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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

JGAD000822

Type of data
NGS (Micro-C and Region Capture Micro-C)
NGS (CITE-seq and 5' single-cell RNA-seq)
NGS (5' and 3' single-cell RNA-seq)
NGS (Multimodal assay including single-nucleus ATAC-seq, 3' and 5' single-nucleus RNA-seq, and 5' single-cell RNA-seq)
NGS (MAS-seq)
NGS (CAGE-seq and NET-CAGE-seq)
Access criteria
Controlled-access (Type I)
Total data volume
17.8 TB
File formats
  • FASTQ
  • BAM
Research
hum0350
Date published
2024-06-14
Date modified
2024-06-14
DDBJ Search
JGAD000822 (opens in a new tab)
JGA Study
JGAS000689 (opens in a new tab)

Analysis method

Micro-C + Region Capture Micro-C

Materials and participants
3 healthy Japanese (17 samples)
  • Health status
    Healthy
  • Subject count
    20 (Mixed)
  • Population
    Japanese
Sample description
genomic DNA extracted from CD4 positive T cells isolated from whole blood
  • Tissue
    CD4+ T cell
  • Tumor / normal
    Normal
Sample provider
N/A
Experimental method
Micro-C
Target
Dovetail Target Enrichment Kit (Cantata Bio, human pan promoter panel)
Reagent kit
Dovetail Micro-C Kit
Fragmentation
MNase
Platform
Illumina NovaSeq 6000
Read type
Paired-end
Read length
400 bp
Data use policy
NBDC data sharing policy (JGAP000001)

scRNA-seq (5' / 3')

Materials and participants
3 healthy Japanese (20 samples)
  • Health status
    Healthy
  • Subject count
    23 (Mixed)
  • Population
    Japanese
Sample description
polyA RNA extracted from CD4 positive T cells isolated from whole blood
  • Tissue
    CD4+ T cell
  • Tumor / normal
    Normal
Sample provider
N/A
Experimental method
scRNA-seq
Target
N/A
Reagent kit
Chromium Single Cell 3'
Chromium Single Cell 5'
Fragmentation
included in the above library construction kit
Platform
Illumina NovaSeq 6000
Read type
Paired-end
Read length
350 bp
Reference genome
GRCh38
Analysis method
Cell Ranger version 5.0.1
Data use policy
NBDC data sharing policy (JGAP000001)

snATAC-seq + snRNA-seq (3'/5') + scRNA-seq (5')

Materials and participants
3 healthy Japanese (9 samples)
  • Health status
    Healthy
  • Subject count
    12 (Mixed)
  • Population
    Japanese
Sample description
polyA RNA and genomic DNA extracted from CD4 positive T cells isolated from whole blood
  • Tissue
    CD4+ T cell
  • 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
Chromium Single Cell 5'
Fragmentation
included in the above library construction kit
Platform
Illumina NovaSeq 6000
Read type
Paired-end
Read length
300 bp
350 bp
Reference genome
GRCh38
Analysis method
Cell Ranger version 5.0.1
Data use policy
NBDC data sharing policy (JGAP000001)

CAGE-seq + NET-CAGE-seq

Materials and participants
2 healthy Japanese (6 samples)
  • Health status
    Healthy
  • Subject count
    8 (Mixed)
  • Population
    Japanese
Sample description
total RNA and nuclear RNA from CD4 positive T cells isolated from whole blood
  • Tissue
    CD4+ T cell
  • Tumor / normal
    Normal
Sample provider
N/A
Experimental method
CAGE-seq
Target
N/A
Reagent kit
CAGE Preparation Kit
Fragmentation
N/A
Platform
Illumina NextSeq 500
Read type
Single-end
Read length
N/A
Reference genome
GRCh38
Mapping
STAR version 2.7.10b
Data use policy
NBDC data sharing policy (JGAP000001)

MAS-seq

Materials and participants
1 healthy Japanese (2 samples)
  • Health status
    Healthy
  • Subject count
    3 (Mixed)
  • Population
    Japanese
Sample description
polyA RNA extracted from CD4 positive T cells isolated from whole blood
  • Tissue
    CD4+ T cell
  • Tumor / normal
    Normal
Sample provider
N/A
Experimental method
scRNA-seq
Target
N/A
Reagent kit
MAS-Seq for 10x Single Cell 3'
Fragmentation
N/A
Platform
PacBio Sequel II
Read type
Paired-end
Read length
N/A
Reference genome
GRCh38
Analysis method
CCS software version 6.3.0, SMRT Link version 12, Stringtie2 version 2.2.1
Data use policy
NBDC data sharing policy (JGAP000001)

CITE-seq + scRNA-seq (5')

Materials and participants
3 healthy Japanese (8 samples)
  • Health status
    Healthy
  • Subject count
    11 (Mixed)
  • Population
    Japanese
Sample description
Cell surface proteins and total RNA of CD4-positive T cells isolated from whole blood
  • Tissue
    CD4+ T cell
  • Tumor / normal
    Normal
Sample provider
N/A
Experimental method
CITE-seq
scRNA-seq
Target
N/A
Reagent kit
Chromium Next GEM Single Cell 5' v2
Fragmentation
included in the above library construction kit
Platform
Illumina NovaSeq 6000
Read type
Paired-end
Read length
73 bp
Reference genome
GRCh38
Analysis method
Cell Ranger version 5.0.1
Data use policy
NBDC data sharing policy (JGAP000001)