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)	NGS (WGBS) NGS (ChIP-seq) NGS (RNA-seq) NGS (miRNA-seq)	Controlled Access (Type I)	2017/12/14

Data Set ID

Type of Data

Criteria

Release Date

JGAS000112

(JGA000122)

Controlled Access (Type I)

2017/12/14

*Release Note

* Data users need to apply an application for Using NBDC Human Data to reach the Controlled-access Data.

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	JGAD000121
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	JGAD000121
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	JGAD000121
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	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

Title

DOI

Data Set ID

Derivation of Human Trophoblast Stem Cells

doi: 10.1016/j.stem.2017.11.004

JGAD000121

JGAD000115 (hum0086)

USERS (Controlled-Access Data)

Principal Investigator	Affiliation	Country/Region	Research Title	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		Derivation of Human Induced Trophoblast Stem Cells from Embryonic Stem Cells	JGAD000121	2020/01/15-2023/12/30
Thorold W. Theunissen	Washington University School of Medicine in St. Louis		Assessment of trophoblast fates derived from human pluripotent stem cells	JGAD000121	2020/01/22-2021/09/16
Lin GAO	The Hong Kong University of Science and Technology		Defining the transcriptional regulatory roles of retrotransposons in human placenta cells.	JGAD000121	2021/08/11-2024/05/28
Gianluca Ursini	Lieber Institute for Brain Development, Johns Hopkins University School of Medicine	United States of America	Analysis of the transcriptional profile of Human Trophoblast Stem Cells	JGAD000121	2022/04/20-2023/03/31
Ming-an Sun	Yangzhou University College of Veterinary Medicine	China	The activation and function of endogenous retroviruses in mammalian placentae	JGAD000121	2022/06/20-2024/06/30