Skip to content
NBDC Human Database

No datasets in the cart.

Go to the cart

We are currently receiving a large number of applications for data submission, and the review process is taking longer than usual.We sincerely apologize for the delay and kindly ask for your understanding. When submitting an application, we would greatly appreciate it if you could allow sufficient time for the processing.

Following a change to our organizational structure effective April 1, 2026, this division has been renamed from the "Database Center for Life Science, Joint Support-Center for Data Science Research" to the "Database Division for Life Science (DBCLS), BioData Science Initiative (BSI), National Institute of Genetics (NIG)". Where the former name still appears in the guidelines, please read it as the new name.

Dataset ID

JGAD000115

Type of data
NGS (PBAT-seq)
NGS (ChIP-seq)
NGS (RNA-seq)
NGS (small RNA-seq)
Access criteria
Controlled-access (Type I)
Total data volume
364 GB
File formats
  • FASTQ
Research
hum0086
Date published
2020-09-28
Date modified
2020-09-28
DDBJ Search
JGAD000115 (opens in a new tab)
JGA Study
JGAS000107 (opens in a new tab)

Analysis method

PBAT-seq

Materials and participants
placenta (cytotrophoblast [normal, fetal growth restriction (ICD10: P059), preeclampsia (ICD10: O149), trisomy 18 (ICD10: Q913)], syncytiotrophoblast, extravillous trophoblast), uterus (endometrium epithelial, stroma), hydatidiform mole (ICD10: O010), female TS, ST from TS and EVT from TS / male TS: total 28 samples
  • Health status
    Mixed
  • Subject count
    28 (Sample)
  • Sex
    Mixed
Disease
  • fetal growth restriction
  • preeclampsia
  • trisomy 18
  • hydatidiform mole
Sample description
DNAs extracted from placenta (cytotrophoblast, syncytiotrophoblast, extravillous trophoblast), uterus (endometrium epithelial, stroma), hydatidiform mole, or trophoblast stem cells
  • Tissue
    Complete hydatidiform mole, Cytotrophoblast, Endometrium, Extravillous trophoblast, Glandular epithelial cell, Placenta, Stromal cell, Syncytiotrophoblast, Trophoblast stem cell
  • Tumor / normal
    Mixed
Cell line
Extravillous trophoblast (EVT)
Syncytiotrophoblast (ST)
Trophoblast stem cell (TS)
Sample provider
N/A
Experimental method
PBAT-seq
Target
N/A
Reagent kit
Post-Bisulfite Adaptor-Tagging (PBAT)
Fragmentation
PBAT method: fragmentation due to bisulfite conversion
Platform
Illumina HiSeq 1500
Illumina HiSeq 2500
Read type
Mixed
Read length
101 bp
Data use policy
NBDC data sharing policy (JGAP000001)

ChIP-seq

Materials and participants
placenta (cytotrophoblast, syncytiotrophoblast, extravillous trophoblast, stroma) and uterus (endometrium epithelial, stroma), female TS, ST from TS, EVT from TS: total 25 samples
  • Subject count
    25 (Sample)
  • Sex
    Female
Sample description
DNAs extracted from placenta (cytotrophoblast, syncytiotrophoblast, extravillous trophoblast, stroma), uterus (endometrium epithelial, stroma), trophoblast stem cells
  • Tissue
    Cytotrophoblast, Endometrium, Extravillous trophoblast, Glandular epithelial cell, Placenta, Stromal cell, Syncytiotrophoblast, Trophoblast stem cell, Villous stromal cell
  • Tumor / normal
    Normal
Sample provider
N/A
Experimental method
ChIP-seq
Target
antibodies: H3K4me3, H3K4me1, H3K9me3, H3K27ac, H3K27me3, H3K36me3
Input
Reagent kit
NEBNext Ultra II DNA Library Prep Kit for Illumina
Ovation Ultralow System V2 Kit
Fragmentation
Ultrasonic fragmentation (Covaris M220)
Platform
Illumina HiSeq 2500
Read type
Mixed
Read length
51–126 bp
Data use policy
NBDC data sharing policy (JGAP000001)

RNA-seq

Materials and participants
placenta (cytotrophoblast [normal, fetal growth restriction (ICD10: P059), preeclampsia (ICD10: O149), trisomy 18 (ICD10: Q913)], syncytiotrophoblast, extravillous trophoblast, stroma) and uterus (endometrium epithelial, stroma), female TS, ST from TS, EVT from TS / male TS, ST from TS, EVT from TS: total 34 samples
  • Health status
    Mixed
  • Subject count
    34 (Sample)
  • Sex
    Mixed
Disease
  • fetal growth restriction
  • preeclampsia
  • trisomy 18
Sample description
mRNAs extracted from placenta (cytotrophoblast, syncytiotrophoblast, extravillous trophoblast, stroma), uterus (endometrium epithelial, stroma), or trophoblast stem cells
  • Tissue
    Cytotrophoblast, Endometrium, Extravillous trophoblast, Glandular epithelial cell, Placenta, Stromal cell, Syncytiotrophoblast, Trophoblast stem cell, Villous stromal cell
  • Tumor / normal
    Normal
Cell line
Trophoblast stem cell (TS)
Sample provider
N/A
Experimental method
RNA-seq
Target
N/A
Reagent kit
TruSeq Stranded mRNA Library Prep Kit
Fragmentation
Heat treatment
Platform
Illumina HiSeq 2500
Read type
Paired-end
Read length
101–126 bp
Data use policy
NBDC data sharing policy (JGAP000001)

small RNA-seq

Materials and participants
placenta (cytotrophoblast [normal, fetal growth restriction (ICD10: P059), preeclampsia (ICD10: O149), trisomy 18 (ICD10: Q913)], syncytiotrophoblast, extravillous trophoblast) and uterus (endometrium epithelial, stroma), female TS, ST from TS, and EVT from TS: total 23 samples
  • Health status
    Mixed
  • Subject count
    23 (Sample)
  • Sex
    Female
Disease
  • fetal growth restriction
  • preeclampsia
  • trisomy 18
Sample description
RNAs extracted from placenta (cytotrophoblast, syncytiotrophoblast, extravillous trophoblast), uterus (endometrium epithelial, stroma), or trophoblast stem cells
  • Tissue
    Cytotrophoblast, Endometrium, Extravillous trophoblast, Glandular epithelial cell, Placenta, Stromal cell, Syncytiotrophoblast, Trophoblast stem cell
  • Tumor / normal
    Normal
Sample provider
N/A
Experimental method
Small RNA-seq
Target
N/A
Reagent kit
NEBNext Small RNA Library Prep Set for Illumina
Fragmentation
N/A
Platform
Illumina HiSeq 1500
Illumina HiSeq 2500
Read type
Single-end
Read length
64 bp (including adapter)
68 bp (including adapter)
Data use policy
NBDC data sharing policy (JGAP000001)