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    Results: 20

    1.

    Rev-Erbs repress macrophage gene expression by inhibiting enhancer-directed transcription

    (Submitter supplied) Rev-Erba and Rev-Erbb are nuclear receptors that regulate the expression of genes involved in the control of circadian rhythm, metabolism, and inflammatory responses. Rev-Erbs function as transcriptional repressors by recruiting NCoR/HDAC3 co-repressor complexes to Rev-Erb response elements in enhancers and promoters of target genes, but the molecular basis for cell-specific programs of repression is not known. more...
    Organism:
    Mus musculus
    Type:
    Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
    Platforms:
    GPL11002 GPL13112
    15 Samples
    Download data:
    GEO (BEDGRAPH, TXT), SRA SRP021025
    Series
    Accession:
    GSE45914
    ID:
    200045914
    2.

    Rev-erb(alpha) and (beta) Coordinately Protect the Circadian Clock and Normal Metabolic Function

    (Submitter supplied) We report the genomic regions enriched for Rev-erb(beta) binding in WT mouse liver, in addition to the false positive regions enriched by ChIP for Rev-erb(alpha) in Rev-erb(alpha) KO liver. In conjunction with previously published data for Rev-erb(alpha) in GSE26345 (GSM647029, GSM647033, and GSM647034), we report the common and subtype specific cistromes for Rev-erb using a quantitative analysis method.
    Organism:
    Mus musculus
    Type:
    Genome binding/occupancy profiling by high throughput sequencing; Third-party reanalysis
    Platforms:
    GPL11002 GPL13112
    3 Samples
    Download data:
    GEO (BED, TXT), SRA SRP011388
    Series
    Accession:
    GSE36375
    ID:
    200036375
    3.

    Diurnal changes of HDAC3, Rev-erbα, NCoR and Pol II recruitment to the mouse liver genome and of H3K9Ac

    (Submitter supplied) We reported a diurnal changes in the recruitment of HDAC3, Rev-erbα, NCoR and Pol II to the mouse liver genome as well as H3K9 acetylation in vivo at ZT10 and ZT22.
    Organism:
    Mus musculus
    Type:
    Genome binding/occupancy profiling by high throughput sequencing
    Platform:
    GPL9250
    18 Samples
    Download data:
    GEO (SAM), SRA SRP008783
    Series
    Accession:
    GSE26345
    ID:
    200026345
    4.

    Gene expression in mouse liver depleted of HDAC3

    (Submitter supplied) Liver-specific depletion of HDAC3 leads to liver steatosis (fatty liver), suggesting disregulation of lipid metabolism. This is correlated with changes in lipid metabolic gene expression. Livers depleted of HDAC3 were removed from 12 week old male HDAC3 fl/fl mice (loxP sites flanking exon 4 to 7 of the HDAC3 gene encoding the catalytic domain of HDAC3) one week after the injection of AAV2/8-Tbg-Cre virus. more...
    Organism:
    Mus musculus
    Type:
    Expression profiling by array
    Platform:
    GPL6246
    10 Samples
    Download data:
    GEO (CEL, CHP)
    Series
    Accession:
    GSE25937
    ID:
    200025937
    5.

    Integral roles for Rev-erb alpha and Rev-erb beta in the circadian clock function

    (Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
    Organism:
    Mus musculus
    Type:
    Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by array
    Platforms:
    GPL9250 GPL6885
    27 Samples
    Download data:
    GEO (BEDGRAPH, TXT)
    Series
    Accession:
    GSE34020
    ID:
    200034020
    6.

    Integral roles for Rev-erb alpha and Rev-erb beta in the circadian clock function [ChIP_seq]

    (Submitter supplied) The circadian clock acts at the genomic level to coordinate internal behavioral and physiologic rhythms via the CLOCK-BMAL transcriptional heterodimer. Although the nuclear receptors REV-ERBα and β have been proposed to contribute to clock function, their precise roles and importance remain unresolved. To establish their regulatory potential we generated comparative cistromes of both Rev-erb isoforms, which revealed shared recognition at over ~50% of their total sites and extensive overlap with the master clock regulator Bmal. more...
    Organism:
    Mus musculus
    Type:
    Genome binding/occupancy profiling by high throughput sequencing
    Platform:
    GPL9250
    3 Samples
    Download data:
    GEO (BEDGRAPH, TXT), SRA SRP009472
    Series
    Accession:
    GSE34019
    ID:
    200034019
    7.

