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Links from GEO DataSets

Items: 20

1.

The glucocorticoid receptor coordinates myofiber-selective transcriptional networks

(Submitter supplied) Muscle fibers have the capacity to modulate their size in response to hormones, including glucocorticoids. Their effects are mediated by the ubiquitously expressed glucocorticoid receptor (GR). However, GR-mediated transcriptional regulation in skeletal muscle at physiological glucocorticoid levels remains elusive. Our study reveals an increased expression of numerous anabolic factors in GR-deficient myofibers, and a reduced expression of antianabolic factors, leading to fiber hypertrophy. more...
Organism:
Mus musculus
Type:
Expression profiling by array
Platform:
GPL1261
8 Samples
Download data: CEL
Series
Accession:
GSE144228
ID:
200144228
2.

Genome-wide GR occupancy and chromatin landscape in skeletal muscles.

(Submitter supplied) Purpose: The aim of this study is to identify the GR genome binding profile as well as that of Pol II, H3K27ac, H3K4me1, H3K4me3 and Ctcf in skeletal muscles. Methods: Libraries were prepared from immunoprecipitated DNA according to standard methods. ChIP-seq libraries were sequenced using a HiSeq 4000 (Illumina) and mapped to the mm10 reference genome using bowtie 2 (Langmead et al., 2009). Data were further analysed using the peak finding algorithm MACS 2 (Zhang et al., 2008) using input as control. more...
Organism:
Mus musculus
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL21103
5 Samples
Download data: BED, WIG
Series
Accession:
GSE164543
ID:
200164543
3.

RNA-seq muscle

(Submitter supplied) Identify the genes modulated by Glucocorticoid Receptor.
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL21103
8 Samples
Download data: XLSX
Series
Accession:
GSE151791
ID:
200151791
4.

ATAC-seq in mouse skeletal muscle

(Submitter supplied) We perfomed ATAC-seq on C57/Bl6 mouse skeletal muscle nuclear extracts
Organism:
Mus musculus
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL21103
1 Sample
Download data: BED, BW, TXT
Series
Accession:
GSE151790
ID:
200151790
5.

The glucocorticoid receptor coordinates myofiber-selective transcriptional networks

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Other
Platform:
GPL21103
22 Samples
Download data: BED, TXT, XLSX
Series
Accession:
GSE142796
ID:
200142796
6.

Genome-wide GR occupancy and chromatin landscape in skeletal muscles

(Submitter supplied) Purpose: The aim of this study is to identify the GR genome binding profile as well as that of Pol II, H3K27ac, H3K4me1, H3K4me3 and Ctcf in skeletal muscles. Methods: Libraries were prepared from immunoprecipitated DNA according to standard methods. ChIP-seq libraries were sequenced using a HiSeq 4000 (Illumina) and mapped to the mm10 reference genome using bowtie 2 (Langmead et al., 2009). Data were further analysed using the peak finding algorithm MACS 2 (Zhang et al., 2008) using input as control. more...
Organism:
Mus musculus
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL21103
8 Samples
Download data: BED, WIG, XLSX
Series
Accession:
GSE142518
ID:
200142518
7.

4C-seq experiment on mouse skeletal muscle and DP thymocytes

(Submitter supplied) Purpose: The aim of this study is to investigate enhancer promoter interactions in skeletal muscle Methods: 50 ng of purified DNA were used as a template for PCR with bait-specific primers (Table S5) containing Illumina adapter termini. PCR reactions were pooled and, after primer removal with 1.8x AMPure XP beads, DNA was sequenced with the HiSeq 4000 (Illumina), as single-end 50 bp reads. Sequences were trimmed to remove primer and bait fragment sequence with the sabre tool (https://github.com/najoshi/sabre), mapped to the genome with Bowtie and converted to restriction fragment space as in van de Werken et al., 2012 (van de Werken et al., 2012). more...
Organism:
Mus musculus
Type:
Other
Platform:
GPL21103
5 Samples
Download data: TXT
8.

