GEO DataSets

(Submitter supplied) Evidence of widespread transcription at active enhancers became apparent. However, our understanding about the functions of enhancer RNAs (eRNAs) and their mechanistic roles remains incomplete. Here, we study eRNA regulation and function using skeletal myoblast differentiation as a paradigm. We provide a panoramic view of enhancer transcription and uncover reprogramming in enhancer transcription occurring during myogenic differentiation. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL13112 GPL18480

13 Samples

Download data: BED, BW, TXT

(Submitter supplied) Evidence of widespread transcription at active enhancers became apparent. However, our understanding about the functions of enhancer RNAs (eRNAs) and their mechanistic roles remains incomplete. Here, we study eRNA regulation and function using skeletal myoblast differentiation as a paradigm. We provide a panoramic view of enhancer transcription and uncover reprogramming in enhancer transcription occurring during myogenic differentiation. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL18480 GPL13112

4 Samples

Download data: TXT

(Submitter supplied) Evidence of widespread transcription at active enhancers became apparent. However, our understanding about the functions of enhancer RNAs (eRNAs) and their mechanistic roles remains incomplete. Here, we study eRNA regulation and function using skeletal myoblast differentiation as a paradigm. We provide a panoramic view of enhancer transcription and uncover reprogramming in enhancer transcription occurring during myogenic differentiation. more...

Organism:

Mus musculus

Type:

Other

Platform:

GPL18480

8 Samples

Download data: BW

(Submitter supplied) Evidence of widespread transcription at active enhancers became apparent. However, our understanding about the functions of enhancer RNAs (eRNAs) and their mechanistic roles remains incomplete. Here, we study eRNA regulation and function using skeletal myoblast differentiation as a paradigm. We provide a panoramic view of enhancer transcription and uncover reprogramming in enhancer transcription occurring during myogenic differentiation. more...

Organism:

Mus musculus

Type:

Other

Platform:

GPL18480

1 Sample

Download data: BED

(Submitter supplied) Gene expression profiling in differentiating C2C12 cells comparing control cells and MUNC-deprived cells

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL6096

4 Samples

Download data: CEL

(Submitter supplied) To check global changes of genes expression correlating with induction of MUNC, we stably overexpressed MUNC in WT cells and in MYOD KO cells. We compared transcriptomes of control cells and cells overexpressing MUNC and distinguished genes that are differentially expressed in different conditions

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

16 Samples

Download data: TSV

(Submitter supplied) Super-enhancers (SEs) are cis-regulatory elements enriching lineage specific key transcription factors (TFs) to form hotspots. A paucity of identification and functional dissection promoted us to investigate SEs during myoblast differentiation. ChIP-seq analysis of histone marks leads to the uncovering of SEs which remodel progressively during the course of differentiation. Further analyses of TF ChIP-seq enable the definition of SE hotspots co-bound by the master TF, MyoD and other TFs, among which we perform in-depth dissection for MyoD/FoxO3 interaction in driving the hotspots formation and SE activation.

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL11002

2 Samples

Download data: BED

(Submitter supplied) Super-enhancers (SEs) are cis-regulatory elements enriching lineage specific key transcription factors (TFs) to form hotspots. A paucity of identification and functional dissection promoted us to investigate SEs during myoblast differentiation. ChIP-seq analysis of histone marks leads to the uncovering of SEs which remodel progressively during the course of differentiation. Further analyses of TF ChIP-seq enable the definition of SE hotspots co-bound by the master TF, MyoD and other TFs, among which we perform in-depth dissection for MyoD/FoxO3 interaction in driving the hotspots formation and SE activation.

