NBDC Research ID: hum0088.v1

 

SUMMARY

Aims: To elucidate the effect and its mechanism of BMP signaling on glioma initiating cells

Methods: Target genes were identified by RNA-seq to elucidate the mechanism of regulation of glioma initiating cells by BMP. Genomic DNA was extracted from glioma initiating cells and whole genome sequencing was performed.

Participants/Materials: Patient-derived glioblastoma cell lines (tumor initiating cells), 2 lines

 

Data Set IDType of DataCriteriaRelease Date
JGAS00000000077 NGS (RNA-seq) Controlled Access (Type I) 2019/02/08
JGAS00000000096 NGS (WGS) Controlled Access (Type I) 2019/02/08

*Release Note

* Data users need to apply the Form 2 (Application Form for Using NBDC Human Data) to reach the Controlled Access Data. Learn more

 

MOLECULAR DATA

JGAS00000000077

Participants/Materials 2 glioblastomas (ICD10:C71.9) (TGS-01, TGS-04)
Targets RNA-seq
Target Loci for Capture Methods -
Platform

Illumina [Genome Analyzer IIx]

Thermo Fisher Scientific [IonProton]

Library Source glioblastoma cell lines were stimulated with BMP-4 for 24 h prior to RNA extraction
Cell Lines -
Library Construction (kit name)

ScriptSeq v2 RNA-seq Library Preparation Kit (Epicentre)

Ion Total RNA-seq Kit v2 (Thermo Fisher Scientific)

Fragmentation Methods

Genome Analyzer IIx: Enzymatic Shearing (included in the kit)

IonProton: Enzymatic Shearing (included in the kit: RNase III)

Spot Type

Genome Analyzer IIx: Paired-end

IonProton: Single-end

Read Length (without Barcodes, Adaptors, Primers, and Linkers)

Genome Analyzer IIx: 76 bp

IonProton: 200 bp

Japanese Genotype-phenotype Archive Data set ID JGAD00000000077
Total Data Volume 43 GB (fastq)
Comments (Policies) NBDC policy

 

JGAS00000000096

Participants/Materials 1 glioblastoma (ICD10:C71.9) (TGS-01)
Targets WGS
Target Loci for Capture Methods -
Platform Thermo Fisher Scientific [IonProton]
Library Source gDNA extracted from glioblastoma cell line (tumor initiating cells)
Cell Lines -
Library Construction (kit name)

Ion Fragment plus library Kit

Ion PI Template OT2 200 Kit v3

Ion PI Sequencing 200 Kit v3

(Thermo Fisher Scientific)

Fragmentation Methods Ultrasonic fragmentation (Bioruptor UCD-200)
Spot Type Single-end
Read Length (without Barcodes, Adaptors, Primers, and Linkers) 200 bp
Japanese Genotype-phenotype Archive Data set ID JGAD00000000096
Total Data Volume 13 GB (fastq)
Comments (Policies) NBDC policy

 

DATA PROVIDER

Principal Investigator: Kohei Miyazono

Affiliation: Department of Molecular Pathology, Graduate School of Medicine, The University of Tokyo

Project / Group Name: -

Funds / Grants (Research Project Number):

NameTitleProject Number
KAKENHI Grant-in-Aid for Scientific Research on Innovative Areas Effects of TGF-β family on cancer microenvironment and strategies for cancer therapy 22112002
KAKENHI Grant-in-Aid for Scientific Research (B) Roles of BMP signaling in maintenance of cell stemness 24390070
KAKENHI Grant-in-Aid for Scientific Research (S) Transcriptional regulation by TGF-β signaling and its relation to progression of cancer 15H05774
JSPS Core-to-Core Program Cooperative International Framework in TGF-beta Family Signaling -

 

PUBLICATIONS

TitleDOIData Set ID
1 Bone morphogenetic protein signaling mediated by ALK-2 and DLX2 regulates apoptosis in glioma-initiating cells. doi: 10.1038/onc.2017.112 JGAD00000000077
2 Identification of a novel fusion gene HMGA2-EGFR in glioblastoma. doi: 10.1002/ijc.31179

JGAD00000000077

JGAD00000000096

 

USRES (Controlled-Access Data)

Principal Investigator: Affiliation: Data in Use (Data Set ID)Period of Data Use