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 |
---|---|---|---|
JGAS000112 (JGA000122) |
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 | JGAD000121 |
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 | JGAD000121 |
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 | JGAD000121 |
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 | JGAD000121 |
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) | Epigenome analysis of cells in the placenta and endometrium forming the fetal-maternal interface | 17gm0510011h0006 |
PUBLICATIONS
Title | DOI | Data Set ID | |
---|---|---|---|
1 | Derivation of Human Trophoblast Stem Cells | doi: 10.1016/j.stem.2017.11.004 |
JGAD000121 JGAD000115 (hum0086) |
2 |
USERS (Controlled-Access Data)
Principal Investigator: | Affiliation: | Data in Use (Data Set ID) | Period of Data Use |
---|---|---|---|
Nehemiah Alvarez | De Novo Genomics Corporation | JGAD000121 | 2018/01/15-2018/12/31 |
R. Michael Roberts | University of Missouri, Animal Sciences / Biochemistry | JGAD000121 | 2018/03/02-2019/02/15 |
Zhigang Xue | School of Medicine and Life Science, Tongji University | JGAD000121 | 2018/12/17-2022/12/31 |
Todd Macfarlan | National Institute of Child Health and Human Development | JGAD000121 | 2018/12/17-2019/10/31 |
Howard Fine | Weill Cornell Medicine | JGAD000121 | 2018/12/18-2023/12/10 |
William S.B. Yeung | Department of Obstetrics and Gynaecology, the University of Hong Kong | JGAD000121 | 2019/02/12-2020/12/13 |
Hui Li | Department of Histoembryology, Genetics and Developmental Biology, Shanghai Jiao Tong University School of Medicine | JGAD000121 | 2020/01/15-2023/12/30 |
Thorold W. Theunissen | Washington University School of Medicine in St. Louis | JGAD000121 | 2020/01/22-2021/09/16 |