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

URL: https://www.h.u-tokyo.ac.jp/english/centers-services/clinical-divisions/allergy-and-rheumatology/index.html

 

Dataset IDType of DataCriteriaRelease Date
E-GEAD-344 NGS (scRNA-seq) Unrestricted-access 2020/10/09

*Release Note

*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

E-GEAD-344

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.

URL: https://www.h.u-tokyo.ac.jp/english/centers-services/clinical-divisions/allergy-and-rheumatology/index.html

Funds / Grants (Research Project Number):

NameTitleProject Number
KAKENHI Grant-in-Aid for Young Scientists (B) Single-cell RNA-seq inquiry into pathogenic immune cells in systemic sclerosis 17K16204

 

PUBLICATIONS

TitleDOIDataset 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

JGAD000309

E-GEAD-344

2