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Due to system maintenance, the application system, application review by the Data Access Committee will be unavailable during the following period.
Schedule: October 5th (Mon), 2026, 9:00 - October 7th (Wed), 2026, 15:00 (JST)
We apologize for any inconvenience this may cause and appreciate your understanding.

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

JGAD000861

Type of data
NGS (scRNA-seq)
Access criteria
Controlled-access (Type I)
Total data volume
71.5 GB
File formats
  • FASTQ
  • CSV
  • HDF5
Research
hum0469
Date published
2024-08-19
Date modified
2024-08-19
DDBJ Search
JGAD000861 (opens in a new tab)
JGA Study
JGAS000728 (opens in a new tab)

Analysis method

scRNA-seq

Materials and participants
Pregnant women undergoing early pregnancy screening (ICD10: O35.3): 10 cases 15 samples
a pair at 12 weeks and 20 weeks: 1 case
a pair at 12 weeks and 36 weeks: 1 case
a pair at 20 weeks and 36 weeks: 2 cases
a pair at 20 weeks and 28 weeks: 1 case
2 specimens around 12 weeks
3 specimens around 20 weeks
  • Health status
    Affected
  • Subject count
    10 (Individual)
  • Sex
    Female
Disease
Pregnant women undergoing early pregnancy screening (O353)
Sample description
RNAs extracted from CD8+ T cells
  • Tissue
    PBMC, Peripheral blood
  • Tumor / normal
    Normal
Sample provider
N/A
Experimental method
scRNA-seq
Target
N/A
Reagent kit
Chromium Next GEM Chip G Single Cell Kit
Chromium Next GEM Single Cell 5' v2
Chromium Single Cell V(D)J
Fragmentation
according to manufacturers' instructions
Platform
Illumina NovaSeq 6000
Read type
Paired-end
Read length
90 bp (28×)
Reference genome
GRCh38
QC and filtering
the following criteria were excluded:
- Number of expressed genes: < 1000 or > 4000
- Total count of gene expression: < 2000 or > 10,000
- Mitochondrial gene expression percentage: > 10%
- TCR fragment genes
Analysis method
- Cell Ranger v6.1.2 (10x Genomics) with the "multi" option
- Python package Scanpy v1.9.3 (scRNA-seq analysis), Scirpy v0.13.0 (TCR genotyping)
Gene count
36,601
Data use policy
NBDC data sharing policy (JGAP000001)