NBDC Research ID: hum0112.v1
SUMMARY
Aims: To establish human trophoblast stem cells from blastocyst, and to characterize them.
Methods: Whole Genome Biosulfite Sequencing (WGBS), ChIP-seq, RNA-seq, and miRNA-seq
Participants/Materials: trophoblast stem cell (TS)
URL： http://ihec-epigenomes.org/ (The processed data will soon be released on the IHEC Data Portal)
| Data Set ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
|
JGAS000000112 (JGA00000000122) |
Controlled Access (Type I) | 2017/12/14 |
* 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
| Participants/Materials: | trophoblast stem cell: 3 samples (1 TS, 3 culture conditions) |
| Targets | WGBS |
| Target Loci for Capture Methods | - |
| Platform | Illumina [HiSeq 1500] |
| Library Source | DNAs extracted from trophoblast stem cell |
| Cell Lines | - |
| Library Construction (kit name) | Post-Bisulfite Adaptor-Tagging (PBAT) |
| Fragmentation Methods | PBAT method: fragmentation due to bisulfite conversion |
| Spot Type | Single-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 101 bp |
| Japanese Genotype-phenotype Archive Data set ID | JGAD00000000121 |
| Total Data Volume | 315 GB |
| Comments (Policies) | NBDC policy |
| Participants/Materials: | trophoblast stem cell: 18 samples (TS: 1, 3 culture conditions, 6 antibodies [anti H3K4me3, H3K4me1, H3K9me3, H3K27ac, H3K27me3, H3K36me3 antibodies]) + 1 negative control |
| Targets | ChIP-seq |
| Target Loci for Capture Methods | - |
| Platform | Illumina [HiSeq 2500] |
| Library Source | DNAs extracted from trophoblast stem cell |
| Cell Lines | - |
| Library Construction (kit name) | Ovation Ultralow System V2 kit (NuGEN) |
| Fragmentation Methods | Ultrasonic fragmentation (Covaris M220) |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 126 bp |
| Japanese Genotype-phenotype Archive Data set ID | JGAD00000000121 |
| Total Data Volume | 315 GB |
| Comments (Policies) | NBDC policy |
| Participants/Materials: | trophoblast stem cell: 6 samples (2 TSs, 3 culture conditions) |
| Targets | RNA-seq |
| Target Loci for Capture Methods | - |
| Platform | Illumina [HiSeq 2500] |
| Library Source | mRNAs extracted from trophoblast stem cell |
| Cell Lines | - |
| Library Construction (kit name) | TruSeq Stranded mRNA LT Sample Prep Kit (Illumina) |
| Fragmentation Methods | Heat treatment |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 101 bp |
| Japanese Genotype-phenotype Archive Data set ID | JGAD00000000121 |
| Total Data Volume | 315 GB |
| Comments (Policies) | NBDC policy |
| Participants/Materials: | trophoblast stem cell: 3 samples (1 TS, 3 culture conditions) |
| Targets | miRNA-seq |
| Target Loci for Capture Methods | - |
| Platform | Illumina [HiSeq 1500] |
| Library Source | RNAs extracted from trophoblast stem cell |
| Cell Lines | - |
| Library Construction (kit name) | NEBNext Small RNA Library Prep Set for Illumina (New England Biolabs) |
| Fragmentation Methods | - |
| Spot Type | Single-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 64 or 68 bp (including adaptor) bp |
| Japanese Genotype-phenotype Archive Data set ID | JGAD00000000121 |
| Total Data Volume | 315 GB |
| Comments (Policies) | NBDC policy |
DATA PROVIDER
Principal Investigator: Takahiro Arima
Affiliation: Department of Informative Genetics, Environment and Genome Research Center,Tohoku University Graduate School of Medicine
Project / Group Name: Core Research and Evolutional Science and Technology (CREST), International Human Epigenome Consortium (IHEC), Sasaki Team
URL： http://crest-ihec.jp/english/index.html, http://ihec-epigenomes.org/
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 | Data Set ID | |
|---|---|---|---|
| 1 | Derivation of Human Trophoblast Stem Cells | doi: 10.1016/j.stem.2017.11.004 | JGAD00000000121 |
| 2 |
USERS (Controlled-Access Data)
| Principal Investigator: | Affiliation: | Data in Use (Data Set ID) | Period of Data Use |
|---|---|---|---|
| Nehemiah Alvarez | De Novo Genomics Corporation | JGAD00000000121 | 2018/01/15-2018/12/31 |
| R. Michael Roberts | University of Missouri, Animal Sciences / Biochemistry | JGAD00000000121 | 2018/03/02-2019/02/15 |
| Zhigang Xue | School of Medicine and Life Science, Tongji University | JGAD00000000121 | 2018/12/17-2022/12/31 |
| Todd Macfarlan | National Institute of Child Health and Human Development | JGAD00000000121 | 2018/12/17-2019/10/31 |
