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| Status |
Public on Jul 19, 2021 |
| Title |
DAA-17 |
| Sample type |
SRA |
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| Source name |
CD3 cells from subject 8 - healthy normal control
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| Organism |
Homo sapiens |
| Characteristics |
subject: 8
time point: Normal
disease: Healthy
cell type: T cells
Sex: male
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| Extracted molecule |
total RNA |
| Extraction protocol |
Cells resuspended in the reaction mix were loaded into the Chromium Single Cell Chip B, as well as the 10x Barcoded Gel Beads and the partitioning oil. The Chip B was placed into the 10x Chromium controller for cell partitioning, targeting a final number of 10 thousand cells per sample. After partition was concluded, the GEMs (Gel Bead-In EMulsions) were transferred to the C1000 Touch Thermal Cycler for the first phase of reverse transcription and samples proceed to library preparation following manufacturer’s instructions.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
DAA-17
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| Data processing |
Illumina BCL files were de-multiplexed and converted to FASTQs using Cell Ranger mkfastq (version 5.0.1, 10X Genomics https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest).
FASTQs were then used to quantify gene expression using Cell Ranger count (version 5.0.1) and the GRCh38 (version refdata-gex-GRCh38-2020-A, 10X Genomics) human genome reference.
Genome_build: GRCh38 (version refdata-gex-GRCh38-2020-A, 10X Genomics)
Supplementary_files_format_and_content: gene expression counts in 10X format (separate barcodes, features, and matrix files for each sample).
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| Submission date |
Jun 23, 2021 |
| Last update date |
Jul 22, 2021 |
| Contact name |
Ana C Maretti-Mira |
| E-mail(s) |
[email protected]
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| Organization name |
USC
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| Department |
Medicine
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| Lab |
Golden Lab
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| Street address |
1450 Biggy Street, NRT 4516
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| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90033 |
| Country |
USA |
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| Platform ID |
GPL24676 |
| Series (1) |
| GSE178756 |
Single-cell transcriptomic analyses of T cells in chronic HCV-infected patients dominated by DAA-induced interferon signaling changes |
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| Relations |
| BioSample |
SAMN19837279 |
| SRA |
SRX11206921 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5396992_DAA-17_barcodes.tsv.gz |
47.7 Kb |
(ftp)(http) |
TSV |
| GSM5396992_DAA-17_features.tsv.gz |
325.6 Kb |
(ftp)(http) |
TSV |
| GSM5396992_DAA-17_matrix.mtx.gz |
63.0 Mb |
(ftp)(http) |
MTX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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