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SRP005604
Mus musculus
11 Downloadable Samples
Illumina Genome Analyzer, Illumina Genome Analyzer II
Description
Transitions between pluripotent stem cells and differentiated cells are executed by key transcription regulators. Comparative measurements of RNA polymerase distribution over the genome’s primary transcription units in different cell states can identify the genes and steps in the transcription cycle that are regulated during such transitions. To identify the complete transcriptional profiles of RNA polymerases with high sensitivity and resolution, as well as the critical regulated steps upon which regulatory factors act, we used genome-wide, nuclear run-on (GRO-seq) to map the density and orientation of transcriptionally-engaged RNA polymerases in mouse embryonic stem cells (ESCs) and embryonic fibroblasts (MEFs). In both cell types, progression of a promoter-proximal, paused RNA polymerase II (Pol II) into productive elongation is a rate-limiting step in transcription of ~40% of mRNA-encoding genes. Importantly, quantitative comparisons between cell types reveal that transcription is controlled frequently at paused Pol II’s entry into elongation. Furthermore, “bivalent” ESC genes (exhibiting both active and repressive histone modifications) bound by Polycomb Group Complexes PRC 1 and PRC2 show dramatically reduced levels of paused Pol II at promoters relative to an average gene. In contrast, bivalent promoters bound by only PRC2 allow Pol II pausing, but it is confined to extremely 5’ proximal regions. Altogether, these findings identify rate-limiting targets for transcription regulation during cell differentiation. Overall design: Mapping engaged RNA polymerase density in two cell types by sequencing run-on transcripts. SUPPLEMENTARY FILES: All fastq files have sanger-fastq format q values. Alignments were generated with eland and the mm9 mouse genome assembly. Reads aligning to regions annotated as similar to rRNA by RepeatMasker were then removed. Wiggle files are in units of RPKM (reads per kilobase per million aligned reads) and are broken up by cell type and chromosome to aid in uploading to UCSC. Each file furthermore contains two tracks - one for each strand. As in the published paper, plus strand RPKM densities are in red with positive values and minus strand RPKM densities are in blue with negative values.
Publication Title
Regulating RNA polymerase pausing and transcription elongation in embryonic stem cells.
Sample Metadata Fields
No sample metadata fields
View Samples- Drosophila melanogaster
- 13 Downloadable Samples
- Illumina Genome Analyzer IIx, Illumina Genome Analyzer
Description
Control of RNA transcription is critical for the development and homeostasis of all organisms, and can occur at multiple steps of the transcription cycle, including RNA polymerase II (Pol II) recruitment, initiation, promoter-proximal pausing, and elongation. That Pol II accumulates on many promoters in metazoans implies that steps other than Pol II recruitment are rate-limiting and regulated 1-6. By integrating genome-wide Pol II chromatin immunoprecipition (ChIP) and Global Run-On (GRO) genomic data sets from Drosophila cells, we examined critical features of Pol II near promoters. The accumulation of promoter-proximal polymerase is widespread, occurring on 70% of active genes; and unlike elongating Pol II within the body of genes, promoter Pol II are held paused by factors like NELF, unable to transcribe unless nuclei are treated with strong detergent. Notably, we find that the vast majority of promoter-proximal Pol II detected by ChIP are paused, thereby identifying the biochemical nature of this rate-limiting step in transcription. Finally, we demonstrate that Drosophila promoters do not have the upstream divergent Pol II that is seen so broadly and prominently on mammalian promoters. We postulate this is a consequence of Drosophila's extensive use of directional core promoter sequence elements, which contrasts with mammals' lack of directional elements and prevalence of CpG island core promoters. In support of this idea, we show that the fraction of mammalian promoters containing a TATA box core element is dramatically depleted of upstream divergent transcription. Overall design: Comparison of multiple GRO-seq data sets
Publication Title
Defining the status of RNA polymerase at promoters.
