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Due to system maintenance, the application system, application review by the Data Access Committee will be unavailable during the following period.
Schedule: October 5th (Mon), 2026, 9:00 - October 7th (Wed), 2026, 15:00 (JST)
We apologize for any inconvenience this may cause and appreciate your understanding.

We are currently receiving a large number of applications for data submission, and the review process is taking longer than usual.We sincerely apologize for the delay and kindly ask for your understanding. When submitting an application, we would greatly appreciate it if you could allow sufficient time for the processing.

Following a change to our organizational structure effective April 1, 2026, this division has been renamed from the "Database Center for Life Science, Joint Support-Center for Data Science Research" to the "Database Division for Life Science (DBCLS), BioData Science Initiative (BSI), National Institute of Genetics (NIG)". Where the former name still appears in the guidelines, please read it as the new name.

Dataset ID

E-GEAD-1086

Type of data
processed data of JGAS000805 / JGAD000947
Read count data of NGS (scRNA-seq, scRNA-TCR-seq, scATAC-RNA-seq)
TCR repertoire clonotype data
open chromatin region data
Access criteria
Unrestricted-access
Total data volume
15.5 GB
File formats
  • TXT
  • CSV
  • TAR
Research
hum0491
Date published
2025-07-03
Date modified
2025-07-03
DDBJ Search
E-GEAD-1086 (opens in a new tab)

Analysis method

scRNA-seq (± CITE-seq)

Materials and participants
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)
  • Health status
    Affected
  • Subject count
    4 (Individual)
Disease
Chronic tonsillitis (J350)
Sample description
CD4+ T cells isolated from tonsil specimens by FACS
  • Tissue
    Tonsil
  • Tumor / normal
    Normal
Sample provider
N/A
Experimental method
CITE-seq
scRNA-seq
Target
N/A
Reagent kit
Chromium Next GEM Single Cell 3' v3.1
TotalSeq-A
TotalSeq-B
Fragmentation
included in the above library construction kit
Platform
Illumina NovaSeq 6000
Read type
Paired-end
Read length
N/A
Reference genome
GRCh38
Mapping
Cell Ranger v6.1.1
QC and filtering
Cell Ranger v6.1.1
Analysis method
Cell Ranger v6.1.1
Gene count
N/A
Data use policy
NBDC data sharing policy (JGAP000001)

scRNA-seq + scTCR-seq (± CITE-seq)

Materials and participants
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)
  • Health status
    Affected
  • Subject count
    5 (Individual)
Disease
Chronic tonsillitis (J350)
Sample description
CD4+ T cells isolated from tonsil specimens by FACS
  • Tissue
    CD4+ T cell, Tonsil
  • Tumor / normal
    Normal
Sample provider
N/A
Experimental method
scRNA-seq
TCR-seq
Target
N/A
Reagent kit
Chromium Next GEM Single Cell 5' v2
TotalSeq-C
Fragmentation
included in the above library construction kit
Platform
Illumina NovaSeq 6000
Read type
Paired-end
Read length
N/A
Reference genome
GRCh38
Mapping
Cell Ranger v6.1.1(10× Genomics)
QC and filtering
Cell Ranger v6.1.1
Analysis method
Cell Ranger v6.1.1
Phenotype data
Included
Data use policy
NBDC data sharing policy (JGAP000001)

scATAC-seq + scRNA-seq

Materials and participants
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)
  • Health status
    Affected
  • Subject count
    2 (Individual)
Disease
Chronic tonsillitis (J350)
Sample description
CD4+ T cells isolated from tonsil specimens by FACS
  • Tissue
    Tonsil
  • Tumor / normal
    Normal
Sample provider
N/A
Experimental method
scATAC-seq
scRNA-seq
Target
N/A
Reagent kit
Chromium Next GEM Single Cell Multiome ATAC + Gene Expression
Fragmentation
included in the above library construction kit
Platform
Illumina NovaSeq 6000
Read type
Paired-end
Read length
N/A
Reference genome
GRCh38
Mapping
Cell Ranger ARC v2.0.0
QC and filtering
Cell Ranger ARC v2.0.0
Analysis method
Cell Ranger ARC v2.0.0
Peak count
N/A
Data use policy
NBDC data sharing policy (JGAP000001)