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GSE94648
Homo sapiens
95 Downloadable Samples
Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Ulcerative colitis (UC) is a chronic inflammatory disease of the colon with preiods of active disease followed by remission.
Publication Title
Usefulness of Transcriptional Blood Biomarkers as a Non-invasive Surrogate Marker of Mucosal Healing and Endoscopic Response in Ulcerative Colitis.
Sample Metadata Fields
Sex, Age, Specimen part, Disease stage, Treatment
View Samples- Homo sapiens
- 12 Downloadable Samples
Illumina HumanMethylation450 BeadChip (HumanMethylation450_15017482), Affymetrix Human Gene 2.0 ST Array (hugene20st)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Profiling of the transcriptional response to all-trans retinoic acid in breast cancer cells reveals RARE-independent mechanisms of gene expression.
Sample Metadata Fields
Cell line
View Samples- Homo sapiens
- 12 Downloadable Samples
- Affymetrix Human Gene 2.0 ST Array (hugene20st), Illumina HumanMethylation450 BeadChip (HumanMethylation450_15017482)
Description
Retinoids, derivatives of vitamin A, are key physiological molecules with regulatory effects on cell differentiation, proliferation and apoptosis. As a result, they are of interest for cancer therapy. Specifically, models of breast cancer have varied responses to manipulations of the retinoid signaling cascade. This study characterizes the transcriptional response of MDA-MB-231 and MDA-MB-468 breast cancer cells to retinaldehyde dehydrogenase 1A3 (ALDH1A3) and to all-trans retinoic acid (atRA). We demonstrate limited overlap between ALDH1A3-induced gene expression and atRA-induced gene expression in both cell lines, suggesting that the function of ALDH1A3 in breast cancer progression extends beyond its role as a retinaldehyde dehydrogenase. Our data reveals divergent transcriptional responses to atRA, which are largely independent of genomic retinoic acid response elements (RAREs) and consistent with the opposing responses of MDA-MB-231 and MDA-MB-468 to in vivo atRA treatment. We identify transcription factors associated with each gene set. Manipulation of one of the transcription factors (i.e. interferon regulatory factor 1; IRF1) demonstrates that it is the level of atRA-inducible and epigenetically regulated transcription factors that determine expression of target genes (e.g. CTSS, cathepsin S). This study provides a paradigm for complex, combinatorial responses of breast cancer models to atRA treatment, and illustrates the need to characterize RARE-independent responses to atRA in a variety of models.
Publication Title
Profiling of the transcriptional response to all-trans retinoic acid in breast cancer cells reveals RARE-independent mechanisms of gene expression.
Sample Metadata Fields
Cell line
View Samples- Bos taurus
- 14 Downloadable Samples
- Affymetrix Bovine Genome Array (bovine)
Description
The potential for dietary supplementation with n-3 polyunsaturated fatty acids (n-3 PUFA) to improve reproductive efficiency in cattle has received much interest. The mechanisms by which n-3 PUFA may affect physiological and biochemical processes in key reproductive tissues are likely to be mediated by significant alterations in gene expression.
Publication Title
Dietary n-3 polyunsaturated fatty acid supplementation alters the expression of genes involved in the control of fertility in the bovine uterine endometrium.
Sample Metadata Fields
Age, Specimen part, Treatment
View Samples- Homo sapiens
- 22 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Central nervous system primitive neuroectodermal tumors (CNS PNET) and medulloblastomas are both embryonal tumors that predominantly occur in children.
Publication Title
The role of the WNT/β-catenin pathway in central nervous system primitive neuroectodermal tumours (CNS PNETs).
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 12 Downloadable Samples
NextSeq 500
Description
We report the results of overexpression of the wildtype and mutant ANT1 (SLC25A4) gene in human embryonic kidney 293T (HEK293T) cells from the cytomegalovirus (CMV) promoter. Libraries were prepared from three independent replicates per condition using stranded RNA sequencing and run at 2 x 75 read length at a targeted output of 60 million paired-end reads per sample. We found only a limited number of nuclear genes whose expression is altered by wildtype ANT1-overexpression. Among the most upregulated genes is the zinc-finger proteins Egr1, a transcriptional factor with diverse cellular functions, including the repression of genes encoding mitochondrial inner membrane protein. The upregulation of EGR1 likely serves as a retrograde mechanism to reduce protein loading on the IMM and to alleviate mPOS. Overexpression of the triple and quadruple mutant alleles altered the expression of 206 and 560 genes, respectively, with 32 commonly up-regulated in both. These include EGR1, ZCCHC12 and SFPQ, which were also upregulated in cells overexpressing the wild-type ANT1. The 32 up-regulated genes are involved in functions including RNA-processing, autophagy/intracellular structure/trafficking, transcriptional control, ribosomal biogenesis/translational control, chaperones/proteasomal function and mitochondrial biogenesis. Upstream regulator analysis subsequently revealed 42 pathways predicted to be either activated or inhibited by these genes, including PPARGC1A, ATF4, Heat Shock Factor 1 (HSF1), mechanistic Target of Rapamycin (mTOR), Myc, EGFR and HMGA1. Overall design: Examination of effects of overexpression of wildtype and mutant ANT1 alleles in HEK293T cells
Publication Title
Mitochondrial carrier protein overloading and misfolding induce aggresomes and proteostatic adaptations in the cytosol.
Sample Metadata Fields
Specimen part, Subject
View Samples- Homo sapiens
- 78 Downloadable Samples
- Affymetrix Human Gene 2.0 ST Array (hugene20st)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
DNA Methylation Predicts the Response of Triple-Negative Breast Cancers to All-Trans Retinoic Acid.
Sample Metadata Fields
Sex, Specimen part, Disease, Cell line, Treatment
View Samples- Mus musculus
- 24 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
Murine GVH-SSc dorsal scapular skin samples were analyzed to determine the effect of IFNAR-1 inhibition on gene expression at day 14 and day 28. Gene expression in GVH-SSc skin from mice treated with a neutralizing IFNAR-1 antibody was compared to that in GVH-SSc skin from mice treated with isotype IgG, with skin from syngeneic graft controls as reference.
Publication Title
Type I IFNs Regulate Inflammation, Vasculopathy, and Fibrosis in Chronic Cutaneous Graft-versus-Host Disease.
Sample Metadata Fields
Sex
View Samples- Homo sapiens
- 77 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
We observed robust overexpression of type I interferon (IFN)inducible genes and genomic signatures that indicate T cell and dendritic cell infiltration in lesional skin. Up-regulation of mRNAs for IFN-a subtypes was observed in lesional skin compared with nonlesional skin. Enrichment of mature dendritic cells and 2 type I IFNinducible proteins, STAT1 and ISG15, were observed in the majority of lesional skin biopsies. Concordant overexpression of IFN-c and TNF-ainducible gene signatures occurred at the same disease sites.
Publication Title
Type I interferon: potential therapeutic target for psoriasis?
Sample Metadata Fields
Disease
View Samples- Homo sapiens
- 19 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf
Publication Title
Mapping and analysis of chromatin state dynamics in nine human cell types.
Sample Metadata Fields
Disease, Cell line
View Samples