    Integral roles for Rev-erb alpha and Rev-erb beta in the circadian clock function [Expression array]

    (Submitter supplied) The circadian clock acts at the genomic level to coordinate internal behavioral and physiologic rhythms via the CLOCK-BMAL transcriptional heterodimer. Although the nuclear receptors REV-ERBα and β have been proposed to contribute to clock function, their precise roles and importance remain unresolved. To establish their regulatory potential we generated comparative cistromes of both Rev-erb isoforms, which revealed shared recognition at over ~50% of their total sites and extensive overlap with the master clock regulator Bmal. more...
    Organism:
    Mus musculus
    Type:
    Expression profiling by array
    Platform:
    GPL6885
    24 Samples
    Download data:
    GEO (TXT)
    Series
    Accession:
    GSE34018
    ID:
    200034018
    8.

    Reprogramming Transcriptional Responses through Functionally-Distinct Classes of Enhancers in Prostate Cancer Cells

    (Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
    Organism:
    Homo sapiens
    Type:
    Expression profiling by array; Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
    Platforms:
    GPL9115 GPL6102
    42 Samples
    Download data:
    GEO (BED, BEDGRAPH, FA)
    Series
    Accession:
    GSE27824
    ID:
    200027824
    9.

    Reprogramming Transcriptional Responses through Functionally-Distinct Classes of Enhancers in Prostate Cancer Cells [ChIP-Seq, Gro-Seq]

    (Submitter supplied) Mammalian genomes are populated with thousands of transcriptional enhancers that orchestrate cell type-specific gene expression programs; however, the potential that there are pre-established enhancers in different functional classes that permit alternative signal-dependent transcriptional responses has remained unexplored. Here we present evidence that cell lineage-specific factors, such as FoxA1, can simultaneously facilitate and restrict key regulated transcription factors, exemplified by the androgen receptor (AR), acting at structurally- and functionally-distinct classes of pre-established enhancers, thus licensing specific signal-activated responses while restricting others. more...
    Organism:
    Homo sapiens
    Type:
    Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
    Platform:
    GPL9115
    30 Samples
    Download data:
    GEO (BED, BEDGRAPH, FA), SRA SRP005967
    Series
    Accession:
    GSE27823
    ID:
    200027823
    10.

    Reprogramming Transcriptional Responses through Functionally-Distinct Classes of Enhancers in Prostate Cancer Cells [gene expression]

    (Submitter supplied) Mammalian genomes are populated with thousands of transcriptional enhancers that orchestrate cell type-specific gene expression programs; however, the potential that there are pre-established enhancers in different functional classes that permit alternative signal-dependent transcriptional responses has remained unexplored. Here we present evidence that cell lineage-specific factors, such as FoxA1, can simultaneously facilitate and restrict key regulated transcription factors, exemplified by the androgen receptor (AR), acting at structurally- and functionally-distinct classes of pre-established enhancers, thus licensing specific signal-activated responses while restricting others. more...
    Organism:
    Homo sapiens
    Type:
    Expression profiling by array
    Platform:
    GPL6102
    12 Samples
    Download data:
    GEO (TXT)
    Series
    Accession:
    GSE27682
    ID:
    200027682
    11.

    Functional Importance of eRNAs for Estrogen-dependent Gene Transcriptional Activation

    (Submitter supplied) The functional importance of gene enhancers in regulated gene expression is well established. In addition to widespread transcription of long non-coding RNA (ncRNA) transcripts in mammalian cells, bidirectional ncRNAs referred to as eRNAs are present on enhancers. However, it has remained unclear whether these eRNAs are functional, or merely a reflection of enhancer activation. Here, we report that 17 β-estradiol (E2)-bound estrogen receptor alpha (ERα) on enhancers causes a global increase in eRNA transcription on enhancers adjacent to E2 upregulated coding genes. more...
    Organism:
    Homo sapiens
    Type:
    Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
    Platforms:
    GPL10999 GPL11154
    11 Samples
    Download data:
    GEO (BIGWIG), SRA SRP020561
    Series
    Accession:
    GSE45822
    ID:
    200045822
    12.

    Widespread transcription at neuronal activity-regulated enhancers

    (Submitter supplied) We used genome-wide sequencing methods to study stimulus-dependent enhancer function in neurons. We identified ~12,000 neuronal activity-regulated enhancers that are bound by the general transcriptional co-activator CBP in an activity-dependent manner. A function of CBP at enhancers may be to recruit RNA polymerase II (RNAPII), as we also observed activity-regulated RNAPII binding to thousands of enhancers. more...
    Organism:
    Mus musculus
    Type:
    Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
    Platform:
    GPL9318
    48 Samples
    Download data:
    GEO (BEDGRAPH, BW), SRA SRP002302
    Series
    Accession:
    GSE21161
    ID:
    200021161
    13.

    Enhancer Transcripts Mark Active Estrogen Receptor Binding Sites using GRO-seq

    (Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
    Organism:
    Homo sapiens
    Type:
    Expression profiling by high throughput sequencing
    Platform:
    GPL9052
    14 Samples
    Download data:
    GEO (BED)
    Series
    Accession:
    GSE43836
    ID:
    200043836
    14.

