NBDC Research ID: hum0413.v1

 

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 cases (skin tissue: 260 samples, PBMC: 461 samples)

          41 healthy controls (skin tissue: 55 samples, PBMC: 41 samples)

 

Dataset IDType of DataCriteriaRelease Date
JGAS000628 NGS (RNA-seq) Controlled-access (Type I) 2023/07/20

*Release Note

* Data users need to apply an application for Using NBDC Human Data to reach the Controlled-access Data. Learn more

 

MOLECULAR DATA

JGAS000628

Participants/Materials

Atopic dermatitis (ICD10: L20.9): 161 cases

   skin tissue: 260 samples, PBMC: 461 samples

41 Healthy controls

   skin tissue: 55 samples, PBMC: 41 samples

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 JGAD000757
Total Data Volume 506.3 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):

NameTitleProject 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

 

PUBLICATIONS

TitleDOIDataset 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 InvestigatorAffiliationCountry/RegionResearch TitleData in Use (Dataset ID)Period of Data Use