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Links from GEO DataSets

Items: 20

1.
Full record GDS5632

In vitro myoblast differentiation: time course

Analysis of myoblasts isolated from a 7 year-old male and cultured in low-serum medium to stimulate myogenic differentiation for up 15 days. Results provide insight into the molecular mechanisms underlying myogenic differentiation.
Organism:
Homo sapiens
Type:
Expression profiling by array, transformed count, 2 protocol, 4 time sets
Platform:
GPL570
Series:
GSE55034
4 Samples
Download data: CEL, CHP
2.

DNA methylation analysis during in vitro myogenic differentiation

(Submitter supplied) DNA methylation has been considered to play an important role in myogenic differentiation. In terminal differentiation of myoblasts, a chronological pattern of DNA methylation changes has been poorly understood. Using Infinium HumanMethylation450 BeadChips, we obtained and evaluated the genome-wide DNA methylation profiles of human myoblast differentiation in vitro.
Organism:
Homo sapiens
Type:
Methylation profiling by genome tiling array
Platform:
GPL13534
7 Samples
Download data: TXT
Series
Accession:
GSE55571
ID:
200055571
3.

DNA methylation and gene expression analysis during myogenic differentiation

(Submitter supplied) DNA methylation has been considered to play an important role during myogenic differentiation. In terminal differentiation of myoblasts, chronological alteration of DNA methylation status was poorly understood. Using Infinium HumanMethylation450 BeadChips, we validated genome wide DNA methylation profiles of human myoblast differentiation models. To investigate correlation between DNA methylation and gene expression, we also assessed gene expression of myoblasts with GeneChip Human Genome U133 Plus 2.0 array.
Organism:
Homo sapiens
Type:
Expression profiling by array
Dataset:
GDS5632
Platform:
GPL570
4 Samples
Download data: CEL, CHP
Series
Accession:
GSE55034
ID:
200055034
4.

Epigenetic analysis reveals the repressive function of MyoD during myogenic differentiation

(Submitter supplied) We identify a subset of highly expressed genes related to muscle development, which show static H3K4me2 enrichment over the gene body and H3K4me3 enrichment towards the gene body during myogenic differentiation. This study reveals that MyoD significantly binds to this particular subset of genes and further systematic analysis shows the repressive role of MyoD. Interestingly, MyoD binds and down-regulates Patz1 which is important for maintaining pluripotency. more...
Organism:
Mus musculus
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL13112
8 Samples
Download data: BED
Series
Accession:
GSE63716
ID:
200063716
5.

WGBS analysis of Landrance and Wuzhishan miniature pig

(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
Series
Accession:
GSE119459
ID:
200119459
6.

Functional consequences of DNA-methylation in response to regular exercise

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Mus musculus
Type:
Expression profiling by array; Methylation profiling by high throughput sequencing
Platforms:
GPL7202 GPL13112
18 Samples
Download data: TXT
Series
Accession:
GSE54278
ID:
200054278
7.

Genome-wide changes in DNA methylation in response to physical exercise

(Submitter supplied) Here we describe a genome-wide analysis of DNA-methylation in muscle of trained mice. In comparison to sedentary controls 2762 genes exhibited differentially methylated CpGs in their putative promoter regions. The majority of these genes were related to muscle growth and differentiation and a minor fraction involved in metabolic regulation. These findings suggest that DNA-methylation is involved in the regulation of muscle adaptation to regular exercise training.
Organism:
Mus musculus
Type:
Methylation profiling by high throughput sequencing
Platform:
GPL13112
6 Samples
Download data: TXT
Series
Accession:
GSE54277
ID:
200054277
8.

Transcriptional changes in skeletal muscle in response to 4 weeks of exercise training

(Submitter supplied) Consequence of physical exercise in skeletal muscle was investigated in C57BL/6 mice after 4 weeks of exercise training and compared to sedentary controls.
Organism:
Mus musculus
Type:
Expression profiling by array
Platform:
GPL7202
12 Samples
Download data: TXT
Series
Accession:
GSE54276
ID:
200054276
9.

Deconstruction of DNA methylation patterns during myogenesis reveals specific epigenetic events in the establishment of the skeletal muscle lineage

(Submitter supplied) Cellular differentiation involves widespread epigenetic reprogramming, including modulation of DNA methylation patterns. We have investigated DNA genome-wide methylation dynamics in embryonic stem cells, primary myoblasts, terminal differentiated myotubes and mature myofibers. About 1.000 differentially methylated regions (DMRs) have been indentified during muscle-lineage determination and terminal differentiation. more...
Organism:
Mus musculus
Type:
Methylation profiling by high throughput sequencing
Platform:
GPL9250
23 Samples
Download data: TAB
Series
Accession:
GSE65037
ID:
200065037
10.

