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| Status |
Public on Dec 18, 2023 |
| Title |
#25-28 TCR |
| Sample type |
SRA |
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| Source name |
PBMC
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| Organism |
Homo sapiens |
| Characteristics |
tissue: PBMC
cell type: T cell
treatment: Mixed sample (3wks, 6wks, 24wks from donor #25,#28)
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| Treatment protocol |
PBMCs were labeled with CellTrace Violet (CTV) and cultured in the presence of SARS-CoV-2 S peptide pool (15-mer, with 11-mer overlap) that covers whole S protein of Wuhan strain, mutations in S proteins of Delta, Omicron BA.1 and BA.2 strains. Human recombinant IL-2 (1ng/ml), IL-7 (5ng/ml) and IL-15 (5ng/ml) were supplemented on day 2, day 5 and day 8 of the culture.
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
On day 10 of the culture, cells were washed and stained with anti-human CD3 and TotalSeq-C antibodies (see ADT/HTO_ information.csv). Proliferated T cells (CD3+CTVlow) were sorted and used for single-cell TCR and RNA sequencing analyses.
Single cell library was prepared using the reagents from 10x Genomics following the manufacturer’s instructions. After reverse transcription, cDNA was amplified for 14 cycles, and up to 50 ng of cDNA was used for construction of gene expression and TCR libraries. Libraries were sequenced in paired-end mode.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
10x Genomics
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| Data processing |
The raw reads were processed by Cell Ranger 6.0.0 (10x Genomics).
Assembly: GRCh38
Supplementary files format and content: CellRanger output files: filtered_feature_bc_matrix.h5 (RNA and feture barcodes)
Supplementary files format and content: CellRanger output files: filtered_contig_annotations.csv (TCR)
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| Submission date |
Oct 30, 2023 |
| Last update date |
Dec 18, 2023 |
| Contact name |
Xiuyuan Lu |
| Organization name |
Osaka University
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| Department |
IFReC
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| Lab |
Molecular Immunology
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| Street address |
3-1 Yamadaoka
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| City |
Suita |
| State/province |
Osaka |
| ZIP/Postal code |
562-0031 |
| Country |
Japan |
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| Platform ID |
GPL24676 |
| Series (1) |
| GSE246535 |
T cell responses in SARS-CoV-2 vaccinees with sustained or declined antibody titer |
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| Relations |
| BioSample |
SAMN38041205 |
| SRA |
SRX22288167 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7870844_25-28_1_filtered_contig_annotations.csv.gz |
1.8 Mb |
(ftp)(http) |
CSV |
| GSM7870844_25-28_2_filtered_contig_annotations.csv.gz |
1.8 Mb |
(ftp)(http) |
CSV |
| GSM7870844_25-28_3_filtered_contig_annotations.csv.gz |
1.7 Mb |
(ftp)(http) |
CSV |
| GSM7870844_25-28_4_filtered_contig_annotations.csv.gz |
1.6 Mb |
(ftp)(http) |
CSV |
| GSM7870844_25-28_5_filtered_contig_annotations.csv.gz |
1.6 Mb |
(ftp)(http) |
CSV |
| GSM7870844_25-28_6_filtered_contig_annotations.csv.gz |
1.6 Mb |
(ftp)(http) |
CSV |
| GSM7870844_25-28_7_filtered_contig_annotations.csv.gz |
1.8 Mb |
(ftp)(http) |
CSV |
| GSM7870844_25-28_8_filtered_contig_annotations.csv.gz |
1.8 Mb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
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