|
| Status |
Public on Jun 12, 2024 |
| Title |
PBMC_2, HTO-derived cDNA |
| Sample type |
SRA |
| |
|
| Source name |
peripheral blood
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: peripheral blood
cell type: T cell
antibodies: Anti CD298 + Anti β2 microglobulin
treatment: none or stimulation with 5-OP-RU or CA7S
fraction: Hashtag oligonucleotide (HTO)
|
| Treatment protocol |
Human PBMCs were prepared from the blood by density gradient centrifugation using Lymphocyte Separation Solution（d=1.077）(Nacalai tesque). PBMCs were stimulated with 5-OP-RU and CA7S at 30 µM or 3000 µM in RPMI 1640 medium (Sigma) supplemented with 10% fetal bovine serum, penicillin (Sigma), streptomycin (MP Biomedicals), and 2-mercaptoethanol (Nacalai tesque). A day later, anti-CD161+MR1-5-OP-RU tetramer+ cells within a CD3+-gated population were sorted by SH800S Cell Sorter (Sony Biotechnology) and used for single-cell TCR- and RNA-seq analyses.
|
| Extracted molecule |
protein |
| Extraction protocol |
Single cell droplets were generated by 10x Genomics Chromium Controller, and cDNAs with UMIs were generated at single-cell level.
The single cell libraries were prepared following the protocol outlined in the Chromium Next GEM Single Cell 5' Reagent Kits v2 User Guide.
|
| |
|
| Library strategy |
OTHER |
| Library source |
other |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Hashtag-condition.xlsx
feature_reference.csv
|
| Data processing |
Sequencing was performed on NovaSeq 6000 platform in a 28+91 base paired-end mode.
Illumina RTA3 v3.4.4 software was used for base calling.
Generated reads were input into the cellranger pipeline (Cell Ranger v.6.0.0, 10x Genomics) for UMI counting for each gene (or tag sequence)-cell (barcode) combination and T cell receptor repertoire profiling.
Assembly: refdata-gex-GRCh38-2020-A and refdata-cellranger-vdj-GRCh38-alts-ensembl-4.0.0
Supplementary files format and content: genematrix.csv: comma-delimited text files including raw counts for all cells detected
Supplementary files format and content: airr_rearrangement.tsv: tab-delimited text file including detected clonotypes for each cell (barcode)
Supplementary files format and content: clonotypes.csv: comma-delimited text file including the TCR clonotype information
Supplementary files format and content: feature_reference.csv: comma-delimited text file including barcode sequences associated with each TotalSeq(BioLegend) hashtag ID and name
Supplementary files format and content: Hashtag-condition.xlsx: Excel file including condition/treatment information for each hashtag
|
| |
|
| Submission date |
Mar 29, 2023 |
| Last update date |
Jun 12, 2024 |
| Contact name |
Daisuke Motooka |
| E-mail(s) |
dry_team@ngs.gen-info.osaka-u.ac.jp
|
| Organization name |
NGS core facility, Research Institute for Microbial Diseases, Osaka University
|
| Street address |
3-1, Yamadaoka
|
| City |
Suita |
| State/province |
Osaka |
| ZIP/Postal code |
5650871 |
| Country |
Japan |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE228498 |
Responses of human MAIT cells to CA7S |
|
| Relations |
| BioSample |
SAMN33970553 |
| SRA |
SRX19809915 |
