GEO DataSets

(Submitter supplied) Systemic sclerosis (SSc) is an incurable autoimmune disease with high morbidity and mortality rates, with no effective treatment. Here, we conducted a population scale single-cell genomic analysis of skin and blood samples of 56 healthy controls, and 97 SSc patients at different stages of disease. We found immune compartment activation in only a subset of diffuse SSc patients, but global dysregulation of the stromal compartment, including a novel subset of LGR5+ scleroderma associated fibroblasts (ScAF). more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL18573 GPL24676

727 Samples

Download data: TAR, TXT

(Submitter supplied) 339 total forearm skin biopsies were obtained from 113 unique SSc patients and 44 matched healthy controls. 105 SSc patients had a 2nd biopsy, 76 patients had a 3rd biopsy, and 1 patient had a 4th biopsy. Global gene expression profiling was performed, and differentially expressed genes and cell type-specific signatures in SSc were evaluated for relationships to skin thickness and other clinical variables. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL13497

339 Samples

Download data: TXT

(Submitter supplied) In this study, we analyzed the gene expression profiles of the lung in mouse bleomycin (BLM)-induced systemic sclerosis (SSc) model treated with MT-7117. Gene array analysis using the BLM-induced SSc model demonstrated changes in numerous categories related to macrophages, monocytes, and neutrophils, followed by endothelial cell-related categories after treatment with MT-7117 (Dersimelagon). In the analysis that focused on biological functions, categories of inflammatory response, activation of antigen-presenting cells, angiogenesis, atherosclerosis, vasculogenesis, and vaso-occlusion were suppressed by MT-7117. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL21163

30 Samples

Download data: TXT

(Submitter supplied) Systemic sclerosis (SSc) is a rare but devastating disease of fibrosis impacting the dermis and multiple organ systems. The prevalence ranges from 4 to 489 cases per million individuals with ten year mortality rates reported around 18 percent. Survival is related to the extent of skin involvement, yet the precise mechanisms driving skin fibrosis in SSc remain unknown. In this study, we analyzed the shared and unique transcriptomic profiles of SSc and normal keratinocytes.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL17692

20 Samples

Download data: CEL, TXT

(Submitter supplied) Myofibroblasts are key effector cells in the extracellular matrix remodeling of systemic sclerosis-associated interstitial lung disease (SSc-ILD), however the diversity of fibroblast populations present in the healthy and SSc-ILD lung is unknown, and has prevented the specific study of the myofibroblast transcriptome. We sought to identify and define the transcriptomes of myofibroblasts and other mesenchymal cell populations in human healthy and SSc-ILD lungs to understand how alterations in fibroblast phenotypes lead to SSc-ILD fibrosis.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

16 Samples

Download data: H5, MTX, TSV

(Submitter supplied) Systemic sclerosis (SSc) is a complex multi-system autoimmune disease characterized by immune dysregulation, vasculopathy, and organ fibrosis. Skin fibrosis causes high morbidity and impaired quality of life in affected individuals. In this study, we identified the COL22α1 gene associated with the pathogenesis of skin fibrosis through high-throughput RNA sequencing of human skin in organ culture. The expression levels of COL22α1 were significantly increased by TGFβ in ex vivo human skin tissues and normal human skin fibroblasts, while other fibrosis growth factors such as IL-6 and bleomycin modestly increased COL22α1 expression.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

4 Samples

Download data: TXT

(Submitter supplied) Systemic sclerosis (SSc) is characterized by vascular damage, autoimmunity and fibrosis and is associated with highly variable clinical presentation and disease course. Aberrant transforming growth factor-ß (TGF-ß) signaling via the early immediate transcription factor Egr-1 is implicated in the pathogenesis of SSc. To shed light on the role of Egr-1 in fibrosis, regulation of gene expression in human skin fibroblasts overexpressing Egr-1 was examined by genome-wide expression analysis. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Datasets:

GDS5191 GDS5192

Platform:

GPL6104

12 Samples

Download data

Analysis of cultured skin fibroblasts overexpressing TGF-ß for 24 and 48 hrs. Results compared to fibroblasts overexpressing Egr-1 (GDS5191). Egr-1 is a zinc finger transcription factor whose expression is induced by TGF-ß. Results examine overlapping Egr-1- and TGF-ß-regulated gene signatures.

Organism:

Homo sapiens

Type:

Expression profiling by array, transformed count, 2 protocol, 2 time sets

Platform:

GPL6104

Series:

GSE27165

8 Samples

Download data

Analysis of cultured skin fibroblasts overexpressing Egr-1 for 24 and 48 hs. Egr-1 is a zinc finger transcription factor whose expression is induced by TGF-ß. Results provide insight into gene targets of Egr-1 and are compared to results of fibroblasts overexpressing TGF-ß (GDS5192).

