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

JGAD000778

Type of data
NGS (scRNA-seq)
Access criteria
Controlled-access (Type I)
Total data volume
40.2 MB
File formats
  • CSV
Research
hum0214
Date published
2024-02-14
Date modified
2024-02-14
DDBJ Search
JGAD000778 (opens in a new tab)
JGA Study
JGAS000648 (opens in a new tab)

Analysis method

scRNA-seq

Materials and participants
Idiopathic Inflammatory Myopathy (ICD10: M339, M332): 6 cases
muscle biopsy: 3 cases, 3 samples
bronchoalveolar lavage fluid: 3 cases, 3 samples
1 healthy control
peripheral blood: 1 sample
  • Health status
    Healthy
  • Subject count
    7 (Individual)
Disease
  • Idiopathic Inflammatory Myopathy
Sample description
Total RNAs extracted from CD4T cells for peripheral blood or CD45-positive cells for muscle tissue and bronchial lavage fluid
Sample provider
N/A
Experimental method
scRNA-seq
Target
N/A
Reagent kit
Chromium Next GEM Single Cell 5' v2
Fragmentation
Chromium Next GEM Single Cell 5' Reagent Kit v2 Dual Index
Platform
Illumina NovaSeq 6000
Read type
Paired-end
Read length
150 bp
Reference genome
GRCh38
Mapping
Cell Ranger (GRCh38)
QC and filtering
For gene detection, a range of 500-3,500 genes from a peripheral blood sample, 1,500-5,500 genes from muscle biopsy samples, 1,000-5,500 genes from bronchoalveolar lavage fluid samples, and less than 5% of cells from mitochondrial genes were analyzed.
Gene count
Peripheral blood: 17,441 genes
Muscle biopsy: 18,184 genes
Bronchoalveolar lavage fluid: 20,314 genes
Processed data type
Count data
Data use policy
NBDC data sharing policy (JGAP000001)