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| Status |
Public on Mar 07, 2022 |
| Title |
PBMC-05-1-GEX-S5 |
| Sample type |
SRA |
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| Source name |
peripheral blood mononuclear cells
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| Organism |
Homo sapiens |
| Characteristics |
batchid: PBMC-05
subbatchid: 1
sequencingrunid: S5
librarytype: Gene Expression
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
A pooled suspension containing 2,000,000 thawed PBMCs from at most 20 subjects (~100,000 per subject) were stained with 282 Totalseq antibodies according to the Totalseq-A protocol (https://www.biolegend.com/en-us/protocols/totalseq-a-antibodies-and-cell-hashing-with-10x-single-cell-3-reagent-kit-v3-3-1-protocol). Stained cells were then loaded onto the Chromium Controller at an input density of 2,500 cells/µL and cDNA libraries were prepared using the 10X Genomics Single Cell 3' v3.1 Assay.
Peripheral blood was collected from each subject in Vacutainer ACD tubes. PBMCs were isolated using a standard Ficoll method and stored in liquid nitrogen.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
PBMC-05-1.barcodes.tsv.gz
PBMC-05-1.features.tsv.gz
PBMC-05-1.matrix.mtx.gz
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| Data processing |
Library strategy: CITE-seq
Raw RNA and ADT fastqs for each Chromium library were respectively aligned to the GRCh38 human genome reference and a reference database of antibody-tag sequences using Cell Ranger 3.1.0
Genome_build: GRCh38
Supplementary_files_format_and_content: CellMetadata_AS_20220103.tsv, CellMetadata_PSA_20220103.tsv: metadata for each barcode (cell type, subject, subject clinical status, whether the cell was identified to be a doublet, etc.); barcodes.tsv.gz: cell barcodes in the sample; features.tsv.gz: Gene and ADT features detected in a sample; matrix.mtx.gz: MTX (MatrixMarket)-formatted read counts in a sample of each feature in the corresponding features.tsv.gz file in each barcode in the corresponding barcodes.tsv.gz file
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| Submission date |
Jan 25, 2022 |
| Last update date |
Mar 07, 2022 |
| Contact name |
Wilson Liao |
| E-mail(s) |
wilson.liao@ucsf.edu
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| Organization name |
University of California, San Francisco
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| Department |
Dermatology
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| Street address |
2340 Sutter St.
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| City |
San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94143 |
| Country |
USA |
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| Platform ID |
GPL24676 |
| Series (1) |
| GSE194315 |
RNA and surface epitope sequencing of single cells involved in spondyloarthritis |
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| Relations |
| BioSample |
SAMN25241918 |
| SRA |
SRX13897066 |
| 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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