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About NBDC Human Database
An enormous amount of human data is being generated with advances in next-generation sequencing and other analytical technologies. We therefore need rules and mechanisms for organizing and storing such data and for effectively utilizing them to make progress in the life sciences.
To promote sharing and utilization of human data while considering the protection of personal information, the Database Center for Life Science (DBCLS) of the Joint Support-Center for Data Science Research, Research Organization of Information and Systems (ROIS-DS) created a platform for sharing various data generated from human specimens, which are available for publicly access in cooperation with the DNA Data Bank of Japan
.
You can apply to use or submit human data through this website.
Violators of the guidelines who have not submitted a report on the deletion of Controlled-access data shall be disclosed here.
What's New
hum0492.v1
NBDC Research ID: hum0492.v1
SUMMARY
Aims: Although advances in our understanding of the disease mechanisms and the development of new drugs has improved the prognosis for patients with immune-inflammatory diseases such as rheumatoid arthritis, inflammatory bowel disease and autoimmune liver disease, there are still some patients who do not respond well to treatment or who are unable to discontinue the use of steroid drugs. This study aims to identify biomarkers, such as genes and proteins, that can be also used as new therapeutic targets in the blood and tissues of patients with these immune-inflammatory diseases who are starting new treatment.
Methods: Single cell RNA sequencing/TCR/BCR repertoire analyses, Spatial transcriptome analysis (Visium)
Participants/Materials: labial salivary glands from 28 patients with Sjögren's syndrome and 10 patients with Sicca
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000773 | Controlled-access (Type I) | 2025/08/12 |
*Data users need to apply an application for Using NBDC Human Data to reach the Controlled-access Data. Learn more
MOLECULAR DATA
| Participants/Materials |
Sjögren's syndrome (ICD10: M350): 19 cases Sicca: 8 cases labial salivary glands: total 27 samples (6 patients with Sjögren's syndrome and 3 patients with Sicca are also used in Visium analysis) |
| Targets | scRNA-seq/TCR/BCR repertoire |
| Target Loci for Capture Methods | - |
| Platform | Illumina [HiSeq X] |
| Library Source | RNAs extracted from T cell or B cell obtained from labial salivary glands |
| Cell Lines | - |
| Library Construction (kit name) | Chromium Next GEM Single Cell 5’ Library & Gel Bead Kit v1.1 |
| Fragmentation Methods | included in the above library construction kit |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 150 bp |
| Mapping Methods | Cell Ranger (version 5.0.1) |
| Reference Genome Sequence | GRCh38 |
| Detecting method for read count (software) | Cell Ranger (version 5.0.1) |
| Gene number | 1478 on average |
| Repertoire analysis Methods (software) | Cell Ranger (version 5.0.1) |
| QC | Cell Ranger (version 5.0.1) |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000915 |
| Total Data Volume | 1.24 TB (bam, csv) |
| Comments (Policies) | NBDC policy |
Visium Spatial Gene Expression, Histological image
| Participants/Materials |
Sjögren's syndrome (ICD10: M350): 15 cases Sicca: 5 cases labial salivary glands: total 20 samples (6 patients with Sjögren's syndrome and 3 patients with Sicca are also used in scRNA-seq/TCR/BCR repertoire analysis) |
| Targets | Visium Spatial Gene Expression, Histological image |
| Target Loci for Capture Methods | - |
| Platform | MGI [DNBSEQ-G400] |
| Library Source | labial salivary glands |
| Cell Lines | - |
| Library Construction (kit name) | Visium CytAssist Spatial Gene Expression for FFPE |
| Fragmentation Methods | included in the above library construction kit |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | read1: 28 bp, read2: 50 bp |
