NBDC Research ID: hum0019.v1

 

SUMMARY

Aims: To identify novel long non-coding RNAs critically involved in gastrointestinal cancer.

Methods: Exome and RNA-seq experiments were performed to investigate quantitative and qualitative abnormalities of long non-coding RNAs in gastrointestinal cancer (Illumina HiSeq 2500)

Participants/Materials: Genomic DNA and polyA RNA were extracted from specimens in 17 gastrointestinal cancer patients. Cancer and non-cancerous tissues were used: total 32 samples)

URL: http://web.sapmed.ac.jp/biochem2/

 

Data Set IDType of DataCriteriaRelease Date
JGAS00000000011 NGS (RNA-seq) Controlled Access (Type I) 2015/04/01

*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

JGAS00000000011

Participants/Materials: 17 gastrointestinal cancer patients
Targets RNA-seq
Target Loci for Capture Methods -
Platform Illumina [HiSeq 2500]
Library Source polyA RNAs were extracted from gastrointestinal cancer and non-cancerous tissues.
Cell Lines -
Library Construction (kit name) Agilent SureSelect XT RNA Target Enrichment for Illumina Multiplexed Sequencing
Fragmentation Methods RNA Seq Fragmentation Mix in the kit
Spot Type Paired-end
Read Length (without Barcodes, Adaptors, Primers, and Linkers) 100bp x 2
Japanese Genotype-phenotype Archive Data set ID JGAD00000000011
Total Data Volume

104 GB (fastq [1,193,969.914 reads / 338 files])

Comments (Policies) NBDC policy

This study was supported by “Genome Science”. “Genome Science” is a part of the “Support Programs for Three Fields in Life Sciences (cancer, genome and brain sciences)” established by the Ministry of Education, Culture, Sports, Science and Technology (MEXT) under the Grant-in-Aid for Scientific Research on Innovative Areas.

 

DATA PROVIDER

Principal Investigator: Yasuhisa Shinomura

Affiliation: Department of Gastroenterology, Rheumatology and Clinical Immunology, Sapporo Medical University

Project / Group Name: Collaborate with Department of Molecular Biology, Sapporo Medical University

URL: http://web.sapmed.ac.jp/biochem2/

Funds / Grants (Research Project Number):

NameTitleProject Number

KAKENHI Grant-in-Aid for Scientific Research (A)

Systematic investigation of quantitative and qualitative abnormalities of long non-coding RNAs critically involved in colorectal cancer 24680092

 

PUBLICATIONS

TitleDOIData Set ID
1 -
2      

 

USERS (Controlled-Access Data)

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