NBDC Research ID: hum0535.v1
SUMMARY
Aims: To perform comprehensive genomic and transcriptomic analyses of DNA and RNA obtained from the skin, blood, and related organs of patients with dermatological diseases, in order to elucidate disease mechanisms and provide a basis for developing novel therapeutic strategies.
Methods: ATAC-seq
Participants/Materials: Epidermal keratinocytes from psoriatic lesions, clinically healed skin of the same patients, and healthy control skin
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000818 | NGS（ATAC-seq） | Controlled-access (Type I) | 2025/10/20 |
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MOLECULAR DATA
| Participants/Materials: |
Psoriasis: 6 cases psoriatic skin: 6 samples clinically healed skin: 6 samples healthy control skin: 5 samples |
| Targets | ATAC-seq |
| Target Loci for Capture Methods | - |
| Platform | Illumina [NovaSeq 6000] |
| Library Source | DNAs extracted from epidermal keratinocytes isolated from skin samples |
| Cell Lines | - |
| Library Construction (kit name) | Tagment DNA TDE1 Enzyme and Buffer Kit |
| Fragmentation Methods | Tn5 transposase-mediated tagmentation |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 150 bp x 2 |
| Software | FastQC, Bowtie2, MACS2 |
| Reference Genome Sequence | GRCh38 |
| QC Methods | Bioanalyzer, FastQC |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000986 |
| Total Data Volume | 69.4 GB (bam) |
| Comments (Policies) | NBDC policy |
DATA PROVIDER
Principal Investigator: Sayaka Shibata
Affiliation: Department of Dermatology, Graduate School of Medicine, The University of Tokyo
Project / Group Name: -
Funds / Grants (Research Project Number):
| Name | Title | Project Number |
|---|---|---|
| KAKENHI Grant-in-Aid for Scientific Research (C) | Mechanisms for Chronic Inflammation of Skin Diseases Due to Resilience Failure and Treatment Strategies | 24K11447 |
| Precursory Research for Innovative Medical care (PRIME), Advanced Research & Development Programs for Medical Innovation, Japan Agency for Medical Research and Development (AMED) | Mechanistic Elucidation of Stress Memory-Driven Chronic Inflammation and Visualization of Stress Sensing | JP24gm6910016 |
| Lydia O’Leary Memorial Pias Dermatological Foundation | Elucidation of the Regulatory Mechanisms of Psoriatic Pathogenesis Mediated by DNA Environment and Super-Enhancers | - |
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 |
USRES (Controlled-access Data)
| Principal Investigator | Affiliation | Country/Region | Research Title | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|---|---|
