NBDC Research ID: hum0218.v1
SUMMARY
Aims: To elucidate the subpopulation of monocytes that are related to the pathophysiology of systemic sclerosis
Methods: Peripheral blood monocytes from 3 systemic sclerosis patients were collected and a single cell RNA-seq was performed for 984 cells.
Participants/Materials: Systemic sclerosis
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| E-GEAD-344 | NGS (scRNA-seq) | Unrestricted-access | 2020/10/09 |
*When the research results including the data which were downloaded from NHA/DRA, are published or presented somewhere, the data user must refer the papers which are related to the data, or include in the acknowledgment. Learn more
MOLECULAR DATA
| Participants/Materials | Systemic sclerosis (ICD10: M340): 3 cases |
| Targets | scRNA-seq |
| Target Loci for Capture Methods | - |
| Platform | Illumina [HiSeq] |
| Library Source | RNAs extracted from a single cell isolated from peripheral blood monocytes |
| Cell Lines | - |
| Library Construction (kit name) |
SMARTer ICELL8 Reagent 3' DE Reagent Kit Nextera XT DNA Library Prep Kit |
| Fragmentation Methods | Nextera XT DNA Library Prep Kit |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) |
Read1: 25 bp Read2: 100 bp |
| Mapping Methods | STAR (GRCh38) |
| QC Methods | The sequencing primer, poly-A, and poly-T were trimmed by Cutadapt and low-quality ends (phred quality score < 25) were also trimmed. After trimming, the read (the length of which was < 20 bases) was also removed. |
| Gene Number | 26288 |
| Genomic Expression Archive ID | E-GEAD-344 |
| Total Data Volume | 49.6 MB (count data, txt) |
| Comments (Policies) | NBDC policy |
DATA PROVIDER
Principal Investigator: Keishi Fujio
Affiliation: Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo
Project / Group Name: Gene expression analysis of systemic sclerosis patients.
Funds / Grants (Research Project Number):
| Name | Title | Project Number |
|---|---|---|
| KAKENHI Grant-in-Aid for Young Scientists (B) | Single-cell RNA-seq inquiry into pathogenic immune cells in systemic sclerosis | 17K16204 |
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | Integrated bulk and single-cell RNA-sequencing identified disease-relevant monocytes and a gene network module underlying systemic sclerosis | doi: 10.1016/j.jaut.2020.102547 |
E-GEAD-344 |
| 2 |
