NBDC Research ID: hum0413.v2
SUMMARY
Aims: To contribute to medical strategies involving disease prediction, prevention, and treatment selection through collecting and analyzing human omics data. We strive to create a novel research field that integrates interdisciplinary studies, with a focus on computational science, using allergy disorders as a model.
Methods: RNA-seq analysis
Participants/Materials:
Atopic dermatitis 161 + 41 cases (skin tissue: 260 + 762 samples, PBMC: 461 samples)
Psoriasis: 18 cases (skin tissue: 36 samples)
41 + 10 healthy controls (skin tissue: 55 + 19 samples, PBMC: 41 samples)
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000628 | NGS (RNA-seq) | Controlled-access (Type I) | 2023/07/20 |
| JGAS000780 | NGS (RNA-seq) | Controlled-access (Type I) | 2025/03/24 |
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MOLECULAR DATA
| Participants/Materials |
[JGAS000628] Atopic dermatitis (ICD10: L20.9): 161 cases skin tissue: 260 samples, PBMC: 461 samples 41 Healthy controls skin tissue: 55 samples, PBMC: 41 samples [JGAS000780] Atopic dermatitis (ICD10: L20.9): 156 cases (115 cases are used in JGAS000628) skin tissue: 951 samples (189 samples are used in JGAS000628) Psoriasis: 18 cases skin tissue: 36 samples 26 Healthy controls (16 individuals are used in JGAS000628) skin tissue: 49 samples (30 samples are used in JGAS000628) |
| Targets | RNA-seq |
| Target Loci for Capture Methods | - |
| Platform | Illumina [HiSeq 1500/2500] |
| Library Source | RNAs extracted from skin tissues or PBMC |
| Cell Lines | - |
| Library Construction (kit name) |
NEBNext Ultra RNA Library Prep Kit for Illumina for skin SureSelect Strand-Specific RNA Library Prep Kit for PBMC |
| Fragmentation Methods | Exposure to divalent cations at elevated temperatures |
| Spot Type | Single-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 50 bp |
| Japanese Genotype-phenotype Archive Dataset ID | |
| Total Data Volume |
JGAD000757: 506.3 GB (fastq) JGAD000922: 553.0 GB (fastq) |
| Comments (Policies) | NBDC policy |
DATA PROVIDER
Principal Investigator: Haruhiko Koseki
Affiliation: Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences
Project / Group Name: Comprehensive analysis on medical and omics data from patients with atopic dermatitis.
Funds / Grants (Research Project Number):
| Name | Title | Project Number |
|---|---|---|
| Practical Research Project for Allergic Diseases and Immunology, Japan Agency for Medical Research and Development (AMED) | Elucidation of pathology of atopic dermatitis involving multiple organ allergy by integrating clinical and omics information | JP22ek0410079 |
| Practical Research Project for Allergic Diseases and Immunology, Japan Agency for Medical Research and Development (AMED) | Analysis on skin microbiome for establishment of precision medicine in atopic dermatitis | JP21ek0410058 |
| Practical Research Project for Allergic Diseases and Immunology, Japan Agency for Medical Research and Development (AMED) | Analysis on skin transcriptome for establishment of precision medicine in atopic dermatitis | JP19ek0410046 |
| Practical Research Project for Allergic Diseases and Immunology, Japan Agency for Medical Research and Development (AMED) | Elucidation of mechanisms underlying progression of atopic dermatitis by analysis on skin and gut microbiome | JP18ek0410028 |
| Project for Development of Innovation Hub, Japan Science and Technology Agency (JST) | Hub for Predictive and Preventative Precision Medicine Driven by Big Data | JPMJIH1504 |
| Practical Research Project for Allergic Diseases and Immunology, Japan Agency for Medical Research and Development (AMED) | Innovation of microbial treatment for atopic dermatitis based on bidirectional understanding of skin microbiota and host | JP22ek0410098 |
| Practical Research Project for Allergic Diseases and Immunology, Japan Agency for Medical Research and Development (AMED) | Interdisciplinary research on atopic dermatitis to elucidate the diversity of allergic pathophysiology and to realize sustainable data-driven precision medicine | JP23ek0410118 |
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | Multifaceted analysis of cross-tissue transcriptomes reveals phenotype–endotype associations in atopic dermatitis. | doi: 10.1038/s41467-023-41857-8 | JGAD000757 |
| 2 |
USRES (Controlled-access Data)
| Principal Investigator | Affiliation | Country/Region | Research Title | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|---|---|
