HCA Data Explorer

Ischaemic sensitivity of human tissue by single cell RNA seq

Assessment of the effect of cold ischaemic time on single cell RNAseq data from human tissues using 10x Genomics 3' single cell RNA sequencing. This project contains data for spleen, oesophagus epithelium and lung parenchyma, three tissues that had previously been reported to have differential sensitivity to ischaemia. Samples were collected into Hypothermasol FRS hypothermic preservation media and dissociated fresh (as soon as possible) or at 12h, 24h, 72h post onset of cold ischaemia in the donor. Single cell and bulk RNA sequencing data was generated at each time point and whole genome sequencing was carried out for each donor.

Anna Wilbrey-ClarkWellcome Sanger Instituteaw24@sanger.ac.uk
Kerstin B MeyerWellcome Sanger Institutekm16@sanger.ac.uk
Elo MadissoonEMBL-EBIem17@sanger.ac.uk
Tracey AndrewWellcome Sanger Instituteta11@sanger.ac.uk
Oliver StegleEMBL-EBIstegle@ebi.ac.uk
Michael JT Stubbington (Co-Investigator)1
Phillipa Harding (Experimental Scientist)1
Anna Wilbrey-Clark (Experimental Scientist)1
Krzysztof Polanski (Computational Scientist)1
Kevin Loudon (Experimental Scientist)2
John R Ferdinand (Experimental Scientist)2
Krishnaa Mahbubani (Clinician)2
Nikitas Georgakopoulos (Clinician)2
Kerstin B Meyer (Principal Investigator)1
Kourosh Saeb-Parsy (Clinician)2
Karol Nowicki-Osuch (Experimental Scientist)3
Rebecca Fitzgerald (Co-Investigator)3
Ricardo J Miragaia (Experimental Scientist)1
Sarah A Teichmann (Co-Investigator)1
Elo Madissoon (Computational Scientist)4
Tracey Andrew (Administrator)1
Anthi Tsingene (Experimental Scientist)1
Emily Relton (Experimental Scientist)1
Liam Bolt (Experimental Scientist)1
Oliver Stegle (Principal Investigator)4
Ni Huang (Computational Scientist)1
1Wellcome Sanger Institute
2University of Cambridge
3MRC Cancer Unit
4EMBL-EBI
Mallory Ann Freeberg
Danielle Welter
Marion F Shadbolt
Zinaida A Perova

To reference this project, please use the following link:

https://explore.data.humancellatlas.org/explore/projects/c4077b3c-5c98-4d26-a614-246d12c2e5d7

Supplementary links are provided by contributors and represent items such as additional data which can’t be hosted here; code that was used to analyze this data; or tools and visualizations associated with this specific dataset.

1.https://www.tissuestabilitycellatlas.org/
INSDC Project Accessions:
ERP114453
INSDC Study Accessions:
PRJEB31843
BioStudies Accessions:
S-SUBS3

For information regarding data sharing and data use, please see our Data Access Policy.

Analysis Portals

CZ CELLxGENECZ CELLxGENE
UCSC Cell BrowserUCSC Cell Browser

Project Label

TissueStability

Species

Homo sapiens

Sample Type

specimens

Anatomical Entity

3 anatomical entities

Organ Part

4 organ parts

Selected Cell Types

2 cell types

Disease Status (Specimen)

Unspecified

Disease Status (Donor)

normal

Development Stage

human adult stage

Library Construction Method

3 library construction methods

Nucleic Acid Source

2 nucleic acid sources

Paired End

false, true

Analysis Protocol

optimus_post_processing_v1.0.0, optimus_v4.2.2

File Format

7 file formats

Cell Count Estimate

199.8k

Donor Count

14
bam67 file(s)csv4 file(s)docx1 file(s)fastq.gz361 file(s)h5ad3 file(s)loom70 file(s)pdf6 file(s)