Show simple item record

Depositordc.contributorWilson-Kanamori, John Roger
Funderdc.contributor.otherMRC - Medical Research Councilen_UK
Funderdc.contributor.otherWellcome Trusten_UK
Funderdc.contributor.otherGuts UKen_UK
Funderdc.contributor.otherAbbVie
Funderdc.contributor.otherTenovus
Funderdc.contributor.otherBritish Heart Foundation
Data Creatordc.creatorRamachandran, Prakash
Data Creatordc.creatorHenderson, Neil
Data Creatordc.creatorWilson-Kanamori, John Roger
Date Accessioneddc.date.accessioned2019-10-25T12:46:43Z
Date Availabledc.date.available2019-10-25T12:46:43Z
Citationdc.identifier.citationRamachandran, Prakash; Henderson, Neil; Wilson-Kanamori, John Roger. (2019). Resolving the fibrotic niche of human liver cirrhosis at single-cell level - Seurat RData object, [dataset]. University of Edinburgh Centre for Inflammation Research. https://doi.org/10.7488/ds/2637.en
Persistent Identifierdc.identifier.urihttp://hdl.handle.net/10283/3433
Persistent Identifierdc.identifier.urihttps://doi.org/10.7488/ds/2637
Dataset Description (abstract)dc.description.abstractWe profile the transcriptomes of non-parenchymal cell types present in healthy and cirrhotic human liver. In particular, we uncover a novel scar-associated TREM2+CD9+ macrophage subpopulation, which expands in liver fibrosis, differentiates from circulating monocytes, has a corollary population in mouse liver fibrosis and is pro-fibrogenic. We also define novel ACKR1+ and PLVAP+ endothelial cells which expand in cirrhosis, are topographically scar-restricted and enhance leucocyte transmigration.en_UK
Dataset Description (TOC)dc.description.tableofcontentstissue.rdata: RData file containing a Seurat object "tissue", which in turn contains the raw and normalised expression values for 58,358 human single cell transcriptomes from healthy and cirrhotic liver. This represents the data after application of all relevant, stringent quality control and doublet removal steps, and thus while it does not wholly correlate to any figure shown in the related publication, may be thought of as the 'final' processed and annotated version of Figure 1. The Seurat object "tissue" also contains metadata fields as follows: - nGene, nUMI, percent.mito: quality control metrics - liver: liver of origin, i.e. Healthy1, Cirrhotic4 (see Extended Data Figure 2f) - dataset: dataset of origin, i.e. Healthy1_Cd45+, Cirrhotic4_Cd45+ - condition: condition of liver of origin, i.e. Uninjured, Cirrhotic - aetiology: aetiology of liver of origin, i.e. NAFLD, PBC - annotation_original: results of initial high-level clustering, i.e. 1-21 - annotation_lineage: results of lineage annotation, i.e. Endothelia, MPs - annotation_indepth: results of detailed low-level clustering, i.e. MPs (1), Endothelia (4)en_UK
Languagedc.language.isoengen_UK
Publisherdc.publisherUniversity of Edinburgh Centre for Inflammation Researchen_UK
Relation (Is Version Of)dc.relation.isversionofhttps://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE136103en_UK
Relation (Is Referenced By)dc.relation.isreferencedbyhttps://www.nature.com/articles/s41586-019-1631-3en_UK
Relation (Is Referenced By)dc.relation.isreferencedbyhttps://www.biorxiv.org/content/10.1101/766113v1en_UK
Rightsdc.rightsCreative Commons Attribution 4.0 International Public Licenseen
Subjectdc.subjectSingle cell transcriptomicsen_UK
Subjectdc.subjectLiver fibrosisen_UK
Subject Classificationdc.subject.classificationMedicine and Dentistry::Clinical Medicineen_UK
Titledc.titleResolving the fibrotic niche of human liver cirrhosis at single-cell level - Seurat RData objecten_UK
Typedc.typedataseten_UK

Download All
zip file MD5 Checksum: 7bee48b1d0dc494ad7168f301cca67e4

Files in this item

Thumbnail
Thumbnail
Thumbnail
Thumbnail

This item appears in the following Collection(s)

Show simple item record