NBDC Research ID: hum0433.v1
SUMMARY
Aims: Trophoblast cells play an essential role in the interactions between the fetus and mother, however, the in vitro model to investigate the nature of human trophoblasts has been limited. In this study, we derived human trophoblast stem cells (hTSCs) from first-trimester cytotrophoblasts (CTs) and blastocysts and revealed their epigenomic landscapes including histone modifications, transcription factor binding sites, and long-range chromatin interactions.
Methods: First-trimester placentas are obtained from elective termination of pregnancies. Placenta and blastocysts after delivery are obtained from the normal and hypertensive disorders of pregnancy (HDP) donors. Whole placental villi are enzymatically digested, and CT cells were immunomagnetically purified using a PE-conjugated anti-ITGA6 antibody. CTs were cultured in TS medium containing EGF, CHIR99021, A83-01, VPA, and Y27632. Differentiated and undifferentiated human trophoblast stem cells (hTSCs) are used to investigate mRNA expression, epigenomic features, proliferation, protein expression, and trophoblast functions.
Participants/Materials: Placenta after artificial abortion or after delivery and a discarded blastocyst
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000659 | NGS (RNA-seq, ChIP-seq, Hi-C) | Controlled-access (Type I) | 2024/09/25 |
| E-GEAD-665 | NGS (RNA-seq, ChIP-seq, Hi-C) | Unrestricted-access | 2024/09/25 |
| JGAS000660 | NGS (RNA-seq) | Controlled-access (Type I) | 2024/09/25 |
| E-GEAD-667 | NGS (RNA-seq) | Unrestricted-access | 2024/09/25 |
| JGAS000667 | NGS (RNA-seq, small RNA-seq, CUT&TAG-seq, Methyl-seq) | Controlled-access (Type I) | 2024/09/25 |
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MOLECULAR DATA
RNA-seq (JGAS000659 / E-GEAD-665)
| Participants/Materials |
trophoblast stem cells derived from placenta after artificial abortion (ICD10: O049): 1 sample trophoblast stem cells derived from a blastocyst: 1 sample |
| Targets | RNA-seq |
| Target Loci for Capture Methods | - |
| Platform | Illumina [NovaSeq 6000] |
| Library Source | RNAs extracted from trophoblast stem cells |
| Cell Lines | - |
| Library Construction (kit name) | NEBNext UltraII Directional RNA Library Prep Kit |
| Fragmentation Methods | included in the above library construction kit |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 150 bp |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000789 |
| Genomic Expression Archive ID | E-GEAD-665 |
| Total Data Volume |
JGAD000789: 337 GB (fastq) E-GEAD-665: 70.7 MB (txt) |
| Comments (Policies) | NBDC policy |
| Participants/Materials |
trophoblast stem cells derived from placenta after artificial abortion (ICD10: O049): 1 sample trophoblast stem cells derived from a blastocyst: 1 sample |
| Targets | ChIP-seq |
| Target Loci for Capture Methods | - |
| Platform | Illumina [NovaSeq 6000, HiSeq 2500] |
| Library Source | DNAs extracted from trophoblast stem cells |
| Cell Lines | - |
| Library Construction (kit name) | NEBNext Ultra II DNA Library Prep Kit for Illumina |
| Fragmentation Methods | Ultrasonic fragmentation |
| Spot Type | Paired-end/Single-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 150 bp |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000789 |
| Genomic Expression Archive ID | E-GEAD-665 |
| Total Data Volume |
JGAD000789: 337 GB (fastq) E-GEAD-665: 3.05 GB (bigwig) |
| Comments (Policies) | NBDC policy |
| Participants/Materials | trophoblast stem cells derived from placenta after artificial abortion (ICD10: O049): 1 sample |
| Targets | Hi-C |
| Target Loci for Capture Methods | - |
| Platform | Illumina [NovaSeq 6000] |
| Library Source | DNAs extracted from trophoblast stem cells |
| Cell Lines | - |
| Library Construction (kit name) | KAPA Hyper Prep Kit |
| Fragmentation Methods | Ultrasonic fragmentation |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 150 bp |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000789 |
| Genomic Expression Archive ID | E-GEAD-665 |
| Total Data Volume |
JGAD000789: 337 GB (fastq) E-GEAD-665: 19.6 MB (bedpe) |
| Comments (Policies) | NBDC policy |
RNA-seq (JGAS000660 / E-GEAD-667)
| Participants/Materials |
hypertensive disorders of pregnancy (ICD10: 149): 10 cases trophoblast stem cells derived from placenta after delivery 3 cases; 3 samples (hTSC, EVT, ST) each 7 cases; 1 sample (ST) each 10 cases; 1 sample (hypoxia-treated hTSCs) each normal pregnancy: 11 subjects trophoblast stem cells derived from placenta after delivery 3 cases; 3 samples (hTSC, EVT, ST) each 8 cases; 1 sample (ST) each 11 cases; 1 sample (hypoxia-treated hTSCs) each |
| Targets | RNA-seq |
| Target Loci for Capture Methods | - |
| Platform | Illumina [NovaSeq 6000] |
| Library Source | RNAs extracted from trophoblast stem cells and CT cells |
| Cell Lines | - |
| Library Construction (kit name) | NEBNext UltraII Directional RNA Library Prep Kit |
