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| Status |
Public on Jul 31, 2022 |
| Title |
KW939_CD4_A7 |
| Sample type |
SRA |
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| Source name |
single cell
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| Organism |
Homo sapiens |
| Characteristics |
cell type: CD4 T
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| 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
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| 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
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
single cell
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| 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
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| Submission date |
Oct 07, 2021 |
| Last update date |
Jul 31, 2022 |
| Contact name |
Paul Moss |
| Organization name |
University of Birmingham
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| Department |
Immunology and Immunotherapy
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| Lab |
Moss
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| Street address |
Vincent Drive
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| City |
Birmingham |
| State/province |
West Midlands |
| ZIP/Postal code |
B152TT |
| Country |
United Kingdom |
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| 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 |
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| Relations |
| BioSample |
SAMN22109295 |
| SRA |
SRX12512794 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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