    Enhancer Transcripts Mark Active Estrogen Receptor Binding Sites

    (Submitter supplied) In this study, we used Global Run-On sequencing (GRO-seq), a method that assays the genome-wide location and orientation of all active RNA polymerases. We generated a global profile of active transcription at ERα binding sites in MCF-7 human breast cancer cells in response to short time course of E2 treatment. This method enabled us to detect active transcription at enhancers and define a class of primary transcripts transcribed uni- or bidirectionally from the ERα binding sites. more...
    Organism:
    Homo sapiens
    Type:
    Expression profiling by high throughput sequencing
    Platform:
    GPL9052
    6 Samples
    Download data:
    GEO (BED), SRA SRP018256
    Series
    Accession:
    GSE43835
    ID:
    200043835
    15.

    Dynamic chromatin connectivity maps reveal lineage specific regulation

    (Submitter supplied) Using genome-wide Chromatin Interaction Analysis with Paired-End-Tag sequencing, we mapped long-range chromatin interactions associated with RNA polymerase II in three different mouse cell lines and uncovered widespread promoter-centered interactions. These interactions further aggregated into higher-order clusters, in which proximal and distant genes are engaged through enhancer-promoter interactions. more...
    Organism:
    Mus musculus
    Type:
    Other
    Platform:
    GPL11002
    5 Samples
    Download data:
    GEO (MAP, TXT, XLS), SRA SRP018770
    Series
    Accession:
    GSE44067
    ID:
    200044067
    16.

    Remodeling of the enhancer landscape during macrophage activation is coupled to enhancer transcription

    (Submitter supplied) Recent studies suggest a hierarchical model in which lineage-determining factors act in a collaborative manner to select and prime cell-specific enhancers, thereby enabling signal-dependent transcription factors to bind and function in a cell type-specific manner. Consistent with this model, TLR4 signaling primarily regulates macrophage gene expression through a pre-existing enhancer landscape. However, TLR4 signaling also induces priming of ~3000 enhancer-like regions de novo, enabling visualization of intermediates in enhancer selection and activation. more...
    Organism:
    Mus musculus
    Type:
    Genome binding/occupancy profiling by high throughput sequencing; Other
    Platforms:
    GPL9250 GPL13112
    139 Samples
    Download data:
    GEO (BEDGRAPH, TXT), SRA SRP026695
    Series
    Accession:
    GSE48759
    ID:
    200048759
    17.

    The polyA+ transcriptomes of mouse embryonic stem cells and their derived neural precursors from strand-specific RNA-Seq

    (Submitter supplied) We have examined the nuclear (nuc) and cytoplasmic (cyt) polyA+ transcriptomes of undifferentiated mouse embryonic stem cells (un) and cells differentiated to neural precursors (d5) using strand-specific RNA-Seq. The 46C mouse embryonic stem cell line was used for this study.
    Organism:
    Mus musculus
    Type:
    Expression profiling by high throughput sequencing
    Platform:
    GPL9318
    11 Samples
    Download data:
    GEO (BED), SRA SRP013997
    Series
    Accession:
    GSE38990
    ID:
    200038990
    18.

    An atlas of active enhancers across human cell types and tissues

    (Submitter supplied) Sequencing of 5' ends of RNA molecules from control and exosome-depleted HeLa-S3 cells.
    Organism:
    Homo sapiens
    Type:
    Expression profiling by high throughput sequencing; Other
    Platform:
    GPL11154
    2 Samples
    Download data:
    GEO (BED), SRA SRP028815
    Series
    Accession:
    GSE49834
    ID:
    200049834
    19.

    An atlas of in vivo transcribed enhancers in human primary cells

    (Submitter supplied) Enhancers are powerful regulatory regions, important for development and the maintenance of differentiated cells and tissues. Here, we generate global maps for two enhancer-associated histone marks, H3K4me1 and H3K27ac for a number of major human blood cell types. This data was generated to show that capped RNAs transcribed bidirectionally can identify known and novel enhancers in vivo.
    Organism:
    Homo sapiens
    Type:
    Genome binding/occupancy profiling by high throughput sequencing
    Platform:
    GPL9052
    21 Samples
    Download data:
    GEO (BED), SRA SRP015454
    Series
    Accession:
    GSE40668
    ID:
    200040668
    20.

    Intragenic enhancers act as alternative promoters

    (Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
    Organism:
    Mus musculus
    Type:
    Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
    Platforms:
    GPL9250 GPL13112
    9 Samples
    Download data:
    GEO (BED, SAM)
    Series
    Accession:
    GSE27921
    ID:
    200027921

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