| Fragmentation Methods | included in the above library construction kit |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 150 bp |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000790 |
| Genomic Expression Archive ID | E-GEAD-667 |
| Total Data Volume |
JGAD000790: 106.3 GB (fastq) E-GEAD-667: 64.7 MB (txt) |
| Comments (Policies) | NBDC policy |
| Participants/Materials |
hypertensive disorders of pregnancy (ICD10: 149): 6 cases CT cells purified from placenta after delivery: 6 samples normal pregnancy: 3 subjects CT cells purified from placenta after delivery: 3 samples |
| Targets | RNA-seq |
| Target Loci for Capture Methods | - |
| Platform | Illumina [NovaSeq 6000, HiSeq 2500] |
| Library Source | RNAs extracted from CT cells |
| Cell Lines | - |
| Library Construction (kit name) | SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing, Nextera XT DNA Library Prep Kit |
| Fragmentation Methods | included in Nextera XT DNA Library Prep Kit |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 101 bp |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000797 |
| Total Data Volume | 621.7 GB (fastq) |
| Comments (Policies) | NBDC policy |
| Participants/Materials |
hypertensive disorders of pregnancy (ICD10: 149): 6 cases CT cells purified from placenta after delivery: 6 samples normal pregnancy: 3 subjects CT cells purified from placenta after delivery: 3 samples trophoblast stem cells derived from HDP placenta after delivery: 3 samples |
| Targets | small RNA-seq |
| Target Loci for Capture Methods | - |
| Platform | Illumina [NovaSeq 6000] |
| Library Source | RNAs extracted from CT cells and trophoblast stem cells |
| Cell Lines | - |
| Library Construction (kit name) | SMARTer smRNA-Seq Kit for Illumina |
| Fragmentation Methods | - |
| Spot Type | Single-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 150 bp |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000797 |
| Total Data Volume | 621.7 GB (fastq) |
| Comments (Policies) | NBDC policy |
| Participants/Materials |
hypertensive disorders of pregnancy (ICD10: 149): 6 cases CT cells purified from placenta after delivery: 6 samples x 6 antibodies, 36 samples in total normal pregnancy: 3 subjects CT cells purified from placenta after delivery: 3 samples x 6 antibodies, 18 samples in total |
| Targets | CUT&TAG-seq |
| Target Loci for Capture Methods | - |
| Platform | Illumina [HiSeq 2500] |
| Library Source | DNA fragments purified from CT cells which are incubated with anti-histone antibodies (K4me1, K4me3, K27ac, K36me3, K27m3, K9me3) and pAG-Tn5 transposase |
| Cell Lines | - |
| Library Construction (kit name) | - |
| Fragmentation Methods | Tn5 transposase |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 26 bp |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000797 |
| Total Data Volume | 621.7 GB (fastq) |
| Comments (Policies) | NBDC policy |
| Participants/Materials |
hypertensive disorders of pregnancy (ICD10: 149): 3 cases CT cells purified from placenta after delivery: 3 samples trophoblast stem cells derived from normal placenta after delivery: 2 samples trophoblast stem cells derived from HDP placenta after delivery: 3 samples |
| Targets | Methyl-seq |
| Target Loci for Capture Methods | - |
| Platform | Illumina [NovaSeq 6000] |
| Library Source | RNAs extracted from CT cells and trophoblast stem cells |
| Cell Lines | - |
| Library Construction (kit name) | Accel-NGS Methyl-Seq DNA Library Kit |
| Fragmentation Methods | fragmentation due to bisulfite conversion (EZ DNA Methylation-Gold Kit) |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 150 bp |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000797 |
| Total Data Volume | 621.7 GB (fastq) |
| Comments (Policies) | NBDC policy |
DATA PROVIDER
Principal Investigator: Eri H Kobayashi
Affiliation: Department of Informative Genetics, Environment and Genome Research Center, Tohoku University Graduate School of Medicine
Project / Group Name: -
Funds / Grants (Research Project Number):
| Name | Title | Project Number |
|---|---|---|
| Advanced Research & Development Programs for Medical Innovation, Japan Agency for Medical Research and Development (AMED) | Elucidation of the mechanisms underlying human placental development and design of a placenta-on-a-chip platform | JP19gm1310001 |
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | Derivation of Human Trophoblast Stem Cells | doi: 10.1016/j.stem.2017.11.004 |
JGAD000789 JGAD000790 JGAD000797 E-GEAD-665 E-GEAD-667 |
| 2 | CRISPR screening in human trophoblast stem cells reveals both shared and distinct aspects of human and mouse placental development | doi: 10.1073/pnas.2311372120 |
JGAD000789 E-GEAD-665 |
USRES (Controlled-access Data)
| Principal Investigator | Affiliation | Country/Region | Research Title | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|---|---|
