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 ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000651 | NGS (RNA-seq) | Controlled-access (Type I) | 2024/01/25 |
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MOLECULAR DATA
| 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):
| Name | Title | Project 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
| Title | DOI | Dataset 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 Investigator | Affiliation | Country/Region | Research Title | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|---|---|
