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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)
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Dataset ID

JGAD000960

Type of data
bulk RNA-seq / bulk ATAC-seq / scCITE-seq of CD4+ / CD3+ T cells from 3 healthy donors following LEF1 siRNA knockdown.
Access criteria
Controlled-access (Type I)
Total data volume
632 GB
File formats
  • FASTQ
  • TSV
  • MTX
  • HDF5
Research
hum0512
Date published
2025-07-31
Date modified
2025-10-27
DDBJ Search
JGAD000960 (opens in a new tab)
JGA Study
JGAS000818 (opens in a new tab)

Analysis method

bulk RNA-seq

Materials and participants
3 healthy donors
CD4+ T cells isolated from donors were activated with CD3/CD28 Dynabeads and cultured in media containing IL-2. Cells were transfected with LEF1-specific siRNA or control siRNA, and harvested at 24, 48, and 72 hours post-knockdown.
1 sample each, total 18 samples
  • Health status
    Healthy
  • Subject count
    3 (Individual)
  • Age group
    Adult
Sample description
RNAs extracted from CD4+ T cells transfected with LEF1-specific siRNA or control siRNA
  • Tissue
    CD4+ T cell
  • Tumor / normal
    Normal
Sample provider
N/A
Experimental method
RNA-seq
Target
N/A
Reagent kit
Nextera XT DNA Library Prep Kit
SMART-Seq mRNA
Fragmentation
Nextera XT
Platform
Illumina NovaSeq 6000
Read type
Paired-end
Read length
100 bp
Reference genome
GRCh38
QC and filtering
FastQC for raw reads; Nextera adapter trimming (min 20bp);
RNASeQC2 for alignment metrics
Analysis method
STAR(v2.7.9a)
RNA-SeQC2(v2.4.2)
Phenotype data
Not included
Data use policy
NBDC data sharing policy (JGAP000001)

bulk ATAC-seq

Materials and participants
3 healthy donors
CD4+ T cells isolated from donors were activated with CD3/CD28 Dynabeads and cultured in media containing IL-2. Cells were transfected with LEF1-specific siRNA or control siRNA, and harvested at 24, 48, and 72 hours post-knockdown.
1 sample each, total 18 samples
  • Health status
    Healthy
  • Subject count
    3 (Individual)
  • Age group
    Adult
Sample description
DNAs extracted from CD4+ T cells transfected with LEF1-specific siRNA or control siRNA
  • Tissue
    CD4+ T cell
  • Tumor / normal
    Normal
Sample provider
N/A
Experimental method
ATAC-seq
Target
N/A
Reagent kit
Nextera XT Index Kit v2
Fragmentation
Tn5 tagmentation with Nextera kit
Platform
Illumina NovaSeq 6000
Read type
Paired-end
Read length
100 bp
Reference genome
GRCh38
QC and filtering
FastQC for raw reads; Nextera adapter trimming (min 20bp);
BAM filtering (samtools -F 1804 -f 2 -q 30);
Blacklist removal;
MACS2 peak calling (q<0.05);
ATACseqQC TSS enrichment score; ataqv metrics;
Analysis method
Bowtie2 (v2.2.6)
MACS2 (v2.2.7.1)
Phenotype data
Not included
Data use policy
NBDC data sharing policy (JGAP000001)

scCITE-seq

Materials and participants
3 healthy donors
CD3+ T cells isolated from donors were activated with CD3/CD28 Dynabeads and cultured in media containing IL-2. Cells were transfected with LEF1-specific siRNA or control siRNA, and harvested at 48 and 72 hours post-knockdown.
1 sample each, total 12 samples (Samples from 3 donors were pooled.)
  • Health status
    Healthy
  • Subject count
    3 (Individual)
  • Age group
    Adult
Sample description
RNAs extracted from CD3+ T cells isolated from samples
  • Tissue
    CD3+ T cell
  • Tumor / normal
    Normal
Sample provider
N/A
Experimental method
CITE-seq
Target
N/A
Reagent kit
Chromium Next GEM Single Cell 5' v2
Fragmentation
Standard protocol of 10x Genomics
Platform
10x Genomics Chromium
Illumina NovaSeq X Plus
Read type
Paired-end
Read length
151 bp
Reference genome
GRCh38
QC and filtering
detected genes, UMI counts, mitochondrial gene percentage,
doublet detection
Analysis method
Cell Ranger 7.0.1
Phenotype data
Not included
Data use policy
NBDC data sharing policy (JGAP000001)