Genome-wide identification of enhancers in skeletal muscle

(Submitter supplied) In an effort to identify the compendium of regulatory elements that govern myogenic differentiation, we generated chromatin state maps based on the recruitment of factors (p300 and PolII) and histone modifications (H3K4me1, H3K27ac) that typify enhancers in myoblasts and myotubes. We found a remarkable concordance between the location of these newly defined, active enhancers and MyoD1 binding events. more...
Organism:
Mus musculus
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platforms:
GPL9250 GPL13112
14 Samples
Download data: BED, TXT
Series
Accession:
GSE37525
ID:
200037525
9.

Conventional and pioneer modes of glucocorticoid receptor interaction with enhancer chromatin in vivo

(Submitter supplied) Here we show how chromatin structure is involved in glucocorticoid receptor (GR) binding in a mouse mammary cell line. We show that GR binds to accessible chromatin sites that are either nucleosome-free or contain a nucleosome.
Organism:
Mus musculus
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL13112
12 Samples
Download data: TDF
Series
Accession:
GSE94562
ID:
200094562
10.

Conventional and pioneer modes of glucocorticoid receptor interaction with enhancer chromatin in vivo

(Submitter supplied) Glucocorticoid hormone plays a major role in metabolism and many related diseases. The hormone-bound glucocorticoid receptor (GR) binds to a specific set of enhancers in different cell types, resulting in unique patterns of gene expression. GR-responsive enhancers have an accessible chromatin structure prior to hormone treatment (“pre-programmed”), whereas unresponsive enhancers specific to other cell types are inaccessible and inactive. more...
Organism:
Mus musculus
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL13112
4 Samples
Download data: TDF
Series
Accession:
GSE92505
ID:
200092505
11.

Enhancer Profiling Reveals Regulators of Skeletal Muscle Identity and Reprogramming [ATAC-seq]

(Submitter supplied) Chromatin immunoprecipitation sequencing of H3K4me2, H3K27ac as well as, ATACseq and RNA-seq reveals regulatory landscapes across different muscle groups, as well as in response to chronic exercise or muscle PGC1a overexpression. This work defines the unique enhancer repetoire of skeletal muscle in vivo and reveals that highly divergent exercise-induced or PGC1a-driven epigenomic programs direct partially convergent transcriptional networks.
Organism:
Mus musculus
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL19057
4 Samples
Download data: BEDGRAPH, TXT
Series
Accession:
GSE134962
ID:
200134962
12.

Enhancer Profiling Reveals Regulators of Skeletal Muscle Identity and Reprogramming [ChIP-Seq]

(Submitter supplied) Chromatin immunoprecipitation sequencing of H3K4me2, H3K27ac as well as, ATACseq and RNA-seq reveals regulatory landscapes across different muscle groups, as well as in response to chronic exercise or muscle PGC1a overexpression. This work defines the unique enhancer repetoire of skeletal muscle in vivo and reveals that highly divergent exercise-induced or PGC1a-driven epigenomic programs direct partially convergent transcriptional networks.
Organism:
Mus musculus
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL19057
6 Samples
Download data: TXT
Series
Accession:
GSE131538
ID:
200131538
13.

Enhancer Profiling Reveals Regulators of Skeletal Muscle Identity and Reprogramming

(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
Platform:
GPL19057
87 Samples
Download data: BEDGRAPH, TXT
Series
Accession:
GSE123879
ID:
200123879
14.

Enhancer Profiling Reveals Regulators of Skeletal Muscle Identity and Reprogramming [RNA-seq]

(Submitter supplied) Chromatin immunoprecipitation sequencing of H3K4me2, H3K27ac as well as, ATACseq and RNA-seq reveals regulatory landscapes across different muscle groups, as well as in response to chronic exercise or muscle PGC1a overexpression. This work defines the unique enhancer repetoire of skeletal muscle in vivo and reveals that highly divergent exercise-induced or PGC1a-driven epigenomic programs direct partially convergent transcriptional networks.
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL19057
15 Samples
Download data: BEDGRAPH, XLSX
Series
Accession:
GSE123878
ID:
200123878
15.

