NBDC Research ID: hum0522.v1
SUMMARY
Aims: To address the dynamics of immune checkpoint inhibitor (ICI)-bound progenitor-exhausted T cells after ICI treatment and analysis of immune cells in autoimmune diseases
Methods: scRNA-seq, TCR-seq, CITE-seq
Participants/Materials: Esophagogastric junction cancer 2 cases, gastric cancer 3 cases
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000720 | NGS（scRNA-seq, TCR-seq, CITE-seq） | Controlled-access (Type I) | 2025/06/26 |
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MOLECULAR DATA
| Participants/Materials |
Esophagogastric junction cancer (ICD10: C15.8): 2 cases 1) Blood, tumor, metastatic lymph nod, and non-metastatic lymph node: total 4 samples 2) Blood, metastatic liver cancer, and non-metastatic lymph node: total 3 samples Gastric cancer (ICD10: C16.9): 3 cases 3) Blood, tumor, and 2 non-metastatic lymph nodes: total 4 samples 4) Blood, tumor, metastatic lymph node, and non-metastatic lymph node: total 4 samples 5) Blood, tumor, and 2 non-metastatic lymph nodes: total 4 samples |
| Targets | scRNA-seq |
| Target Loci for Capture Methods | - |
| Platform |
Illumina [Novaseq 6000] MGI [DNBSEQ-G400] |
| Library Source | RNAs extracted from T cells isolated from peripheral blood sample |
| Cell Lines | - |
| Library Construction (kit name) | Chromium Next GEM Single Cell 5' Kit v2 Chromium Next GEM Chip K Single Cell Kit |
| Fragmentation Methods | included in the above library construction kit |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 91 bp |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000853 |
| Total Data Volume | 482.4 GB（fastq） |
| Comments (Policies) | NBDC policy |
| Participants/Materials |
Esophagogastric junction cancer (ICD10: C15.8): 2 cases 1) Blood, tumor, metastatic lymph nod, and non-metastatic lymph node: total 4 samples 2) Blood, metastatic liver cancer, and non-metastatic lymph node: total 3 samples Gastric cancer (ICD10: C16.9): 3 cases 3) Blood, tumor, and 2 non-metastatic lymph nodes: total 4 samples 4) Blood, tumor, metastatic lymph node, and non-metastatic lymph node: total 4 samples 5) Blood, tumor, and 2 non-metastatic lymph nodes: total 4 samples |
| Targets | TCR-seq |
| Target Loci for Capture Methods | - |
| Platform |
Illumina [Novaseq 6000] MGI [DNBSEQ-G400] |
| Library Source | RNAs extracted from T cells isolated from samples |
| Cell Lines | - |
| Library Construction (kit name) | Chromium Single Cell Human TCR Amplification Kit Chromium Next GEM Chip K Single Cell Kit |
| Fragmentation Methods | included in the above library construction kit |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 91 bp |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000853 |
| Total Data Volume | 482.4 GB（fastq） |
| Comments (Policies) | NBDC policy |
| Participants/Materials |
Esophagogastric junction cancer (ICD10: C15.8): 2 cases 1) Blood, tumor, metastatic lymph nod, and non-metastatic lymph node: total 4 samples 2) Blood, metastatic liver cancer, and non-metastatic lymph node: total 3 samples Gastric cancer (ICD10: C16.9): 3 cases 3) Blood, tumor, and 2 non-metastatic lymph nodes: total 4 samples 4) Blood, tumor, metastatic lymph node, and non-metastatic lymph node: total 4 samples 5) Blood, tumor, and 2 non-metastatic lymph nodes: total 4 samples |
| Targets | CITE-seq |
| Target Loci for Capture Methods | - |
| Platform |
Illumina [Novaseq 6000] MGI [DNBSEQ-G400] |
| Library Source | RNAs extracted from T cells isolated from samples |
| Cell Lines | - |
| Library Construction (kit name) | Chromium Next GEM Single Cell 5' Kit v2 Chromium Next GEM Chip K Single Cell Kit |
| Fragmentation Methods | included in the above library construction kit |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 91 bp |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000853 |
| Total Data Volume | 482.4 GB（fastq） |
| Comments (Policies) | NBDC policy |
DATA PROVIDER
Principal Investigator: Takuro Saito
Affiliation: Department of gastroenterological surgery, Osaka University
Project / Group Name: -
| Name | Title | Project Number |
|---|---|---|
| KAKENHI Grant-in-Aid for Early-Career Scientists | Immune status of lymph nodes in gastric cancer and the effect of checkpoint inhibitors on lymph nodes | 23K15472 |
| KAKENHI Grant-in-Aid for Early-Career Scientists | The analysis for the suppressive mechanism of antitumor immunity in lymph nods of gastric cancer | 20K17685 |
| KAKENHI Grant-in-Aid for Scientific Research (C) | Elucidating the Mechanism of effect of Immune Checkpoint Inhibitors Through Detection of Nivolumab-Bound T Cells | 23K08194 |
| Medical research grant, Takeda Science Foundation | Mechanistic Insights into Antitumor Lymphocyte Regulation in Gastric Cancer by Spatial Mapping of Lymph Nodes | - |
| Medical research grant, Chubei Itoh Foundation | - | - |
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 |
USRES (Controlled-access Data)
| Principal Investigator | Affiliation | Country/Region | Research Title | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|---|---|
