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| Status |
Public on Nov 26, 2024 |
| Title |
BCR, PBMC, healthy, donor2 |
| Sample type |
SRA |
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| Source name |
PBMC
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| Organism |
Homo sapiens |
| Characteristics |
cell type: PBMC
Sex: Male
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| Extracted molecule |
total RNA |
| Extraction protocol |
PBMCs were isolated from blood samples from six COVID-19 inpatients admitted to Juntendo University Hospital in Tokyo, Japan, using BD Vacutainer CPT mononuclear cell preparation tubes containing sodium heparin. The isolated cells were washed with Dalbeccos' phosphate buffered saline (PBS), resuspended in 1 mL of CELLBANKER 1 Plus, and stored at -80°C until further use.
scRNA libraries were constructed with library-associated unique indexes, using the library construction kit (1000196), the Single Index Kit T Set A (1000213), and SI primer (2000095)
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| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
DNBSEQ-G400 |
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| Description |
healthy2_control2
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| Data processing |
Cell Ranger v 6.1.2 (multi)
Quality control, mapping to human genome reference, and read count exctraction were performed using Cell Ranger multi
Assembly: hg38
Supplementary files format and content: Comma-delimited text files include clonotype information for each Sample
Supplementary files format and content: Comma-delimited text files include VDJ sequences and annotation for each barcode
Supplementary files format and content: Tab-delimited text files include CDR sequences with start and end sites for each VDJ gene
Library strategy: BCR
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| Submission date |
May 16, 2024 |
| Last update date |
Nov 26, 2024 |
| Contact name |
Yoko Tabe |
| Organization name |
Juntendo University
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| Department |
Department of Clinical Laboratory Medicine
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| Street address |
2 Chome-1-1 Hongo
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| City |
Bunkyo |
| State/province |
Tokyo |
| ZIP/Postal code |
113-8421 |
| Country |
Japan |
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| Platform ID |
GPL28038 |
| Series (1) |
| GSE267642 |
BCR, not TCR, repertoire diversity is associated with favorable COVID-19 [BCR-Seq] |
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| Relations |
| BioSample |
SAMN41274741 |
| SRA |
SRX24576625 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8271487_hc2_BCR_airr_rearrangement.tsv.gz |
209.2 Kb |
(ftp)(http) |
TSV |
| GSM8271487_hc2_BCR_clonotypes.csv.gz |
12.1 Kb |
(ftp)(http) |
CSV |
| GSM8271487_hc2_BCR_filtered_contig_annotations.csv.gz |
71.6 Kb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
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