|
| Status |
Public on Dec 21, 2022 |
| Title |
TCR repertoire of P7-post [P7-post-TCR] |
| Sample type |
SRA |
| |
|
| Source name |
CD62Llow CD4+ T cells
|
| Organism |
Homo sapiens |
| Characteristics |
diagnosis: Lung cancer
cell type: CD62Llow CD4+ T cells
|
| Treatment protocol |
Pre-treatment samples.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Manufactured protocol of Chromium system (10x Genomics).
Manufactured protocol of Chromium Next GEM Single Cell V(D)J Reagent Kit v1.1 with Feature Barcoding technology (10x Genomics).
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
P7-post-TCR
RNA of TCR genes
Peripheral Blood Mononuclear Cells
An antigen stimulation experiment using Dynabeads Human T-Activator CD3/CD28 was performed on T cells obtained from patient #7. "P7-post" indicates post-stimulated.
|
| Data processing |
Library strategy: TCR repertoire
10x Genomics cellranger (4.0.0) mkfastq used for basecalling.
Sequenced reads were processed with cellranger (4.0.0) count using the GRCh38 reference dataset (version 2020-A; downloaded from 10x Genomics) to derive gene expression and feature barcode UMI count matrix.
Sequenced reads were processed with cellranger (4.0.0) vdj using the GRCh38 reference dataset (version 4.0.0; downloaded from 10x Genomics) to derive TCR clonotype data.
Genome_build: GRCh38
Supplementary_files_format_and_content: *_matrix.mtx.gz: MatrixMarket format files include UMI count matrixes of gene expressions and feature barcodes for each sample. Row and column names of matrix are separately recorded in following two files.
Supplementary_files_format_and_content: *_barcodes.tsv.gz: Tab-separated text files include cell barcodes for each sample.
Supplementary_files_format_and_content: *_features.tsv.gz: Tab-separated text files include gene names and feature barcode names for each sample.
Supplementary_files_format_and_content: *_filtered_contig_annotations.csv.gz: Comma-separated text files include TCR clonotype data for each sample.
|
| |
|
| Submission date |
Mar 12, 2021 |
| Last update date |
Dec 21, 2022 |
| Contact name |
Satoshi Yamasaki |
| E-mail(s) |
s_ymsk@saitama-med.ac.jp
|
| Organization name |
Saitama Medical University
|
| Department |
Department of Respiratory Medicine
|
| Street address |
1397-1, Yamane
|
| City |
Hidaka-City, Saitama |
| ZIP/Postal code |
350-1298 |
| Country |
Japan |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE168844 |
Identification of a novel antitumor CD4+ T cell cluster orchestrating antitumor immunity |
|
| Relations |
| BioSample |
SAMN18290674 |
| SRA |
SRX10335858 |
