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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

JGAD000121

Type of data
NGS (PBAT-seq)
NGS (ChIP-seq)
NGS (RNA-seq)
NGS (miRNA-seq)
Access criteria
Controlled-access (Type I)
Total data volume
339 GB
File formats
  • FASTQ
Research
hum0112
Date published
2020-09-28
Date modified
2020-09-28
DDBJ Search
JGAD000121 (opens in a new tab)
JGA Study
JGAS000112 (opens in a new tab)

Analysis method

PBAT-seq

Materials and participants
trophoblast stem cell: 3 samples (1 TS, 3 culture conditions)
  • Subject count
    3 (Sample)
Sample description
DNAs extracted from trophoblast stem cell
  • Tissue
    Placenta
  • Tumor / normal
    Normal
Cell line
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
Read type
Single-end
Read length
101 bp
Data use policy
NBDC data sharing policy (JGAP000001)

ChIP-seq

Materials and participants
trophoblast stem cell: 18 samples (TS: 1, 3 culture conditions, 6 antibodies [anti H3K4me3, H3K4me1, H3K9me3, H3K27ac, H3K27me3, H3K36me3 antibodies]) + 1 negative control
  • Subject count
    18 (Sample)
Sample description
DNAs extracted from trophoblast stem cell
  • Tissue
    Placenta, Trophoblast stem cell
  • Tumor / normal
    Normal
Cell line
Trophoblast stem cell (TS)
Sample provider
N/A
Experimental method
ChIP-seq
Target
N/A
Reagent kit
Ovation Ultralow System V2 Kit
Fragmentation
Ultrasonic fragmentation (Covaris M220)
Platform
Illumina HiSeq 2500
Read type
Paired-end
Read length
126 bp
Data use policy
NBDC data sharing policy (JGAP000001)

RNA-seq

Materials and participants
trophoblast stem cell: 6 samples (2 TSs, 3 culture conditions)
  • Subject count
    6 (Sample)
Sample description
mRNAs extracted from trophoblast stem cell
  • Tissue
    Placental stem cell, Trophoblast stem cell
  • Tumor / normal
    Normal
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 bp
Data use policy
NBDC data sharing policy (JGAP000001)

miRNA-seq

Materials and participants
trophoblast stem cell: 3 samples (1 TS, 3 culture conditions)
  • Subject count
    3 (Sample)
Sample description
RNAs extracted from trophoblast stem cell
  • Tissue
    Placenta
  • Tumor / normal
    Normal
Cell line
Trophoblast stem cell (TS)
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
Read type
Single-end
Read length
64 bp (including adapter)
68 bp (including adapter)
Data use policy
NBDC data sharing policy (JGAP000001)