NBDC Research ID: hum0521.v1
SUMMARY
Aims: This study aims to clarify tumor immunity in uterine cancer. In particular, we aim to describe the characteristics of B cells and T cells in the tumor microenvironment of uterine cancer and to deepen our understanding of them.
Methods: Uterine specimens were digested with enzymes to separate CD45+ lymphocytes using MACS (Magnetic cell sorting). Subsequently, CD19+ B cells and CD3+ T cells were separated using FACS (Fluorescence-activated cell sorting). Isolated B and T cells were then analyzed using single-cell RNA-seq, single-cell BCR-seq, single-cell TCR-seq, and CITE-seq.
Participants/Materials: tumor tissues of 10 uterine cancer patients, normal uterine tissue from 1 patient with hereditary breast and ovarian cancer syndrome
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000827 | NGS (scRNA-seq, scBCR-seq, scTCR-seq, CITE-seq) | Controlled-access (Type I) | 2025/08/29 |
| E-GEAD-1121 | NGS (scRNA-seq, scBCR-seq, scTCR-seq, CITE-seq) | Unrestricted-access | 2025/08/29 |
*Data users need to apply an application for Using NBDC Human Data to reach the Controlled-access Data. Learn more
*When the research results including the data which were downloaded from NHA/DRA, are published or presented somewhere, the data user must refer the papers which are related to the data, or include in the acknowledgment. Learn more
MOLECULAR DATA
scRNA-seq (JGAS000827 / E-GEAD-1121)
| Participants/Materials |
uterine cancer (ICD10: C549): 10 cases B cells isolated from tumor tissues: 10 cases, 11 samples (one of them acquired scRNA-seq data twice) T cells isolated from tumor tissues: 5 cases, 5 samples hereditary breast and ovarian cancer syndrome (ICD10: R798): 1 case B cells isolated from non-tumor tissues: 1 case, 1 sample T cells isolated from non-tumor tissues: 1 case, 1 sample |
| Targets | scRNA-seq |
| Target Loci for Capture Methods | - |
| Platform | Illumina [NovaSeq 6000] |
| Library Source | B and T cells isolated from uterine tissue |
| Cell Lines | - |
| Library Construction (kit name) | Chromium Next GEM Single Cell 3' v3.1 or 5' v2 |
| Fragmentation Methods | included in the above library construction kit |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | - |
| Mapping Methods | Cell Ranger v5.0.1 |
| Reference Genome Sequence | GRCh38-3.0.0 |
| Detecting method for read count (software) | Cell Ranger v5.0.1 |
| QC Methods | Cell Ranger v5.0.1 |
| Gene Number | - |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000969 |
| Genomic Expression Archive ID | E-GEAD-1121 |
| Total Data Volume |
JGAD000969: 1.2 TB (fastq, csv) E-GEAD-1121: 2 GB (h5, csv, tsv) |
| Comments (Policies) | NBDC policy |
scBCR-seq (JGAS000827 / E-GEAD-1121)
| Participants/Materials |
uterine cancer (ICD10: C549): 4 cases B cells isolated from tumor tissues: 4 cases, 4 samples hereditary breast and ovarian cancer syndrome (ICD10: R798): 1 case B cells isolated from non-tumor tissues: 1 case, 1 sample |
| Targets | scBCR-seq |
| Target Loci for Capture Methods | - |
| Platform | Illumina [NovaSeq 6000] |
| Library Source | B cells isolated from uterine tissue |
| Cell Lines | - |
| Library Construction (kit name) | Chromium Next GEM Single Cell 5' v2 |
| Fragmentation Methods | included in the above library construction kit |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | - |
| Mapping Methods | Cell Ranger v5.0.1 |
| Reference Genome Sequence | refdata-cellranger-vdj-GRCh38-alts-ensembl-5.0.0 |
| Detecting method for read count (software) | Cell Ranger v5.0.1 |
| QC Methods | Cell Ranger v5.0.1 |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000969 |
| Genomic Expression Archive ID | E-GEAD-1121 |
| Total Data Volume |
JGAD000969: 1.2 TB (fastq, csv) E-GEAD-1121: 2 GB (h5, csv, tsv) |
| Comments (Policies) | NBDC policy |
scTCR-seq (JGAS000827 / E-GEAD-1121)
| Participants/Materials |
uterine cancer (ICD10: C549): 5 cases T cells isolated from tumor tissues: 5 cases, 5 samples hereditary breast and ovarian cancer syndrome (ICD10: R798): 1 case T cells isolated from non-tumor tissues: 1 case, 1 sample |
| Targets | scTCR-seq |
| Target Loci for Capture Methods | - |
| Platform | Illumina [NovaSeq 6000] |
| Library Source | T cells isolated from uterine tissue |
| Cell Lines | - |
| Library Construction (kit name) | Chromium Next GEM Single Cell 5' v2 |
| Fragmentation Methods | included in the above library construction kit |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | - |
| Mapping Methods | Cell Ranger v5.0.1 |
| Reference Genome Sequence | refdata-cellranger-vdj-GRCh38-alts-ensembl-5.0.0 |
| Detecting method for read count (software) | Cell Ranger v5.0.1 |
| QC Methods | Cell Ranger v5.0.1 |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000969 |
| Genomic Expression Archive ID | E-GEAD-1121 |
| Total Data Volume |
JGAD000969: 1.2 TB (fastq, csv) E-GEAD-1121: 2 GB (h5, csv, tsv) |
| Comments (Policies) | NBDC policy |
CITE-seq (JGAS000827 / E-GEAD-1121)
| Participants/Materials |
uterine cancer (ICD10: C549): 6 cases B cells isolated from tumor tissues: 6 cases, 6 samples T cells isolated from tumor tissues: 5 cases, 5 samples |
| Targets | scRNA-seq |
| Target Loci for Capture Methods | - |
| Platform | Illumina [NovaSeq 6000] |
| Library Source | B and T cells isolated from uterine tissue |
| Cell Lines | - |
| Library Construction (kit name) | Chromium Next GEM Single Cell 3' v3.1 or 5' v2; BioLegend TotalSeq-B or -C |
| Fragmentation Methods | included in the above library construction kit |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | - |
| Mapping Methods | Cell Ranger v5.0.1 |
| Reference Genome Sequence | - |
| Detecting method for read count (software) | Cell Ranger v5.0.1 |
| QC Methods | Cell Ranger v5.0.1 |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000969 |
| Genomic Expression Archive ID | E-GEAD-1121 |
| Total Data Volume |
JGAD000969: 1.2 TB (fastq, csv) E-GEAD-1121: 2 GB (h5, csv, tsv) |
| Comments (Policies) | NBDC policy |
DATA PROVIDER
Principal Investigator: Hideki Ueno
Affiliation: Department of Immunology, Graduate School of Medicine, Kyoto University
Project / Group Name: -
Funds / Grants (Research Project Number):
| Name | Title | Project Number |
|---|---|---|
| - | - | - |
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | Oligoclonal expansion of IgG+ B cells along with Tfh cell response is associated with a better outcome in endometrial cancer | doi: 10.1093/intimm/dxaf049 | JGAD000969 E-GEAD-1121 |
| 2 |
USRES (Controlled-access Data)
| Principal Investigator | Affiliation | Country/Region | Research Title | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|---|---|
