NBDC Research ID: hum0214.v2
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SUMMARY
Aims: To elucidate the regulation of gene expression in each immune cell subset and its contribution to autoimmune diseases.
Methods: Various immune cell subsets from 21 systemic sclerosis patients, 26 ANCA associated vasculitis, and 28 healthy controls were collected (Naive_B, SM_B, USM_B, DN_B, Plasmablast, Th1, Th2, Th17, Tfh, Naive_CD4, Mem_CD4, Fr._II_eTreg, Naive_CD8, Mem_CD8, mDC, pDC, CD16p_Mono, CD16n_Mono, NK, Neu) and total RNAs were extracted from each subset. RNA-seq was performed for each sample.
Participants/Materials: Systemic Sclerosis, ANCA-associated Vasculitis, healthy individuals
| Data Set ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000220 | NGS (RNA-seq) Systemic sclerosis | Controlled Access (Type I) | 2020/10/09 |
| JGAS000220 | NGS (RNA-seq) ANCA-associated Vasculitis | Controlled Access (Type I) | 2021/03/05 |
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MOLECULAR DATA
| Participants/Materials |
Systemic Sclerosis (ICD10: M340): 21 cases 13 healthy controls |
| Targets | RNA-seq |
| Target Loci for Capture Methods | - |
| Platform | Illumina [HiSeq 2500] |
| Library Source | Total RNAs extracted from 19 immune cell subsets (Naive_B, SM_B, USM_B, DN_B, Plasmablast, Th1, Th2, Th17, Tfh, Naive_CD4, Mem_CD4, Fr._II_eTreg, Naive_CD8, Mem_CD8, mDC, pDC, CD16p_Mono, CD16n_Mono, NK) |
| Cell Lines | - |
| Library Construction (kit name) | SMART-seq v4 Ultra Low Input RNA Kit |
| Fragmentation Methods | SMART-seq v4 Ultra Low Input RNA Kit |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 100 bp |
| Mapping Methods | STAR (hg38) |
| QC Methods | The adaptor sequences and 3’ low quality bases (Phred quality score < 20) were trimmed. Short reads (< 50bp) and reads containing many low quality bases (Phred quality score < 20 in > 20% of the bases) were removed. If the uniquely mapped rate was less than 80%, or the number of uniquely mapped reads was 5.00 x 106 reads, the sample was removed before further analysis. The correlation coefficient of the expression data between two samples belonging to the same cell subset and calculated the average of the correlation coefficient (Di). Samples for which Di was less than 0.9 were removed. |
| Gene Number | 26353 |
| Japanese Genotype-phenotype Archive Data set ID | JGAD000309 |
| Total Data Volume | 125 MB (count data, txt) |
| Comments (Policies) | NBDC policy |
RNA-seq (ANCA-associated Vasculitis)
| Participants/Materials |
ANCA-associated Vasculitis (ICD10: M318): 26 cases 28 healthy controls (including above 13 individuals) |
| Targets | RNA-seq |
| Target Loci for Capture Methods | - |
| Platform | Illumina [HiSeq 2500] |
| Library Source | Total RNAs extracted from 20 immune cell subsets (Naive_B, SM_B, USM_B, DN_B, Plasmablast, Th1, Th2, Th17, Tfh, Naive_CD4, Mem_CD4, Fr._II_eTreg, Naive_CD8, Mem_CD8, mDC, pDC, CD16p_Mono, CD16n_Mono, NK, Neu) |
| Cell Lines | - |
| Library Construction (kit name) | SMART-seq v4 Ultra Low Input RNA Kit |
| Fragmentation Methods | SMART-seq v4 Ultra Low Input RNA Kit |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 100 bp |
| Mapping Methods | STAR (hg38) |
| QC Methods | The adaptor sequences and 3’ low quality bases (Phred quality score < 20) were trimmed. Short reads (< 50bp) and reads containing many low quality bases (Phred quality score < 20 in > 20% of the bases) were removed. If the uniquely mapped rate was less than 80%, or the number of uniquely mapped reads was 5.00 x 106 reads, the sample was removed before further analysis. The correlation coefficient of the expression data between two samples belonging to the same cell subset and calculated the average of the correlation coefficient (Di). Samples for which Di was less than 0.9 were removed. |
| Gene Number | 26353 |
| Japanese Genotype-phenotype Archive Data set ID | JGAD000310 |
| Total Data Volume | 125 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: Immune cell multi-omics analysis of immune-mediated diseases
Funds / Grants (Research Project Number):
| Name | Title | Project Number |
|---|---|---|
| Collaborative research fund with Chugai Pharmaceutical Co., Ltd. | - | - |
PUBLICATIONS
| Title | DOI | Data Set 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 |
| 2 | Identifying the most influential gene expression profile in distinguishing ANCA-associated vasculitis from healthy controls | doi: 10.1016/j.jaut.2021.102617 | JGAD000310 |
USRES (Controlled-Access Data)
| Principal Investigator: | Affiliation: | Data in Use (Data Set ID) | Period of Data Use |
|---|---|---|---|