Organism:

Homo sapiens

Type:

Expression profiling by array, transformed count, 2 protocol, 2 time sets

Platform:

GPL6104

Series:

GSE27165

8 Samples

Download data

(Submitter supplied) We assessed genome-wide chromatin accessibility and transcription factor footprinting in endothelial cells and fibroblasts isolated from skin biopsies from healthy subjects and diffuse cutaneous scleroderma patients.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24676

24 Samples

Download data: NARROWPEAK

(Submitter supplied) To investigate the miRNA signature in the serum of systemic sclerosis (SSc) patients. The levels of 758 miRNAs were evaluated in the serum of 26 SSc patients as compared to 9 healthy controls by using an Openarray platform. Patients fulfilling the ACR/EULAR 2013 classification criteria were classified in relation to the extent of skin fibrosis as limited cutaneous (lcSSc) or diffuse cutaneous SSc (dcSSc); patients fulfilling the classification criteria without skin fibrosis will be referred to as non-cutaneous SSc (ncSSc). more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL22992

35 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens

Type:

Expression profiling by array

7 related Platforms

577 Samples

Download data: CEL, GPR, TXT

(Submitter supplied) Systemic sclerosis (SSc) is an autoimmune disease characterized by clinical heterogeneity, multi-organ involvement, and complex genetic risk. Here, we report the first multi-tissue meta-analysis of ten independent SSc gene expression datasets. We identify a common immune-fibrotic expression axis across all tissues that is associated with the most severe disease phenotypes. The coexpression patterns conserved across tissues and phenotypes were used to query functional genomic networks, which allowed us to identify common and tissue-specific disease drivers. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6480

15 Samples

Download data: TXT

(Submitter supplied) Systemic sclerosis (SSc) is an autoimmune disease characterized by clinical heterogeneity, multi-organ involvement, and complex genetic risk. Here, we report the first multi-tissue meta-analysis of ten independent SSc gene expression datasets. We identify a common immune-fibrotic expression axis across all tissues that is associated with the most severe disease phenotypes. The coexpression patterns conserved across tissues and phenotypes were used to query functional genomic networks, which allowed us to identify common and tissue-specific disease drivers. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL14550

24 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL7202

34 Samples

Download data: GPR, XLS

(Submitter supplied) Systemic sclerosis (SSc) is confounded by considerable disease heterogeneity. Animal models of SSc that recapitulate distinct subsets of disease at the molecular level have not delineated. We applied interspecies comparative analysis of genomic data from multiple mouse models of SSc and patients with SSc to determine which animal models best reflect the SSc intrinsic gene expression subsets.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL7202

20 Samples

Download data: GPR, XLS

(Submitter supplied) Systemic sclerosis (SSc) is confounded by considerable disease heterogeneity. Animal models of SSc that recapitulate distinct subsets of disease at the molecular level have not delineated. We applied interspecies comparative analysis of genomic data from multiple mouse models of SSc and patients with SSc to determine which animal models best reflect the SSc intrinsic gene expression subsets.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL7202

10 Samples

Download data: GPR

(Submitter supplied) Systemic sclerosis (SSc) is confounded by considerable disease heterogeneity. Animal models of SSc that recapitulate distinct subsets of disease at the molecular level have not delineated. We applied interspecies comparative analysis of genomic data from multiple mouse models of SSc and patients with SSc to determine which animal models best reflect the SSc intrinsic gene expression subsets.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL7202

4 Samples

Download data: GPR

(Submitter supplied) Normal fibroblasts and SSc fibroblasts between the third and six subpassages were used for experiments. Total RNA was extracted from culture cells with ISOGEN (Nippon Gene, Tokyo, Japan). MicroRNA isolation from total RNA was performed using RT2 qPCR-Grade miRNA Isolation Kit (SA Bioscience). For RT2 Profiler PCR Array (SABioscience), microRNAs were reverse-transcribed into first strand cDNA using RT2 miRNA First Strand Kit (SABiosciences). more...

Organism:

Homo sapiens

Type:

Expression profiling by RT-PCR

Platform:

GPL14956

2 Samples

Download data: TXT

(Submitter supplied) We examined the effect of IL-17 signaling pathway on extracellular matrix (ECM) expression and the involvement of IL-17 signaling pathway in pathogenesis of SSc. To identify differences in the expression pattern of ECM genes in IL-17A- or IL-17F-treated cells, we performed PCR array analysis, consisting of 84 ECM-related genes. Normal human dermal fibroblasts were cultured until they were confluent, and then stimulated with IL-17A or IL-17F for 12 hours, and total RNA was extracted. more...

Organism:

Homo sapiens

Type:

Expression profiling by RT-PCR

Platform:

GPL14864

3 Samples

Download data: TXT