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 IDType of DataCriteriaRelease Date
JGAS000197 NGS (PBAT-seq, RNA-seq, ChIP-seq) Controlled-access (Type I) 2020/04/27

*Release Note

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

 

MOLECULAR DATA

PBAT-seq

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

 

RNA-seq

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

 

ChIP-seq

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 DOIDataset 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 InvestigatorAffiliationCountry/RegionResearch TitleData 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