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Sample GSM3140593 Query DataSets for GSM3140593
Status Public on Sep 27, 2018
Title Human_HC_1
Sample type SRA
 
Source name Colon
Organism Homo sapiens
Characteristics tissue: Colon
disease state: Healthy
Treatment protocol Cells isolated from colonic tissues, untreated, directly used for chip loading.
Extracted molecule total RNA
Extraction protocol Single cell suspension derived from enzymatic digestion of colonic biopsies and enrichment for stromal fraction by MACS-depletion of epithelial and immune cells and red blood cells.
Libraruy construction by 3’ prime V2 chemistry Chromium single cell gene expression kit.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 4000
 
Data processing Basecalling was performed using Illumina Casava software
Samples were demultiplexed using Illumina bcl2fasq software
Sequenced reads were processed, aligned and counts summarised using Cellranger 2.1 pipeline
Seurat r package was used to process raw UMI matrices and procude UMI counts per 10,000 unique molecules identified per cell
Genome_build: hg38, mm10
Supplementary_files_format_and_content: tab-delimited UMI counts per 10,000 unique molecules detected
 
Submission date May 13, 2018
Last update date Sep 27, 2018
Contact name Alison Simmons
E-mail alison.simmons@ndm.ox.ac.uk
Organization name University of Oxford
Department The MRC Weatherall Institute of Molecular Medicine
Street address John Radcliffe Hospital/Headley Way
City Oxford
ZIP/Postal code OX3 9DS
Country United Kingdom
 
Platform ID GPL20301
Series (1)
GSE114374 Composition of the Colonic Mesenchyme and the Nature of its Plasticity in Inflammatory Bowel Disease
Relations
BioSample SAMN09204837
SRA SRX4079052

Supplementary data files not provided
Raw data are available in SRA
Processed data are available on Series record

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