NBDC Research ID: hum0431.v1

 

SUMMARY

Aims: Identification of susceptibility gene clusters for neuropsychiatric disorders such as schizophrenia, mood disorders (bipolar disorder, major depressive disorder), developmental disorders, and epilepsy.

Methods: RNA-seq analysis

Participants/Materials:

We introduced single variants identified in patients with Autism Spectrum Disorder (ASD) into human iPSCs (HPS4290:201B7-Ff]) using the CRISPR/Cas9 system. Variants at the protospacer adjacent motif (PAM) sequence were also introduced.

          1) Mutant iPSC lines with the chr7:g.26200781C>T variant and the single PAM sequence: 2 samples

              Control lines with a single PAM sequence: 2 samples

          2) Mutant iPSC lines with the chr22:g.19179942C>T variant and the single PAM sequence: 3 samples

              Control lines with a single PAM sequence: 2 samples

 

Dataset IDType of DataCriteriaRelease Date
JGAS000651 NGS (RNA-seq) Controlled-access (Type I) 2024/01/25

*Release Note

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

 

MOLECULAR DATA

JGAS000651

Participants/Materials

Human iPSCs (HPS4290:201B7-Ff]) introduced single variants identified in patients with ASD (ICD10: F840)

    1) Mutant iPSC lines with the chr7:g.26200781C>T variant and the single PAM sequence: 2 samples

        Control lines with a single PAM sequence: 2 samples

    2) Mutant iPSC lines with the chr22:g.19179942C>T variant and the single PAM sequence: 3 samples

        Control lines with a single PAM sequence: 2 samples

Targets RNA-seq
Target Loci for Capture Methods -
Platform Illumina [NovaSeq 6000]
Library Source RNAs extracted from mutant iPSCs
Cell Lines RIKEN BRC
Library Construction (kit name) NEBNext Ultra RNA Library Prep Kit for Illumina
Fragmentation Methods included in the above library construction kit
Spot Type Paired-end
Read Length (without Barcodes, Adaptors, Primers, and Linkers) 150 bp x 2
Japanese Genotype-phenotype Archive Dataset ID JGAD000781
Total Data Volume 90.8 GB (fastq)
Comments (Policies) NBDC policy

 

DATA PROVIDER

Principal Investigator: Atsushi Takata

Affiliation: Laboratory for Molecular Pathology of Psychiatric Disorders, RIKEN Center for Brain Science

Project / Group Name: -

URL: https://cbs.riken.jp/en/faculty/a.takata/

Funds / Grants (Research Project Number):

NameTitleProject Number
Strategic Research Program for Brain Sciences, Japan Agency for Medical Research and Development (AMED) Identification of genetically defined subgroups of bipolar disorder by sequence analysis of trio samples JP20dm0107133
Advanced Genome Research and Bioinformatics Study to Facilitate Medical Innovation (GRIFIN), Platform Program for Promotion of Genome Medicine, Japan Agency for Medical Research and Development (AMED) Analysis of the genetic architectures of human diseases based on the oligogenic model JP22km0405214
The Strategic International Brain Science Research Promotion Program (Brain/MINDS Beyond), Japan Agency for Medical Research and Development (AMED) Analysis of somatic mutations in bipolar disorder and methodological development of genomic neuropathology JP20dm0307028
KAKENHI Grant-in-Aid for Transformative Research Areas (B) Identification of genes and key molecular pathways determining cluster/hub cells and analysis of their relationship to human diseases 20H05777
KAKENHI Grant-in-Aid for Scientific Research (B) Comprehensive study of rare germline and somatic mutations by large-scale sequence analysis for bipolar disorder 21H02855
KAKENHI Grant-in-Aid for Early-Career Scientists Molecular pathological analysis of a histone methyltransferase associated with autism spectrum disorder 21K15752
KAKENHI Grant-in-Aid for Research Activity Start-up Identification of loci associated with paternal age effect of Denovo mutation by large-scale family genome data analysis 22K20751

 

PUBLICATIONS

TitleDOIDataset ID
1 Topologically associating domains define the impact of de novo promoter variants on autism spectrum disorder risk doi: 10.1016/j.xgen.2024.100488 JGAD000781
2

 

USRES (Controlled-access Data)

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