Enhancer Profiling Reveals Regulators of Skeletal Muscle Identity and Reprogramming [ChIP-seq, ATAC-seq]

(Submitter supplied) Chromatin immunoprecipitation sequencing of H3K4me2, H3K27ac as well as, ATACseq and RNA-seq reveals regulatory landscapes across different muscle groups, as well as in response to chronic exercise or muscle PGC1a overexpression. This work defines the unique enhancer repetoire of skeletal muscle in vivo and reveals that highly divergent exercise-induced or PGC1a-driven epigenomic programs direct partially convergent transcriptional networks.
Organism:
Mus musculus
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL19057
62 Samples
Download data: BED, BEDGRAPH, TXT
Series
Accession:
GSE123877
ID:
200123877
16.

Characterization of chromatin and gene expression changes during fasting in mouse liver

(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:
GPL19057 GPL13112
50 Samples
Download data: BEDGRAPH, CSV, FPKM_TRACKING
Series
Accession:
GSE72087
ID:
200072087
17.

Characterization of chromatin and gene expression changes during fasting in mouse liver [RNA-Seq]

(Submitter supplied) During fasting the liver supplies the organism’s energy demands by producing glucose and ketones. Fuel production during fasting is temporally organized whereby glucose serves as the major fuel produced in short-term fasting while ketones are produced in longer fasts as gluconeogenic precursors deplete1. However, the regulatory process dictating this temporally-organized metabolic output is unexplored. more...
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL13112
6 Samples
Download data: FPKM_TRACKING
Series
Accession:
GSE72086
ID:
200072086
18.

Characterization of chromatin and gene expression changes during fasting in mouse liver [Dnase-Seq]

(Submitter supplied) During fasting the liver supplies the organism’s energy demands by producing glucose and ketones. Fuel production during fasting is temporally organized whereby glucose serves as the major fuel produced in short-term fasting while ketones are produced in longer fasts as gluconeogenic precursors deplete1. However, the regulatory process dictating this temporally-organized metabolic output is unexplored. more...
Organism:
Mus musculus
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL13112
6 Samples
Download data: BEDGRAPH, CSV
Series
Accession:
GSE72085
ID:
200072085
19.

Characterization of chromatin and gene expression changes during fasting in mouse liver [ChIP-Seq]

(Submitter supplied) During fasting transcriptional programs lead to glucose and ketone production. The major TFs, their crosstalk and the enhancers driving it are unknown. We show that fasting massively reorganizes liver chromatin to expose 'fasting enhancers'. By tracking TF footprints, we implicated the major TFs regulating fuel production by two modules. The ketogenic module is executed by a temporally-organized TF cascade. more...
Organism:
Mus musculus
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platforms:
GPL19057 GPL13112
38 Samples
Download data: BEDGRAPH, CSV
Series
Accession:
GSE72084
ID:
200072084
20.

GR and LSD1/KDM1A-targeted gene activation requires selective H3K4me2 demethylation at enhancers

(Submitter supplied) KDM1A-mediated H3K4 demethylation is a well-established mechanism underlying transcriptional gene repression, but its role in gene activation is less clear. Here we report a critical function and novel mechanism of action of KDM1A in glucocorticoid receptor (GR)-mediated gene transcription. Biochemical purification of the nuclear GR complex revealed KDM1A as an integral component. In cell-free assays, GR modulates KDM1A-catalyzed H3K4 progressive demethylation by limiting loss of H3K4me1. more...
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms:
GPL20795 GPL16791
40 Samples
Download data: BEDGRAPH, CSV
Series
Accession:
GSE108588
ID:
200108588
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