NBDC Research ID: hum0180.v1
SUMMARY
Aims: Gene expression analysis of diseases caused by abnormal RNA splicing
Methods: RNA-Seq for a cellular RNA
Participants/Materials: Familial Dysautonomia
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000170 | NGS (RNA-seq) | Controlled-access (Type I) | 2021/03/12 |
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MOLECULAR DATA
| Participants/Materials |
Familial Dysautonomia (ICD10: G90.1): 2 cases (6 samples) under DMSO, RECTAS and TG003 treatment |
| Targets | RNA-seq |
| Target Loci for Capture Methods | GM04663, GM04589, GM04899, GM02343, 41865, 41866, 35659, 35673, 35677, GM03987, GM04664, GM00850, GM02342, HD100CAU, HD100AA (provided by Coriell institute) |
| Platform | Thermo Fisher Scientific [Ion Proton] |
| Library Source | RNAs extracted from fibroblasts |
| Cell Lines | - |
| Library Construction (kit name) | Ion Total RNA-Seq Kit v2 |
| Fragmentation Methods | |
| Spot Type | Single-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | |
| QC | |
| Deduplication | |
| Calibration of re-alignment and base quality | |
| Mapping Methods | |
| Reference Genome Sequence | |
| Coverage (Depth) | |
| Detecting Methods for Transcripts | |
| Total Reads / Uniquely Mapped Reads | |
| Gene Numbers | |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000248 |
| Total Data Volume |
50 GB Data files: 6 (fastq) Analysis files: 6 (transcripts per million: TPM [txt]) |
| Comments (Policies) | NBDC policy |
DATA PROVIDER
Principal Investigator: Masahiko Ajiro
Affiliation: Department of Drug Discovery Medicine, Kyoto University Graduate School of Medicine
Project / Group Name:
URL: http://www.anat1dadb.med.kyoto-u.ac.jp/?lang=en
Funds / Grants (Research Project Number):
| Name | Title | Project Number |
|---|---|---|
| Program for Promoting Platform of Genomics based Drug Discovery, Japan Agency for Medical Research and Development (AMED) | Development of genetic disease medicine by pharmacogenomics analysis ofspliceswitching compounds | JP18kk0305003 |
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | Therapeutic manipulation of IKBKAP mis-splicing with a small molecule to cure familial dysautonomia. | doi: 10.1038/s41467-021-24705-5 | JGAD000248 |
| 2 |
USRES (Controlled-access Data)
| Principal Investigator | Affiliation | Country/Region | Research Title | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|---|---|
| Michiaki Hamada | Faculty of Science and Engineering, Waseda University | Japan | Construction of RNA-targeted Drug Discovery Database | JGAD000248 | 2022/12/26-2025/03/31 |
