NBDC Research ID: hum0512.v1
SUMMARY
Aims: Autoimmune diseases occur when the immune system damages the body's tissues, affecting over 1% of the population. Genomic polymorphisms strongly influence autoimmune disease risk, with many identified through large-scale genomic analyses. Since these risk polymorphisms often cluster in gene expression regulatory regions of immune cells, evaluating their relationship with gene regulation in these cells is essential for understanding their functions. This research aims to elucidate risk polymorphism functions using both natural polymorphisms and artificial ones introduced through genome editing. We will analyze multi-omics data from various cells and employ comprehensive genomic analysis to precisely identify risk polymorphism locations and understand their functions.
Methods: bulk RNA-seq, bulk ATAC-seq, single cell CITE-seq (RNA-seq)
Participants/Materials: 3 healthy donors
URL: https://immunogenetics.med.keio.ac.jp/en
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000818 | NGS（bulk RNA-seq, bulk ATAC-seq, scCITE-seq） | Controlled-access (Type I) | 2025/07/30 |
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MOLECULAR DATA
| Participants/Materials: |
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 |
| Targets | RNA-seq |
| Target Loci for Capture Methods | - |
| Platform | Illumina [NovaSeq 6000] |
| Library Source | RNAs extracted from CD4+ T cells transfected with LEF1-specific siRNA or control siRNA |
| Cell Lines | - |
| Library Construction (kit name) |
SMART-seq mRNA Nextera XT DNA Library Prep Kit |
| Fragmentation Methods | Nextera XT |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 100 bp |
| Software |
STAR(v2.7.9a) RNA-SeQC2(v2.4.2) |
| Reference Genome Sequence | GRCh38 |
| QC Methods |
FastQC for raw reads; Nextera adapter trimming (min 20bp); RNASeQC2 for alignment metrics |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000960 |
| Total Data Volume | 631.6 GB (fastq, tab) |
| Comments (Policies) | NBDC policy |
| Participants/Materials: |
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 |
| Targets | ATAC-seq |
| Target Loci for Capture Methods | - |
| Platform | Illumina [NovaSeq 6000] |
| Library Source | DNAs extracted from CD4+ T cells transfected with LEF1-specific siRNA or control siRNA |
| Cell Lines | - |
| Library Construction (kit name) | Nextera XT Index Kit v2 |
| Fragmentation Methods | Tn5 tagmentation with Nextera kit |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 100 bp |
| Software |
Bowtie2 (v2.2.6) MACS2 (v2.2.7.1) |
| Reference Genome Sequence | GRCh38 |
| QC Methods |
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; |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000960 |
| Total Data Volume | 631.6 GB (fastq, tab) |
| Comments (Policies) | NBDC policy |
| Participants/Materials: |
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.) |
| Targets | CITE-seq |
| Target Loci for Capture Methods | - |
| Platform |
Illumina [NovaSeq X Plus] 10x Genomics [Chromium] |
| Library Source | RNAs extracted from CD3+ T cells isolated from samples |
| Cell Lines | - |
| Library Construction (kit name) | Chromium Next GEM Single Cell 5' Kit v2 |
| Fragmentation Methods | Standard protocol of 10x Genomics |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 151 bp |
| Software | Cell Ranger 7.0.1 |
| Reference Genome Sequence | GRCh38 |
| QC Methods |
detected genes, UMI counts, mitochondrial gene percentage, doublet detection |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000960 |
| Total Data Volume | 631.6 GB（fastq, tab, other） |
| Comments (Policies) | NBDC policy |
DATA PROVIDER
Principal Investigator: Kazuyoshi Ishigaki
Affiliation: Laboratory for Human Immunogenetics, RIKEN Center for Integrative Medical Sciences
Project / Group Name: -
Funds / Grants (Research Project Number):
| Name | Title | Project Number |
|---|---|---|
| KAKENHI Grant-in-Aid for Scientific Research (B) | Establishment of personalized anti-cytokine therapy through functional analysis of autoimmune disease risk polymorphisms | 22H03114 |
| KAKENHI Grant-in-Aid for Research Activity Start-up | Identification of transcription factor controlling autoimmunity risk allele's pathogenic function | 21K20647 |
| KAKENHI Grant-in-Aid for Early-Career Scientists | Functional analysis of rheumatoid arthritis risk polymorphisms using genome editing technology and targeted analysis | 25K19621 |
| Biobank - Construction and Utilization biobank for genomic medicine REalization (B-Cure), Japan Agency for Medical Research and Development (AMED) | Development of technology for evaluating the impact of polygenic risk scores on biological systems | JP22tm0424223 |
| Practical Research Project for Allergic Diseases and Immunology, Japan Agency for Medical Research and Development (AMED) | Elucidation of rheumatoid arthritis pathogenesis through functional analysis of risk polymorphisms combined with genome editing technology | JP22ek0410099 |
| Research and Development Program for Translating Genomic Research into Drug Discovery and Other Applications, Japan Agency for Medical Research and Development (AMED) | Identification of novel diagnostic markers for rheumatoid arthritis based on T cell receptor sequence information using biobanks | JP23tm0524005 |
| Practical Research Project for Allergic Diseases and Immunology, Japan Agency for Medical Research and Development (AMED) | Comprehensive elucidation of T cell-level immune tolerance breakdown through interaction between HLA gene polymorphisms and smoking in rheumatoid arthritis | JP25ek0410139 |
| Basis for Supporting Innovative Drug Discovery and Life Science Research (BINDS), Japan Agency for Medical Research and Development (AMED) | Support for large-scale functional genomics analysis using biological samples and advancement of human immune function evaluation platform | JP22ama121015 |
| Japan Initiative for World-leading Vaccine Research and Development Centers, Japan Agency for Medical Research and Development (AMED) | Support organization for establishment and implementation of human immune evaluation methods centered on multi-omics of genetic diversity and function | JP223fa627010 |
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | Accurate, sensitive, and efficient chromatin accessibility quantification at target loci using UNIChro-seq | JGAD000960 |
USRES (Controlled-Access Data)
| Principal Investigator | Affiliation | Country/Region | Research Title | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|---|---|
