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GSE65336
Homo sapiens
78 Downloadable Samples
Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Type I IFNs are implicated in the pathophysiology of systemic sclerosis (SSc). Recently, a Phase I open-label trial was conducted with an anti-IFNAR1 receptor antibody (anifrolumab) in adult SSc patients. In this study, we aim to assess the downstream effects of anifrolumab and elucidate the role of type I IFN in SSc. Serum proteins and extracellular matrix (ECM) markers were measured in relation to IFN pathway activation status and SSc disease activity. Our results demonstrated a robust overexpression of multiple serum proteins in SSc patients, particularly those with an elevated baseline type I IFN gene signature. Anifrolumab administration was associated with significant downregulation of T cellassociated proteins and upregulation of type III collagen degradation marker. Whole-blood and skin microarray results also indicated the inhibition of T cell receptor and ECMrelated transcripts by anifrolumab. In summary, our study demonstrates suppressive effects of anifrolumab on T cell activation and collagen accumulation through which tissue fibrosis may be reduced in SSc patients. The relationship between these peripheral markers and the clinical response to anifrolumab may be examined in larger double-blind, placebo-controlled trials.
Publication Title
Suppression of T Cell Activation and Collagen Accumulation by an Anti-IFNAR1 mAb, Anifrolumab, in Adult Patients with Systemic Sclerosis.
Sample Metadata Fields
Specimen part, Disease, Disease stage, Time
View Samples- Sus scrofa
- 19 Downloadable Samples
- Affymetrix Porcine Genome Array (porcine)
Description
The use of cDNA microarrays has made it possible to analyze expression of thousands of genes simultaneously. We employed microarray gene expression profiling of porcine cDNA to compare myocardial gene expression in infarct core and remote myocardium at 1 week (n=3), 4 weeks (n=3), and 6 weeks (n=3) after surgically induced myocardial infarction (MI) and in sham-operated controls (n=3). More than 8,000 cDNA sequences were identified in myocardium that showed differential expression in response to MI. Different temporal and spatial patterns of gene expression were recognized in the infarct core tissue within this large set of data. Microarray gene profiling revealed candidate genes, some of them described for the first time, which elucidate changes in biological processes at different stages after MI.
Publication Title
Identification of temporal and region-specific myocardial gene expression patterns in response to infarction in swine.
Sample Metadata Fields
Sex, Specimen part, Treatment, Time
View Samples- Homo sapiens
- 6 Downloadable Samples
Affymetrix Human Gene 1.0 ST Array (hugene10st), Illumina HiSeq 2000
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
A comparative study of RNA-Seq and microarray data analysis on the two examples of rectal-cancer patients and Burkitt Lymphoma cells.
Sample Metadata Fields
Cell line, Treatment
View Samples- Arabidopsis thaliana
- 6 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
Early establishment of the apical-basal axis is prerequesite for correct embryonic development in Arabidopsis. The hypophysis is derived from the basal cell of the early embryo and is indispensible for root development; it gives rise to the root quiescent center and the central columella. Arabidopsis pvip1 pvip2 mutants show defects in embryonic root development and give rise to rootless seedlings.
Publication Title
Arabidopsis plant homeodomain finger proteins operate downstream of auxin accumulation in specifying the vasculature and primary root meristem.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 6 Downloadable Samples
- Illumina HiSeq 2000
Description
RNA-Seq profiling of Burkitt Lymphoma cell line (BL2) with B-cell activating factor (BAFF) for 24 hrs . The Burkitt Lymphoma cell line were either only cultured in cell culture medium supplemented with 10 mM HEPES at 1 × 106 cells/ml or additionally incubated with B-cell activating factor (BAFF) for 24 hrs Overall design: Two conditions of BL2 cells each in 3 replicates: 1. non-stimulated control (BL2), 2. Baff stimulated (BL2Baff)
Publication Title
A comparative study of RNA-Seq and microarray data analysis on the two examples of rectal-cancer patients and Burkitt Lymphoma cells.
Sample Metadata Fields
Treatment, Subject
View Samples- Homo sapiens
- 6 Downloadable Samples
- Affymetrix Human Gene 1.0 ST Array (hugene10st)
Description
Microarray profiling of Burkitt Lymphoma cell line (BL2) with B-cell activating factor (BAFF) for 24 hrs .
Publication Title
A comparative study of RNA-Seq and microarray data analysis on the two examples of rectal-cancer patients and Burkitt Lymphoma cells.
Sample Metadata Fields
Cell line
View Samples- Homo sapiens
- 5 Downloadable Samples
- IlluminaHiSeq2000
Description
RNA-Seq profiling of MCF-7 and MDA-MB-231. We profiled RNA expression in the estrogen-receptor-positive (ER+) MCF-7 and the triple-negative MDA-MB-231 breast cancer cells. The objective was to find genes differentially expressed between these cell lines as potential drivers of invasiveness of the triple-negative MDA-MB-231. We further utilized the identified differential genes to validate expression-responsive module of non-canonical Wnt signaling pathway. Overall design: 2 biological replicates of MCF-7 and 3 biological replicates of MDA-MB-231
Publication Title
Newly Constructed Network Models of Different WNT Signaling Cascades Applied to Breast Cancer Expression Data.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 12 Downloadable Samples
- IlluminaHiSeq2000
Description
RNA-Seq profiling of estrogen-receptor-positive MCF-7 cell lines with different perturbations of non-canonical WNT signaling . The MCF-7 cells were either transfected with an empty vector (pcDNA) or with a ROR2 overexpression construct, in parallel with or without stimulation with recombinant WNT5A. The objective was to find expression-responsive targets of these perturbations as potential drivers of increased cell invasiveness. Overall design: Four conditions of MCF-7 cells each in 3 replicates: 1. empty vector (pcDNA), 2. empty vector (pcDNA) with WNT5A stimulation, 3. ROR2 overexpression construct, 4. ROR2 overexpression construct with WNT5A stimulation
Publication Title
Ror2 Signaling and Its Relevance in Breast Cancer Progression.
Sample Metadata Fields
No sample metadata fields
View Samples- Drosophila melanogaster
- 9 Downloadable Samples
- Illumina HiSeq 2500
Description
N6-methyladenosine RNA (m6A) is the most abundant internal mRNA modification in mammals. While its role in the regulation of posttranscriptional gene expression is beginning to be unveiled, its function during development of complex organisms is poorly understood. Here, we identify Spenito as a novel member of the methyltransferase complex and show that m6A in Drosophila is necessary for proper synaptic growth, and in regulation of early steps of pre-mRNA splicing. Splicing of Sex-lethal and of its downstream targets are defective in animals lacking m6A, revealing also important roles in sex determination and dosage compensation. Finally, we implicate the nuclear m6A reader protein, YT521-B, as a crucial effector of m6A modifications in vivo. Altogether, our work provides important novel insights into m6A biology through identification and characterization of both m6A-writing and -reading proteins in Drosophila and their effects on splicing, neurogenesis and sex-determination within the context of the whole animal. Overall design: RNA seq in Drosophila melanogaster (flies) (3 Conditions, triplicates)
Publication Title
m<sup>6</sup>A modulates neuronal functions and sex determination in Drosophila.
Sample Metadata Fields
Sex, Specimen part, Subject
View Samples- Homo sapiens
- 54 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Detailed longitudinal sampling of glioma stem cells in situ reveals Chr7 gain and Chr10 loss as repeated events in primary tumor formation and recurrence.
Sample Metadata Fields
Specimen part, Disease
View Samples