| Software | spaceranger-2.0.1 |
| Reference | GRCh38 |
| Tissue Image | hematoxylin-eosin staining |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000915 |
| Total Data Volume | 1.24 TB (fastq, jpg/tiff) |
| Comments (Policies) | NBDC policy |
DATA PROVIDER
Principal Investigator: Masaru Takeshita
Affiliation: Division of Rheumatology, Department of Internal Medicine, Keio University School of Medicine
Project / Group Name: -
| Name | Title | Project Number |
|---|---|---|
| KAKENHI Grant-in-Aid for Early-Career Scientists | Single cell integrated analysis of antigen specificity and gene expression for the cure of autoimmune diseases | 20K17430 |
| KAKENHI Grant-in-Aid for Scientific Research (C) | Elucidation of the Mechanisms of Autoantibody Production at Lesion Sites in Autoimmune Diseases | 22K08528 |
| KAKENHI Grant-in-Aid for JSPS Fellows | Elucidation of Sjögren's syndrome pathogenesis through retrotransposon sequences | 21J00596 |
| KAKENHI Grant-in-Aid for Scientific Research (B) | Molecular signatures in pre-RA patients by multi-omics analysis | 20H03720 |
| Keio University Academic Promotion Fund | Elucidation of Autoimmune Mechanisms at Lesion Sites in Autoimmune Diseases and Development of Antigen-Specific Immunosuppressive Therapies | - |
| Keio University Fukuzawa Memorial Fund | Comprehensive Understanding of Autoimmunity and Practical Application of Antigen-Specific Immunosuppressive Therapies | - |
| Keio University Next-Generation Research Promotion Program | Comprehensive Analysis of Salivary Gland Lesions as Sites of Autoimmune Responses | - |
| Mochida Memorial Foundation for Medical and Pharmaceutical Research — Research Grant — | lucidation of Autoimmune Mechanisms in Lesional Tissues of Sjögren’s Syndrome and Development of Antigen-Specific Immunosuppressive Therapies | - |
| Kowa Life Science Foundation — Research Grant — | Elucidation of Molecular Mechanisms Involved in Autoimmune Responses at Lesion Sites in Sjögren’s Syndrome | - |
| Takeda Science Foundation — Medical Research Grant — | Elucidation of Autoimmune Mechanisms at Lesion Sites in Autoimmune Diseases | - |
| Japan Rheumatism Foundation — Research Grant for Rheumatic Disease Investigation — | Elucidation of Molecular Mechanisms Involved in Autoantigen-Specific B Cell Immune Responses in Various Autoimmune Diseases and Identification of Therapeutic Targets | - |
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | |||
| 2 |
USRES (Controlled-access Data)
| Principal Investigator | Affiliation | Country/Region | Research Title | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|---|---|
hum0497.v2_release note
hum0492 Release Note
| Research ID | Release Date | Type of Data |
|---|---|---|
| hum0492.v1 | 2025/08/12 | NGS (scRNA-seq/TCR/BCR repertoire, Visium Spatial Gene Expression), Histological image |
hum0492.v1
- RNAs extracted from labial salivary glands from 19 patients with Sjögren's syndrome and 8 patients with Sicca were used for the single-cell RNA sequencing/TCR/BCR repertoire analyses. Bam and csv files are provided.
- Labial salivary glands from 15 patients with Sjögren's syndrome and 5 patients with Sicca were used for Visium Spatial Gene Expression Assays. Fastq and jpg/tiff files are provided.
Note:
hum0497.v1_release note
hum0497 Release Note
| Research ID | Release Date | Type of Data |
|---|---|---|
| hum0497.v1 | 2025/08/06 | NGS (RNA-seq) |
hum0497.v1
RNAs extracted from trophoblast stem cell lines derived from the chorion of term placentas from three individuals and their differentiated extravillous trophoblast cells and syncytiotrophoblast cells, as well as trophoblast stem cell lines obtained from RIKEN BRC and their differentiated extravillous trophoblast cells and syncytiotrophoblast cells were used for RNA-sequencing analysis. Fastq and csv files are provided.
