NBDC Research ID: hum0091.v1
SUMMARY
Aims: The aim of this study is to participate in International Human Epigenome Consortium (http://ihec-epigenomes.org/), through disclosure of quality reference epigenome profiles in normal and diseased cells obtained from multiple Japanese people.
Methods: ChIP-Seq, RNA-seq and PBAT-seq analysis about normal human foveolar epithelial cells of the stomach purified from gastrectomy specimens using crypt isolation method.
Participants/Materials: Normal human foveolar epithelial cells of the stomach purified from gastrectomy specimens using crypt isolation method : 14 cells
URL: http://crest-ihec.jp/english/project/index.html
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000082 | NGS (PBAT-seq) | Controlled-access (Type I) | 2021/03/12 |
| JGAS000165 | NGS (ChIP-seq) | Controlled-access (Type I) | 2021/03/12 |
| JGAS000081 | NGS (RNA-seq) | Controlled-access (Type I) | 2021/03/12 |
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MOLECULAR DATA
| Participants/Materials: | Normal human foveolar epithelial cells of the stomach purified from gastrectomy specimens using crypt isolation method : 14 |
| Targets | PBAT-seq |
| Target Loci for Capture Methods | - |
| Platform | Illumina [HiSeq 2000] |
| Library Source | gDNAs extracted from normal human foveolar epithelial cells |
| Cell Lines | - |
| Library Construction (kit name) |
Post-Bisulfite Adaptor-Tagging (PBAT) method |
| Fragmentation Methods | PBAT method: fragmentation due to bisulfite conversion |
| Spot Type | Single-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 100 bp |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000082 |
| Total Data Volume | 1 TB (fastq [41 files / 25,928,851,326 reads]） |
| Comments (Policies) | NBDC policy |
| Participants/Materials: | Normal human foveolar epithelial cells of the stomach purified from gastrectomy specimens using crypt isolation method : 14 |
| Targets | ChIP-seq |
| Target Loci for Capture Methods | - |
| Platform | Illumina [HiSeq 2500] |
| Library Source | gDNAs extracted from normal human foveolar epithelial cells |
| Cell Lines | - |
| Library Construction (kit name) |
Anti H3K4me3, H3K9me3, H3K27me3, H3K27ac, H3K4me1 and H3K36me3 mouse monoclonal antibodies, kindly provided by Dr. Hiroshi Kimura, Tokyo Institute of Technology, were used for immunoprecipitation. |
| Fragmentation Methods | Ultrasonic fragmentation (BRANSON SLPe, amplitude 40%, on 30 sec and off 30 sec, 10 cycles, on ice) |
| Spot Type | Single-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 36 bp |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000243 |
| Total Data Volume | 65 GB (fastq [49 files / 1,981,314,349 reads]) |
| Comments (Policies) | NBDC policy |
| Participants/Materials: | Normal human foveolar epithelial cells of the stomach purified from gastrectomy specimens using crypt isolation method : 14 |
| Targets | RNA-seq |
| Target Loci for Capture Methods | - |
| Platform | Illumina [HiSeq 2000] |
| Library Source/span> | Total RNA extracted from normal human foveolar epithelial cells |
| Cell Lines | - |
| Library Construction (kit name) | SureSelect Strand Specific RNA kit |
| Fragmentation Methods | Purified poly-A RNA was fragmented with heat treatment and divalent cations. |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 100 bp |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000081 |
| Total Data Volume | 79 GB(fastq [22 files / 1,202,044,862 reads]） |
| Comments (Policies) | NBDC policy |
DATA PROVIDER
Principal Investigator: Yae Kanai
Affiliation: Department of Pathology, Keio University School of Medicine
Project / Group Name: AMED-CREST International Human Epigenome Consortium (IHEC) Team Kanai
URL: http://crest-ihec.jp/english/index.html
URL: http://www.jst.go.jp/kisoken/crest/en/research_area/completed/areah23-4.html
URL: https://pathology.med.keio.ac.jp/home-e/
Funds / Grants (Research Project Number):
| Name | Title | Project Number |
|---|---|---|
| Core Research and Evolutional Science and Technology, Advanced Research & Development Programs for Medical Innovation, Japan Agency for Medical Research and Development (AMED-CREST) | Development of Fundamental Technologies for Diagnosis and Therapy Based upon Epigenome Analysis | - |
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 | JGAD000081 | 2022/12/26-2025/03/31 |
