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/
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000011 | NGS (RNA-seq) | Controlled-access (Type I) | 2015/04/01 |
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MOLECULAR DATA
| 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) | 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 Dataset ID | JGAD000011 |
| 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):
| Name | Title | Project 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
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | - | ||
| 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 | JGAD000011 | 2022/12/26-2025/03/31 |
