GEO DataSets

(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

(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

(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

(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

(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

(Submitter supplied) Histone variants complement and integrate histone post-translational modifications in regulating transcription. The histone variant macroH2A1 (mH2A1) is almost three times the size of its canonical H2A counterpart due to the presence of a ~25kDa evolutionarily conserved non-histone macro domain. Strikingly, mH2A1 can mediate both gene repression and activation. However, the molecular determinants conferring these alternative functions remain elusive. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing

Platforms:

GPL17021 GPL13112

41 Samples

Download data: BED, BW, TXT

(Submitter supplied) This experiment was conducted to identify novel MLL4 targets in skeletal muscle Enhancers play central role in controlling gene expression in time and space. Primed enhancers are marked by histone H3 lysine 4 (H3K4) mono/di-methylation (H3K4me1/2). Mixed-lineage leukemia 4 (MLL4/KMT2D) is an evolutionarily conserved H3K4me1/2 methyltransferase that is required for enhancer activation. Here, we identified the genome-wide MLL4 occupancy in mouse skeletal muscle by ChIP-seq coupled with RNA-seq analysis. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL17021

3 Samples

Download data: BEDGRAPH, XLS

(Submitter supplied) This experiment was conducted to identify mRNA transcripts alteration in skeletal muscle of MLL4SET muscle-specific knockout mice. Enhancers play central role in controlling gene expression in time and space. Primed enhancers are marked by histone H3 lysine 4 (H3K4) mono/di-methylation (H3K4me1/2). Mixed-lineage leukemia 4 (MLL4/KMT2D) is an evolutionarily conserved H3K4me1/2 methyltransferase that is required for enhancer activation. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21103

6 Samples

Download data: FPKM_TRACKING, XLSX

(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

(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

(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

(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

(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

(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

(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

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

synthetic construct; Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing; Other; Expression profiling by high throughput sequencing

Platforms:

GPL19057 GPL24247 GPL26526

82 Samples

Download data: BW, TXT

(Submitter supplied) Measurement the activity of candidate CSEs in aCMs and vCMs.

Organism:

Mus musculus; synthetic construct

Type:

Other

Platforms:

GPL24247 GPL26526

15 Samples

Download data: TXT

(Submitter supplied) Investigate the sequence features required for CSE activity and selectivity.

Organism:

Mus musculus; synthetic construct

Type:

Other

Platforms:

GPL24247 GPL26526

14 Samples

Download data: TXT

(Submitter supplied) Examination of chamber selective chromatin accessibility and investigate if chromatin accessibility regulates CSEs.

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL19057

4 Samples

Download data: BW

(Submitter supplied) To investigate the chamber selective transcriptional programs, we performed RNA-seq on purified cardiomyocytes. Totally we have 5 replicates for atrial cardiomyocytes and 5 replicates for ventricular cardiomyocytes.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

10 Samples

Download data: TXT