Sample Metadata Fields
Cell line, Treatment, Subject
View Samples- Homo sapiens
- 24 Downloadable Samples
- Illumina HiSeq 2500
Description
To understand the nature of glucocorticoids targeting non-immune cell function, we generate RNA sequencing data from 3 human podocyte cell lines derived from 3 kidney transplant donors and identify the genes that are significantly regulated in dexamethasone-treated podocytes compared to vehicle-treated cells.Our results represent a significant step forward in the genome-wide characterization of the molecular effects of glucocorticoids on human podocytes. The resource generated in this study is important for understanding the targeting of non-immune cell function by glucocorticoids and also for designing more specific podocyte-targeted agents for MCN therapy. Overall design: Transcriptome profiles of human podocytes treated with vehicle and dexamethasone were generated by RNA-sequencing using Illumina HiSeq 2500
Publication Title
RNA sequencing analysis of human podocytes reveals glucocorticoid regulated gene networks targeting non-immune pathways.
Sample Metadata Fields
Specimen part, Subject
View Samples- Mus musculus
- 14 Downloadable Samples
Affymetrix Mouse Gene 2.1 ST Array (mogene21st)
Description
The histone methyltransferase Suv39h1 silences transcriptional programs during CD8+-T cell differentiation
Publication Title
The epigenetic control of stemness in CD8<sup>+</sup> T cell fate commitment.
Sample Metadata Fields
Specimen part
View Samples- Rattus norvegicus
- 48 Downloadable Samples
- Affymetrix Rat Genome 230 2.0 Array (rat2302)
Description
To investigate the molecular mechanisms associated with initial dose-related events that are linked to the development of liver tumours: liver growth; cell proliferation; changes in histopathology such as hypertrophy
Publication Title
An integrated functional genomic study of acute phenobarbital exposure in the rat.
Sample Metadata Fields
Specimen part, Time
View Samples- Mus musculus
- 6 Downloadable Samples
- Illumina MouseRef-8 v2.0 expression beadchip
Description
Microarray gene expression was performed on mouse livers. Gene expression profiles were studies on 3 PTU treated and 3 PTU followed by T3 treated mice.
Publication Title
Transcriptional activation by the thyroid hormone receptor through ligand-dependent receptor recruitment and chromatin remodelling.
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 19 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Pediatric GIST commonly harbors a disabled succinate dehydrogenase complex (SDH), which yields tumors with highly conserved genomes but characteristic epigenomic signatures. Mysteriously, nearly half of such SDH-deficient GIST, including tumors from Carney Triad patients, lack identifiable mutations in SDH component genes and genes required for complex assembly (SDHA, SDHB, SDHC, SDHD, SDHAF, termed SDHx). Genomic sequencing coupled with DNA methylation and transcriptional profiling have exposed SDHC promoter-specific CpG island epimutation and concomitant gene silencing in the majority of SDHx-WT GIST.
Publication Title
Recurrent epimutation of SDHC in gastrointestinal stromal tumors.
Sample Metadata Fields
No sample metadata fields
View Samples- Arabidopsis thaliana
- 17 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
Fe deficiency stimulates a coordinated response involving reduction, transport and redistribution of Fe in the roots. The expression of genes regulated by Fe deficiency in the two contrasting Arabidopsis thaliana ecotypes, Tsu-1 and Kas-1, shows that different ecotypes can respond in diverse ways, with different Fe regulated overrepresented categories.
Publication Title
Use of natural variation reveals core genes in the transcriptome of iron-deficient Arabidopsis thaliana roots.
