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Sample GSM5616296 Query DataSets for GSM5616296
Status Public on Jul 31, 2022
Title KW939_CD4_B7
Sample type SRA
 
Source name single cell
Organism Homo sapiens
Characteristics cell type: CD4 T
Treatment protocol Single cell RNA sequencing was performed in 3 patients on T cells isolated from 30–50 ml peripheral blood collected at two weeks after transplantation
Extracted molecule total RNA
Extraction protocol Peripheral blood mononuclear cells (PBMCs) were isolated by density gradient centrifugation and frozen in FCS containing 10% DMSO and stored at –80°C for later use. T cells were sorted on the FACS Aria fusion (BD, USA) using CD3-PERCPCy5.5 (Biolegend, clone HIT3A), CD4-APC/Cy7 (BD Biosciences, clone RPA-T4), and CD8-Viogreen (Miltneyi Biotec, clone BW135/80). CD56-FITC (Biolegend, clone 5.1H11) was used to gate out NK cells and propidium iodide to exclude dead cells (Miltenyi Biotec).
Single cells were sorted into a 96 well plate directly into 3ul of lysis buffer. Library preparation and sequencing was performed by Oxford Genomics Centre (Oxford University, United Kingdom)
Paired end single cell sequencing using Smartseq2
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Description single cell
Data processing Reads were aligned to the human genome (hg38) using BWA-MEM with default parameters. Reads aligning to features were counted from the alignment bam files with the htseq-count script from HTSeq(17) with parameters: -r pos -m union -s no. Counts were aggregated accross the 2 lanes for each cell to give the raw counts matrix
Genome_build: hg38
Supplementary_files_format_and_content: Counts matrix with raw feature counts for each cell
 
Submission date Oct 07, 2021
Last update date Jul 31, 2022
Contact name Paul Moss
Organization name University of Birmingham
Department Immunology and Immunotherapy
Lab Moss
Street address Vincent Drive
City Birmingham
State/province West Midlands
ZIP/Postal code B152TT
Country United Kingdom
 
Platform ID GPL24676
Series (1)
GSE185498 Expression of CD94 and CD96 on CD8+ T cells early after allogeneic stem cell transplantation is predictive of subsequent disease relapse and survival
Relations
BioSample SAMN22109293
SRA SRX12512796

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

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