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Using genetics to identify cell types and mechanisms underlying susceptibility to primary sclerosing cholangitis

Primary sclerosing cholangitis (PSC) is a T-cell mediated, chronic inflammatory condition of the biliary tree that is strongly associated with inflammatory bowel disease. Genome-wide association studies have identified 22 non-HLA genetic risk variants associated PSC. Identifying the genes impacted by these variants has proven difficult as the majority lie in non-coding regions of the genome. Knowledge of the genes and biological pathways these non-coding variants are perturbing is vital to understanding the disease biology. One means of assessing the impact of non-coding variants within disease associated loci upon genes is via colocalisation with eQTL. Many eQTL are cell-type specific, requiring the analysis of disease relevant cell types to detect colocalisation. We have collected PSC-relevant T-cell-subtypes from the peripheral blood of PSC patients via fluorescence activated cell sorting in preparation for RNA sequencing and mapping of eQTL. Samples were collected at the Norfolk and Norwich University Hopital, for which local ethical approval has been granted. Lysed cell samples will be transferred to WTSI and DNA/RNA will be extracted from lysed cell samples by T143 before genotyping (DNA) and custom library preparation and sequencing (RNA). This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/

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Studies are experimental investigations of a particular phenomenon, e.g., case-control studies on a particular trait or cancer research projects reporting matching cancer normal genomes from patients.

Study ID Study Title Study Type
EGAS00001002642 Transcriptome Analysis

This table displays only public information pertaining to the files in the dataset. If you wish to access this dataset, please submit a request. If you already have access to these data files, please consult the download documentation.

ID File Type Size Located in
EGAF00008257726 cram 826.8 MB
EGAF00008257727 cram 817.4 MB
EGAF00008257728 cram 584.7 MB
EGAF00008257729 cram 803.2 MB
EGAF00008257730 cram 736.5 MB
EGAF00008257731 cram 973.0 MB
EGAF00008257732 cram 955.9 MB
EGAF00008257733 cram 845.1 MB
EGAF00008257734 cram 1.1 GB
EGAF00008257735 cram 1.8 GB
EGAF00008257736 cram 796.1 MB
EGAF00008257737 cram 811.9 MB
EGAF00008257738 cram 790.9 MB
EGAF00008257739 cram 789.3 MB
EGAF00008257740 cram 566.7 MB
EGAF00008257741 cram 771.0 MB
EGAF00008257742 cram 706.5 MB
EGAF00008257743 cram 938.8 MB
EGAF00008257744 cram 915.9 MB
EGAF00008257745 cram 814.1 MB
EGAF00008257746 cram 1.0 GB
EGAF00008257747 cram 1.7 GB
EGAF00008257748 cram 765.0 MB
EGAF00008257749 cram 779.5 MB
24 Files (21.6 GB)