We performed a polysomal RNA-Seq screen in non-malignant breast epithelial (MCF10A) and TNBC (MDA-MB-231) cells exposed to normoxic or hypoxic conditions and/or treated with an mTOR pathway inhibitor. Analysis of both the transcriptome and the translatome identified mRNA transcripts translationally activated or repressed by hypoxia in an mTOR-dependent or -independent manner. The mRNA populations of each sample were converted to cDNA libraries using the TruSeq protocol and then sequenced using a HiSeq 2000 machine. Paired-end reads were mapped against the reference human genome (GRCh38) with STAR v2.5.1b (ENCODE parameters for long RNA) and GENCODE v24 annotation. Gene quantification was performed using RSEM v1.2.28 with default parameters. Only protein-coding genes were included in the analysis. Normalization of the count matrix was performed with the TMM method of the edgeR R package. Polysomal RNA (P) and RNA total (T) fold changes across conditions were calculated with edgeR. Significant genes (FDR < 5% for MCF10A cells and FDR < 10% for MDA-MB-231 cells) in polysomes were selected for translational efficiency calculation (log2FC RNA polysomes/log2FC RNA total). Genes with a z-score > 1.5 were considered to have an increased translational efficiency and genes with a z-score < –1.5 were considered to have a decreased translational efficiency. GO enrichment analysis of significant genes was performed with the DAVID database. Overall design: RNA-Seq profiles in polysomes vs total in Normoxia, Hypoxia, Hypoxia + PP242, Normoxia + PP242 in MCF10A and MDA-MB-231 cell lines
Hypoxia-mediated translational activation of ITGB3 in breast cancer cells enhances TGF-β signaling and malignant features <i>in vitro</i> and <i>in vivo</i>.
Cell line, Treatment, Subject
View SamplesWe analyzed the role of the histone lysine methyltransferase Set7/9 in the differentiation of human embryonic stem (ES) cells. Human ES cell lines expressing a control short hairpin and a short hairpin against Set7/9 were established and the genome wide expression profile was compared between both cell lines at different days during differentiation. Analysis of both profiles indicates that in the absence of Set7/9 there is a delay in the silencing of self-renewal factors as well as in the induction of differentiation markers. These results indicate that Set7/9 plays an active role in the differentiation of human ES cells.
SETD7 Regulates the Differentiation of Human Embryonic Stem Cells.
Specimen part, Cell line
View SamplesObjective Telmisartan, an angiotensin II type 1 (AT1) receptor blocker, and amlodipine, a calcium channel blocker, are antihypertensive agents clinically used as monotherapy or in combination. They exert beneficial cardiovascular effects independently of blood pressure lowering and classic mechanisms of action. In this study, we investigate molecular mechanisms responsible for the off-target effects of telmisartan and telmisartan-amlodipine in endothelial cells (EC), using an unbiased approach.
Telmisartan exerts pleiotropic effects in endothelial cells and promotes endothelial cell quiescence and survival.
Specimen part, Disease, Treatment
View SamplesmiR-29 can target many gene transcripts encoding extracellular matrix proteins. To unravel novel targets, we used microarray analysis to detect global gene expression changes when inhibiting endogenous miR-29.
Ten-eleven translocation (Tet) and thymine DNA glycosylase (TDG), components of the demethylation pathway, are direct targets of miRNA-29a.
Specimen part, Treatment
View SamplesThis SuperSeries is composed of the SubSeries listed below.
Deconvolution of blood microarray data identifies cellular activation patterns in systemic lupus erythematosus.
Specimen part, Disease
View SamplesMicroarray deconvolution is a technique for quantifying the relative abundance of constituent cells in a mixture based on that mixture's microarray signature and the signatures of the purified constituents. It has been applied to yeast and other systems but not to blood samples.
Deconvolution of blood microarray data identifies cellular activation patterns in systemic lupus erythematosus.
Specimen part, Disease
View SamplesMicroarray deconvolution is a technique for quantifying the relative abundance of constituent cells in a mixture based on that mixture's microarray signature and the signatures of the purified constituents. Its ability to discriminate related human cells is unknown.
Deconvolution of blood microarray data identifies cellular activation patterns in systemic lupus erythematosus.
No sample metadata fields
View SamplesSingle-cell RNA-Seq RNA from medial ganglionic eminence at E11.5, E13.5, E15.5 or E17.5. The ID of this project in Genentech''s ExpressionPlot database is PRJ0007389 Overall design: Single-cell RNA-Seq from medial ganglionic eminence at E11.5, E13.5, E15.5 or E17.5.
Single-cell RNA sequencing identifies distinct mouse medial ganglionic eminence cell types.
Specimen part, Subject
View SamplesJ14 ES cells differentiated into MGE-like cells. Three groups of single-cell preparations were analyzed: ES cells (undifferentiated), differentiated cells (unsorted, of which less than 10% are GFP+) and GFP+ differentiated cells. These are specified in the "group" sample characteristic, with values "ES", "Unsorted" and "GFP+" respectively. The "SAMPLE_ID" sample characteristic is a sample identifier internal to Genentech. The ID of this project in Genentech''s ExpressionPlot database is PRJ0007904 Overall design: J14 ES cells differentiated into MGE-like cells
Single-cell RNA sequencing identifies distinct mouse medial ganglionic eminence cell types.
Cell line, Subject
View SamplesMouse bone marrow-derived macrophages (BMDM) grown in macrophage colony-stimulating factor (CSF-1) have been used widely in studies of macrophage biology and the response to toll-like receptor agonists. We investigated whether similar cells could be derived from the domestic pig. Cultivation of pig bone marrow cells for 5-7 days in presence of rhCSF-1 generated a pure population of BMDM that expressed the usual macrophage markers (CD14, CD16, CD163, CD172a), are potent phagocytic cells and produced tumor necrosis factor (TNF) in response to lipopolysaccharide (LPS). Bone marrow cells could be stored frozen and thawed, providing a renewable resource.
Pig bone marrow-derived macrophages resemble human macrophages in their response to bacterial lipopolysaccharide.
Sex, Specimen part, Time
View Samples