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| Status |
Public on Apr 15, 2024 |
| Title |
PWH P5 CSF scTCRseq |
| Sample type |
SRA |
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| Source name |
CSF
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| Organism |
Homo sapiens |
| Characteristics |
donor: P5
tissue: CSF
cell type: T cell
disease status: chronic HIV
study id: HIV-1017
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| 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.
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| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 4000 |
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| Description |
P5_1_7_CSF_TCR
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| 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
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| Submission date |
Sep 24, 2023 |
| Last update date |
Apr 15, 2024 |
| Contact name |
Shelli Farhadian |
| Organization name |
Yale University
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| Street address |
135 College St.
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| City |
New Haven |
| State/province |
CT |
| ZIP/Postal code |
06511 |
| Country |
USA |
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| 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 |
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| Relations |
| BioSample |
SAMN37525455 |
| SRA |
SRX21870120 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7798126_P5_1_7_CSF_TCR.tar.gz |
1.5 Mb |
(ftp)(http) |
TAR |
SRA Run Selector |
| Raw data are available in SRA |
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