Sample Metadata Fields
Age, Specimen part, Time
View Samples- Bos taurus
- 40 Downloadable Samples
- Illumina HiSeq 2000
Description
The objective of this study was to examine the effect of dietary restriction and subsequent re-alimentation induced compensatory growth on the global gene expression profile of jejunum epithelial Holstein Friesian bulls (n=40) were assigned to one of two groups: restricted feed allowance (RES; n=20) for 125 days (Period 1) followed by ad libitum access to feed for 55 days (Period 2) or (ii) ad libitum access to feed throughout (ADLIB; n=20). All bulls received the same diet of 70% concentrate 30% grass silage through out the experimental trial,with the amount of feed provided different dependent on each treatment group. At the end ofeach period, 10 animals from each treatment group (RES, ADLIB) were slaughtered, and jejunum epithelial collected from all animals. RNA was extracted and jejununal epithelium gene expression was examined using RNAseq technology on all samles collected (end of Period 1: 10 samples each from ADLIB and RES groups; end of Period 2: 10 samples each from ADLIB and RES groups). Dietary restriction and subsequent re-alimentation were associated with altered expression of genes involved in digestion and metabolism, aswell as cellular protection and detoxification in jejunal epithelia. This information may be exploited in genomic breeding programmes to assist selection of cattle with a greater ability to compensate following a period dietary restriction. Overall design: 40 jejunumal epithelium RNA samples were analysed in total. 10 samples were from jejunum epithelium collected at the end of a period of dietary restriction (d 125; Period 1) and 10 samples were from jejunum epithelium collected after 55 days of compensatory growth (d 55 of re-alimentation, Period 2). In addition, RNA was also anlaysed from 10 samples collected from animals fed ad libitum at the end of both Period 1 and Period 2.
Publication Title
Gene co-expression networks contributing to the expression of compensatory growth in metabolically active tissues in cattle.
Sample Metadata Fields
Specimen part, Subject
View Samples- Bos taurus
- 34 Downloadable Samples
- Illumina HiSeq 2000
Description
The objective of this study was to examine the effect of dietary restriction and subsequent re-alimentation induced compensatory growth on the global gene expression profile of ruminal epithelial papillae. Holstein Friesian bulls (n=38) were assigned to one of two groups: restricted feed allowance (RES; n=19) for 125 days (Period 1) followed by ad libitum access to feed for 55 days (Period 2) or (ii) ad libitum access to feed throughout (ADLIB; n=19). All bulls received the same diet of 70% concentrate 30% grass silage through out the experimental trial,with the amount of feed provided different dependent on each treatment group. At the end of Period 1, 9 animals from each treatment group were slaughtered, with 10 animals from each treatment slaughtered at the end of Period 2. Rumen epithelium was collected from all animals within thirty minutes of slaughter. RNA was extracted and rumen epithelium gene expression was examined using RNAseq technology on all samles collected (end of Period 1: 9 samples each from ADLIB and RES groups; end of Period 2: 10 samples each from ADLIB and RES groups). Genes identified as differentially expressed in response to both dietary restriction and subsequent compensatory growth included those involved in processes such as cellular interactions and transport, protein folding and gene expression, as well as immune response. This information can be exploited in genomic breeding programmes to assist selection of cattle with a greater ability to compensate following a period dietary restriction. Overall design: 38 rumen epithelium RNA samples were analyzed in total. Purebred Holstein Friesian bulls were assigned to one of two feeding treatments (i) restricted feed allowance for 125 days (n=9) followed by ad libitum access to feed for a further 55 days (n=10) or (ii) a control group with ad libitum access to feed through out the 180 days trial (n=19). The first 125 days of the trial were denoted as Period 1, during which treatment groups were fed differentially. The subsequent 55 days, denoted as Period 2 during which all bulls were fed ad libitum. All bulls received the same diet of 70% concentrate 30% grass silage through out the experimental trial, with the amount of feed provided different dependent on each treatment group. Restricted fed animals were fed to grow at 0.6 kg /day during Period 1, with ad libitum animals expected to gain in excess of 1.5 to 2 kg/day.
Publication Title
Gene co-expression networks contributing to the expression of compensatory growth in metabolically active tissues in cattle.
Sample Metadata Fields
Sex, Specimen part, Subject
View Samples