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL18480 GPL19057

13 Samples

Download data: BED

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

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL26167 GPL24676

13 Samples

Download data: GTF, TXT

(Submitter supplied) We identified a novel muscle-specific lncRNA, lncFAM71E1-2:2 (lncFAM), which increased robustly during early human myogenesis. Overexpression of lncFAM promoted differentiation of human myoblasts into myotubes, while silencing lncFAM suppressed this process. A nucleus-resident lncRNA, lncFAMwas studied using chromatin isolation by RNA purification followed by mass spectrometry (ChIRP-ms) analysis to identify the molecular mechanisms whereby it might promote myogenesis. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26167

1 Sample

Download data: GTF

(Submitter supplied) We identified a novel muscle-specific lncRNA, lncFAM71E1-2:2 (lncFAM), which increased robustly during early human myogenesis. Overexpression of lncFAM promoted differentiation of human myoblasts into myotubes, while silencing lncFAM suppressed this process. A nucleus-resident lncRNA, lncFAM was studied using chromatin isolation by RNA purification followed by mass spectrometry (ChIRP-ms) analysis to identify the molecular mechanisms whereby it might promote myogenesis. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

12 Samples

Download data: TXT

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

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL24676 GPL16791

18 Samples

Download data: TXT

(Submitter supplied) The goals of this study are to compare differentially expressed RNAs during OIP5-AS1:MIR-7 TSB treated myoblasts and control myoblasts during myogenesis and further investigate functional regulatory network of those RNAs in myogenesis in vitro and in vivo.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

12 Samples

Download data: TXT

(Submitter supplied) The goals of this study are to compare differentially expressed RNAs during human myogenesis and further investigate functional regulatory network of those RNAs in myogenesis in vitro and in vivo.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

6 Samples

Download data: TXT

(Submitter supplied) In skeletal myogenesis, the transcription factor MyoD, activates distinct transcriptional programs in progenitors compared to terminally differentiated cells. Using ChIP-seq and gene expression analyses, we show that in primary myoblasts, Snai1/2-HDAC1/2 repressive complex bind and exclude MyoD from its targets. Notably, Snail binds E-box motifs that are G/C-rich in their central dinucleotides, and such sites are almost exclusively associated with genes expressed during differentiation. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11002

4 Samples

Download data: TXT

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

Organism:

Mus musculus

Type:

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

Platforms:

GPL11002 GPL9250 GPL6246

27 Samples

Download data: BW, CEL, TXT

(Submitter supplied) In skeletal myogenesis, the transcription factor MyoD activates distinct transcriptional programs in progenitors compared to terminally differentiated cells. Using ChIP-seq and gene expression analyses, we show that in primary myoblasts, Snail-HDAC1/2 repressive complex bind and exclude MyoD from its targets. Notably, Snail binds E-box motifs that are G/C-rich in their central dinucleotides, and such sites are almost exclusively associated with genes expressed during differentiation. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL9250 GPL11002

14 Samples

Download data: BW, TXT

(Submitter supplied) In skeletal myogenesis, the transcription factor MyoD activates distinct transcriptional programs in progenitors compared to terminally differentiated cells. Using ChIP-seq and gene expression analyses, we show that in primary myoblasts, Snail-HDAC1/2 repressive complex bind and exclude MyoD from its targets. Notably, Snail binds E-box motifs that are G/C-rich in their central dinucleotides, and such sites are almost exclusively associated with genes expressed during differentiation. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL6246

9 Samples

Download data: CEL

(Submitter supplied) Transcription factors and DNA regulatory binding motifs are fundamental components of the gene regulatory network (GRN). Here, by using genome-wide occupancy profiling of master regulators of MyoGenesis (MyoD and MyoGenin), we show their extensive occupancy in the extragenic enhancer regions coinciding with RNA synthesis (i.e. eRNA). In particular, multiple regions coding for eRNAs were observed within regulatory region of MYOD1, including previously characterized Distal Regulatory Regions (DRR) and Core Enhancer (CE). more...

Organism:

Mus musculus

Type:

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

Platforms:

GPL11002 GPL13112

11 Samples

Download data: BED, BIGWIG, TXT, WIG

(Submitter supplied) Here, we performed the first whole-genome bisulfite sequencing (WGBS) of longissimus dorsi muscle (LDM) from Landrace (LR) and Wuzhishan (WZS) miniature pig during early embryonic stages (18, 21 and 28 dpc (days post coitum)).

Organism:

Sus scrofa

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL9126

6 Samples

Download data: TAR