Note:
hum0497.v1
NBDC Research ID: hum0497.v1
SUMMARY
Aims: Establishing trophoblast stem cells from the human term placenta contributes to elucidating the pathophysiology of placenta-related pregnancy complications, such as preeclampsia, which commonly occur in late pregnancy.
Methods: RNA sequencing
Participants/Materials: Three trophoblast stem cell (Ch-TS) lines derived from the chorion of term placentas from three individuals, as well as differentiated extravillous trophoblast cells (Ch-EVT) and syncytiotrophoblast cells (Ch-ST). Additionally, three trophoblast stem cell lines obtained from RIKEN BRC (CT27, CT29, bTS5) and their differentiated extravillous trophoblast cells and syncytiotrophoblast cells.
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000777 | NGS (RNA-seq) | Controlled-access (Type I) | 2025/08/06 |
*Data users need to apply an application for Using NBDC Human Data to reach the Controlled-access Data. Learn more
MOLECULAR DATA
| Participants/Materials |
human term placentas from three individuals (ICD10: O82.0, O80.0) trophoblast stem cell (Ch-TS) lines derived from the chorion: 3 samples differentiated extravillous trophoblast cells (Ch-EVT): 3 samples differentiated syncytiotrophoblast cells (Ch-ST): 3 samples human trophoblast stem cell lines from RIKEN BRC (CT27, CT29, bTS5) trophoblast stem cells: 3 samples differentiated extravillous trophoblast cells: 2 samples differentiated syncytiotrophoblast cells: 2 samples |
| Targets | RNA-seq |
| Target Loci for Capture Methods | - |
| Platform | Illumina [NovaSeq 6000] |
| Library Source | total RNA extracted from trophoblast stem cells, extravillous trophoblast cells and syncytiotrophoblast cells |
| Cell Lines | RIKEN BRC (CT27 [RCB4936], CT29 [RCB4937], bTS5 [RCB4940]) |
| Library Construction (kit name) | NEBNext Poly(A) mRNA Magnetic Isolation Module, NEBNext Ultra II Directional RNA Library Prep Kit, NEBNext Multiplex Oligos for Illumina (96 Unique Dual Index Primer Pairs) |
| Fragmentation Methods | chemical fragmentation at 94℃ |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 100 bp |
| Mapping Methods | HISAT2 |
| Mapping Quality | Mapping rate>98% |
| Reference Sequence | GRCh38/hg38 |
| Analysis Methods | featureCounts (GRCh38.106) |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000919 |
| Total Data Volume | 68.3 GB (fastq, csv) |
| Comments (Policies) | NBDC policy |
DATA PROVIDER
Principal Investigator: Masatsugu Ema
Affiliation: Department of Stem Cells and Human Disease Models, Research Center for Animal Life Science, Shiga University of Medical Science
Project / Group Name: -
Funds / Grants (Research Project Number):
| Name | Title | Project Number |
|---|---|---|
| KAKENHI Grant-in-Aid for Scientific Research (C) | Establishment of trophoblast stem cells derived from patients with hypertensive disorders of pregnancy | 22K09639 |
| KAKENHI Grant-in-Aid for Challenging Research (Pioneering) | Elucidation of implantation and placental development mechanisms in non-human primates and their application to human biology | 24K21265 |
| KAKENHI Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area) | Inner cell mass dynamism and totipotency in primate | 22H04669 |
| KAKENHI Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area) | Origin of placental tissues in cynomolgus monkey | 20H05359 |
| The Seiichi Imai Memorial Foundation | Generation of Trophoblast Stem Cell from Preeclampsia | - |
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | Establishment of Human Trophoblast Stem Cells from Term Smooth Chorion | doi: 10.1016/j.placenta.2025.07.090 | JGAD000919 |
| 2 |
USRES (Controlled-access Data)
| Principal Investigator | Affiliation | Country/Region | Research Title | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|---|---|
hum0521.v1
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 |
|---|---|---|---|---|---|
