immune cells from the lamina propria of colon and matching mesenteric lymph nodes


ABSTRACT: 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.

INSTRUMENT(S): Illumina HiSeq 4000, Agilent Bravo NGS workstation, Microlab STAR automated liquid handler (Hamilton Robotics), PCR machine (MJ Research Peltier Thermal Cycler), BD Influx sorter

ORGANISM(S): Homo sapiens  

SUBMITTER: Kylie R James  

PROVIDER: E-MTAB-8486 | ArrayExpress | 2020-01-01

SECONDARY ACCESSION(S): ERP118273

REPOSITORIES: ArrayExpress, ENA

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