This SuperSeries is composed of the SubSeries listed below.
Poised RNA polymerase II changes over developmental time and prepares genes for future expression.
Specimen part, Cell line, Treatment, Time
View SamplesMurine ES cell gene expression before RA induction are used to compare gene expression for time-points of 8, 12, 16, 24, 36, 48, 60 and 72 hours post-induction.
Poised RNA polymerase II changes over developmental time and prepares genes for future expression.
Cell line, Treatment, Time
View SamplesPoised RNA polymerase II is predominantly found at developmental control genes and is thought to allow their rapid and synchronous induction in response to extracellular signals. How the recruitment of poised RNA Pol II is regulated during development is not known. By isolating muscle tissue from Drosophila embryos at five stages of differentiation, we show that the recruitment of poised Pol II occurs at many genes de novo and this makes them permissive for future gene expression. When compared to other tissues, these changes are stage-specific and not tissue-specific. In contrast, Polycomb group repression is tissue-specific and in combination with Pol II (the balanced state) marks genes with highly dynamic expression. This suggests that poised Pol II is temporally regulated and is held in check in a tissue-specific fashion. We compare our data to mammalian embryonic stem cells and discuss a framework for predicting developmental programs based on chromatin state. Overall design: mRNA-seq of Drosophila tissues during development
Poised RNA polymerase II changes over developmental time and prepares genes for future expression.
Specimen part, Subject, Time
View SamplesThe physiological responses to B cell receptors (BCR) and Toll-like receptors (TLRs) so vital to immunity are well known but the transcriptional signatures and regulatory mechanisms that initiate activation and release cells from quiescence remain unclear. Here, we show that BCR- or TLR-mediated activation of B cells involves a large shared transcriptional signature and a smaller subset of distinct signal-specific transcriptional responses. Signal-specific transcription is observable within 2 hours of ligand exposure; suggesting different modes of activation begin soon after ligand binding and long before the well-documented BCR and TLR-dependent physiological responses occur. Ligand-specific differences in regulatory mechanisms including RNA Pol II recruitment, activating (H3K4me3) and repressing (H3K27me3) histone marks, transcription factor binding sites in responsive gene promoters, and miRNA expression were observed. These results begin to define the transcriptional landscape of early B cell activation revealing more ligand-specific regulation and character than occurs much earlier than previously expected. Overall design: CD43- mouse resting B cells were stimulated with ligands against the B cell receptor and TLR4 (LPS). RNA-sequencing was performed to describe differential transcription and ChIP-sequencing was performed to describe regulatory mechanism responses.
Divergence of transcriptional landscape occurs early in B cell activation.
No sample metadata fields
View SamplesThree groups of male +b and bb rats were obtained (ages between 6 and 14 months) and intestinal scrapes were taken. Tissues was combined from 3 rats per group and processed for gene chip analysis.
Induction of arachidonate 12-lipoxygenase (Alox15) in intestine of iron-deficient rats correlates with the production of biologically active lipid mediators.
No sample metadata fields
View SamplesHuman umbilical cord Whartons jelly stem cells (WHJSC) are gaining attention as a possible clinical source of mesenchymal stem cells for use in cell therapy and tissue engineering due to their high accessibility, expansion potential and plasticity. However, the cell viability changes that are associated to sequential cell passage of these cells are not known. In this analysis, we have identified the gene expression changes that are associated to cell passage in WHJSC.
Evaluation of the cell viability of human Wharton's jelly stem cells for use in cell therapy.
Specimen part
View SamplesEts1-/- mice have an increase in B cell differentiation to plasma cells and increased serum immunoglobulin levels. The genes in B cells that are transcriptionally regulated by Ets1 and help regulate B cell differentiation are largely unknown. Here, we identify Ets1-regulated target genes in B cells using ChIP-seq and RNA-seq analysis. We found that Ets1 targets genes associated with immune response, mature B cell differentiation and regulation of B cell activation. Overall design: Quiescent follicular B cells were sorted from the spleens of wild-type and Ets1-/- mice using the following markers B220+ CD23-high CD21-low CD80-negative IgA-negative IgE-negative IgG1-negative IgG2a-negative IgG2b-negative IgG3-negative. Total RNA was prepared from sorted cells and subjected to RNA-sequencing.
Genome-Wide Identification of Target Genes for the Key B Cell Transcription Factor <i>Ets1</i>.
Specimen part, Cell line, Subject
View SamplesReproductive success depends on a functional oviduct for gamete storage, maturation, fertilization, and early embryonic development. The ovarian-derived sex steroids estrogen and progesterone have been found to influence cell proliferation, differentiation and functionality of the oviduct. The objective of this study was to investigate steroidal regulation of oviductal epithelial cell function by using the Bovine Gene 1.0 ST array (Affymetrix Inc., CA) for transcriptional profiling. Our overall goals were to increase our understanding of known epithelial cell processes critical for fertility, and to identify novel genes and biochemical processes for future analysis. Transcripts were annotated using NetAffx annotation database for the Bovine gene 1.0 ST array and last updated in June 2014.
A transcriptomal analysis of bovine oviductal epithelial cells collected during the follicular phase versus the luteal phase of the estrous cycle.
Specimen part
View SamplesIn the present study, we sought to understand the impact of obesity/metabolic disease (high-fat induced) on spinal cord injury (SCI) by examining transcriptome. Adult, male Long Evans rats received either thoracic level contusion of the spinal cord or sham laminectomy and then were allowed to recover on normal rat chow for 4 weeks and further on HFD for an additional 8 weeks. Spinal cord tissues harvested from the rats were processed for Affymetrix microarray and further transcriptomic analysis.
Chronic spinal cord changes in a high-fat diet-fed male rat model of thoracic spinal contusion.
Sex, Specimen part
View SamplesTissue samples were collected from patients diagnosed with HNSCC (oropharynx, hypopharynx, larynx). Samples were taken from the tumor site (tumor samples) and from a site distant to the tumor (normal samples) prior to therapy.
Prognostic biomarkers for HNSCC using quantitative real-time PCR and microarray analysis: β-tubulin isotypes and the p53 interactome.
Age, Specimen part, Subject
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