NBDC Research ID: hum0491.v1
SUMMARY
Aims: Germinal center reactions in secondary lymphoid tissues are those responsible for the production of high-affinity antibodies and are primarily regulated by CD4+ T cells. However, the biology of CD4+ T cells in secondary lymphoid tissues has not been well described in humans. In particular, the differentiation, localization, and heterogeneity of IL10+ Foxp3- follicular CD4+ T cells (T follicular regulatory type 1, Tfr1 cells), which suppress the germinal center response, remain unresolved. This study aims to describe CD4+ T cells in human secondary lymphoid tissues in detail and to elucidate the differentiation, localization and heterogeneity of IL10+ Foxp3- follicular CD4+ T cells.
Methods: CD4+ T cells (whole or Tfr1-enriched) were isolated from tonsil specimens by FACS and subjected to the following single-cell multi-omics analyses: scRNA-seq, scRNA-TCR-seq, scATAC-RNA-seq. In some experiments, CITE-seq was combined.
Participants/Materials: Chronic tonsillitis 8 cases
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000805 | NGS (scRNA-seq, scRNA-TCR-seq, scATAC-RNA-seq) | Controlled-access (Type I) | 2025/07/04 |
| E-GEAD-1086 |
processed data of JGAS000805 / JGAD000947 Read count data of NGS (scRNA-seq, scRNA-TCR-seq, scATAC-RNA-seq) |
Unrestricted-access | 2025/07/04 |
*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 with/without CITE-seq (JGAS000805 / E-GEAD-1086)
| Participants/Materials |
Chronic tonsillitis (ICD10: J35.0): 4 cases CD4+ T cells were isolated from tonsil specimens by FACS: 8 samples (whole 4 samples, Tfr1-enriched 4 samples) |
| Targets | scRNA-seq with/without CITE-seq |
| Target Loci for Capture Methods | - |
| Platform | Illumina [Novaseq 6000] |
| Library Source | CD4+ T cells isolated from tonsil specimens by FACS |
| Cell Lines | - |
| Library Construction (kit name) | 10× Genomics, Chromium Next GEM Single Cell 3' v3.1 and BioLegend, TotalSeq-A, -B |
| 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 v6.1.1(10× Genomics) |
| Reference Genome Sequence | GRCh38-2020-A (GENCODE v32/Ensembl 98) |
| Detecting method for read count (software) | Cell Ranger v6.1.1(10× Genomics) |
| QC Methods | Cell Ranger v6.1.1(10× Genomics) |
| Gene Number | - |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000947 |
| Genomic Expression Archive ID | E-GEAD-1086 |
| Total Data Volume |
JGAD000947: 1.8 TB (fastq, csv) E-GEAD-1086: 16 GB (h5, csv, tsv.gz, tsv.gz.tbi) |
| Comments (Policies) | NBDC policy |
scRNA-TCR-seq with/without CITE-seq (JGAS000805 / E-GEAD-1086)
| Participants/Materials |
Chronic tonsillitis (ICD10: J35.0): 5 cases CD4+ T cells were isolated from tonsil specimens by FACS: 10 samples (whole 5 samples, Tfr1-enriched 5 samples) |
| Targets | scRNA-TCR-seq with/without CITE-seq |
| Target Loci for Capture Methods | - |
| Platform | Illumina [Novaseq 6000] |
| Library Source | CD4+ T cells isolated from tonsil specimens by FACS |
| Cell Lines | - |
| Library Construction (kit name) | 10× Genomics, Chromium Next GEM Single Cell 5' v2 and BioLegend, TotalSeq-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 v6.1.1(10× Genomics) |
| Reference Genome Sequence | GRCh38-2020-A (GENCODE v32/Ensembl 98) and refdata-cellranger-vdj-GRCh38-alts-ensembl-5.0.0 |
| Detecting method for read count (software) | Cell Ranger v6.1.1(10× Genomics) |
| QC Methods | Cell Ranger v6.1.1(10× Genomics) |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000947 |
| Genomic Expression Archive ID | E-GEAD-1086 |
| Total Data Volume |
JGAD000947: 1.8 TB (fastq, csv) E-GEAD-1086: 16 GB (h5, csv, tsv.gz, tsv.gz.tbi) |
| Comments (Policies) | NBDC policy |
scATAC-RNA-seq (JGAS000805 / E-GEAD-1086)
| Participants/Materials |
Chronic tonsillitis (ICD10: J35.0): 2 cases CD4+ T cells were isolated from tonsil specimens by FACS: 4 samples (whole 2 samples, Tfr1-enriched 2 samples) |
| Targets | scATAC-RNA-seq |
| Target Loci for Capture Methods | - |
| Platform | Illumina [Novaseq 6000] |
| Library Source | CD4+ T cells isolated from tonsil specimens by FACS |
| Cell Lines | - |
| Library Construction (kit name) | 10x Genomics, Chromium Next GEM Multiome |
| 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 ARC v2.0.0 (10x Genomics) |
| Reference Genome Sequence | GRCh38-2020-A (GENCODE v32/Ensembl 98) |
| Detecting method for open chromatin region (software) | Cell Ranger ARC v2.0.0 (10x Genomics) |
| QC Methods | Cell Ranger ARC v2.0.0 (10x Genomics) |
| Peak Number | - |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000947 |
| Genomic Expression Archive ID | E-GEAD-1086 |
| Total Data Volume |
JGAD000947: 1.8 TB (fastq, csv) E-GEAD-1086: 16 GB (h5, csv, tsv.gz, tsv.gz.tbi) |
| 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 | Single-cell multiomic analysis revealed the differentiation, localization, and heterogeneity of IL10+ Foxp3– follicular T cells in humans. | doi: 10.1093/intimm/dxaf014 | JGAD000947 E-GEAD-1086 |
| 2 |
