NBDC Research ID: hum0177.v1
SUMMARY
Aims: DNA methylome analyses and expression analysis for malignant glioma harbouring H3F3A gene mutation
Methods: PBAT-seq, RNA-seq and ChIP-seq
Participants/Materials: 14 Malignant glioma patients and 1 cell line
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000197 | NGS (PBAT-seq, RNA-seq, ChIP-seq) | Controlled-access (Type I) | 2020/04/27 |
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MOLECULAR DATA
| Participants/Materials: | Malignant glioma (ICD10: C71.9): 14 cases + 1 cell line |
| Targets | PBAT-seq |
| Target Loci for Capture Methods | - |
| Platform | Illumina [HiSeq X Ten] |
| Library Source | DNAs extracted from tumor tissues of malignant glioma and a cell line |
| Cell Lines | IFO50356 (JCRB) |
| Library Construction (kit name) | TACS ligation-mediated PBAT*ref1 |
| Fragmentation Methods | Ultrasonic fragmentation (Covaris S220) |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 150 bp |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000280 |
| Total Data Volume | 1 TB (fastq) |
| Comments (Policies) | NBDC policy |
| Participants/Materials: | Malignant glioma (ICD10: C71.9): 5 cases + 1 cell line |
| Targets | RNA-seq |
| Target Loci for Capture Methods | - |
| Platform | Illumina [NovaSeq 6000] |
| Library Source | RNAs extracted from tumor tissues of malignant glioma and a cell line |
| Cell Lines | IFO50356 (JCRB) |
| Library Construction (kit name) | TruSeq stranded mRNA Kit |
| Fragmentation Methods | - |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 100 bp |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000281 |
| Total Data Volume | 1 TB (fastq) |
| Comments (Policies) | NBDC policy |
| Participants/Materials: | 1 Cell line of malignant glioma (ICD10: C71.9) |
| Targets | ChIP-seq |
| Target Loci for Capture Methods | - |
| Platform | Illumina [NovaSeq 6000] |
| Library Source | DNAs extracted from a cell line of malignant glioma (1 control [whole cell lysate] and 2 immunoprecipitation samples). Anti- histone H3.3 rabbit monoclonal antibody and anti- histone H3.3 G34V rabbit monoclonal antibody were used for immunoprecipitation. |
| Cell Lines | IFO50356 (JCRB) |
| Library Construction (kit name) | SMARTer ThruPLEX DNA-seq Kit |
| Fragmentation Methods | Ultrasonic fragmentation (Covaris S220) |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 150 bp |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000282 |
| Total Data Volume | 1 TB (fastq) |
| Comments (Policies) | NBDC policy |
DATA PROVIDER
Principal Investigator: Takashi Ito
Affiliation: Department of Medical Biochemistry, Graduate School of Medical Sciences, Kyushu University
Project / Group Name: -
Funds / Grants (Research Project Number):
| Name | Title | Project Number |
|---|---|---|
| Platform Project for Supporting Drug Discovery and Life Science Research, Japan Agency for Medical Research and Development (AMED) | Improvements and support in methylome analysis | JP16am0101059 |
| Platform Project for Supporting Drug Discovery and Life Science Research, Japan Agency for Medical Research and Development (AMED) | Advanced methylomics: support and development | JP19am0101103 |
| KAKENHI Grant-in-Aid for Scientific Research on Priority Areas (Research in a proposed research area) | Development and applications of next generation epigenome analysis technologies | 17H06305 |
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | Highly efficient single-stranded DNA ligation technique improves low-input whole-genome bisulfite sequencing by post-bisulfite adaptor tagging | doi: 10.1093/nar/gkz435 | |
| 2 |
USERS (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 | JGAD000281 | 2022/12/26-2025/03/31 |
