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Sample GSM7798092 Query DataSets for GSM7798092
Status Public on Apr 15, 2024
Title PWH P1 Visit 2 CSF scTCRseq
Sample type SRA
 
Source name CSF
Organism Homo sapiens
Characteristics donor: P1
tissue: CSF
cell type: T cell
disease status: chronic HIV
study id: HIV-1102v2
Extracted molecule total RNA
Extraction protocol Fresh CSF and blood were processed within one hour of collection. CSF was centrifuged at 300g for 10 minutes at room temperature (25°C). The supernatant was aspirated to 40 µl and the pelleted cells were used for single-cell RNA sequencing. Peripheral blood mononuclear cells (PBMCs) were isolated from whole blood via Ficoll gradient with Sepmate tubes and resuspended in .04% PBS-BSA for single-cell RNA sequencing.
For blood, approximately 8000 single cells per sample were processed using the Chromium 5′ single-cell expression system (10x Genomics). For CSF, the entire cell pellet was processed for 10X. Samples were sequenced on Illumina HiSeq 4000 or Illumina HiSeq2500 at an average depth of 30-50,000 reads per cell.
 
Library strategy OTHER
Library source transcriptomic
Library selection other
Instrument model Illumina HiSeq 4000
 
Description P1_1_2_CSF_TCR
Data processing Cell Ranger 7.0.0 count subcommand was used to generate the count matrices, barcode assignments, and feature calls for gene expression data.
Cell Ranger 7.0.0 vdj subcommand was used to assemble TCR and BCR sequences.
Cell Ranger 7.0.0 aggr subcommand was used to aggregate samples into a single data matrix
Seurat v4 was used to filter out low quality cells and Azimuth was used to perform cell type annotations.
Assembly: GCRhg38
Supplementary files format and content: cell ranger count matrix in h5 file format, cell ranger vdj clonotype files, seurat object in RDS format
Library strategy: scTCRseq
 
Submission date Sep 24, 2023
Last update date Apr 15, 2024
Contact name Shelli Farhadian
Organization name Yale University
Street address 135 College St.
City New Haven
State/province CT
ZIP/Postal code 06511
Country USA
 
Platform ID GPL20301
Series (1)
GSE243905 Single-cell TCR profiling of CSF and blood cells of PWH reveals persistent and shared infected T cell clones across tissue compartments even after ART
Relations
BioSample SAMN37525489
SRA SRX21870165

Supplementary file Size Download File type/resource
GSM7798092_P1_1_2_CSF_TCR.tar.gz 1.7 Mb (ftp)(http) TAR
SRA Run SelectorHelp
Raw data are available in SRA

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