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 IDType of DataCriteriaRelease Date

JGAS000000112

(JGA00000000122)

NGS (WGBS)

NGS (ChIP-seq)

NGS (RNA-seq)

NGS (miRNA-seq)

Controlled Access (Type I) 2017/12/14

*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

NGS (WGBS)

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

 

NGS (ChIP-seq)

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

 

NGS (RNA-seq)

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

 

NGS (miRNA-seq)

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 DOIData 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