Comparison of Genome-Wide Binding of MyoD in Normal Human Myogenic Cells and Rhabdomyosarcomas Identifies Regional and Local Suppression of Promyogenic Transcription Factors

(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
Platforms:
GPL10558 GPL10999
10 Samples
Download data: TXT
Series
Accession:
GSE50415
ID:
200050415
11.

Comparison of Genome-Wide Binding of MyoD in Normal Human Myogenic Cells and Rhabdomyosarcomas Identifies Regional and Local Suppression of Promyogenic Transcription Factors (MyoD ChIP-Seq profiling)

(Submitter supplied) Rhabdomyosarcoma is a pediatric tumor of skeletal muscle that expresses the myogenic basic helix-loop-helix protein MyoD but fails to undergo terminal differentiation. Prior work has determined that DNA binding by MyoD occurs in the tumor cells, but myogenic targets fail to activate. Using MyoD chromatin immunoprecipitation coupled to high-throughput sequencing and gene expression analysis in both primary human muscle cells and RD rhabdomyosarcoma cells, we demonstrate that MyoD binds in a similar genome-wide pattern in both tumor and normal cells but binds poorly at a subset of myogenic genes that fail to activate in the tumor cells. more...
Organism:
Homo sapiens
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL10999
4 Samples
Download data: TXT
Series
Accession:
GSE50413
ID:
200050413
12.

Comparison of Genome-Wide Binding of MyoD in Normal Human Myogenic Cells and Rhabdomyosarcomas Identifies Regional and Local Suppression of Promyogenic Transcription Factors (expression)

(Submitter supplied) Rhabdomyosarcoma is a pediatric tumor of skeletal muscle that expresses the myogenic basic helix-loop-helix protein MyoD but fails to undergo terminal differentiation. Prior work has determined that DNA binding by MyoD occurs in the tumor cells, but myogenic targets fail to activate. Using MyoD chromatin immunoprecipitation coupled to high-throughput sequencing and gene expression analysis in both primary human muscle cells and RD rhabdomyosarcoma cells, we demonstrate that MyoD binds in a similar genome-wide pattern in both tumor and normal cells but binds poorly at a subset of myogenic genes that fail to activate in the tumor cells. more...
Organism:
Homo sapiens
Type:
Expression profiling by array
Platform:
GPL10558
6 Samples
Download data: TXT
Series
Accession:
GSE50411
ID:
200050411
13.

Genome-wide maps of Twist2-binding, MyoD-binding and chromatin state in Twist2-overexpressing Twist2+ cells

(Submitter supplied) Integrated analysis of genome-wide ChIP-Seq and RNA-Seq data revealed the first dynamic chromatin and transcriptional landscape of Twist2 binding during myogenic differentiation. During differentiation, Twist2 competes with MyoD at shared DNA motifs to direct global gene transcription and repression of the myogenic program. Additionally, TWIST2 shapes the epigenetic landscape to drive chromatin opening at oncogenic loci and chromatin closing at myogenic loci. more...
Organism:
Mus musculus
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL19057
34 Samples
Download data: BIGWIG
Series
Accession:
GSE127998
ID:
200127998
14.

MicroRNA expression in bovine satellite cells at 6th day of in vitro differentiation - myotubes (Hereford & Limousin vs Holstein-Freisian cattle)

(Submitter supplied) miRNA profiling of bovine satellite cells (BSC) differentiated into myotubes (6th day of in vitro differentiation). BSC isolated from m. semitendinosus of beef (Hereford & Limousine) and dairy (Holstein-Friesian) cattle. Goal was to determine differences in miRNA expresion during in vitro myogenesis in beef vs dairy cattle used as a control.
Organism:
Bos taurus
Type:
Non-coding RNA profiling by array
Platform:
GPL19028
24 Samples
Download data: TXT
Series
Accession:
GSE73778
ID:
200073778
15.

MeDIP-on-chip and Pol-II ChIP-on-chip during C2C12 myogenic and BMP2-induced osteogenic differentiation

(Submitter supplied) Differentiation of pluripotent embryonic stem cells, via more restricted multipotent adult stem cells, towards the multitude of terminally differentiated, specialized cell types that make up the adult body is a multi-step process characterized by a progressive restriction of differentiation potential. Previous studies have demonstrated tissue-specific differences in DNA methylation patterns that might play a role in lineage restriction and tissue-specific gene expression. more...
Organism:
Mus musculus
Type:
Genome binding/occupancy profiling by genome tiling array; Methylation profiling by genome tiling array
Platform:
GPL5811
14 Samples
Download data: BAR, BED, CEL
Series
Accession:
GSE22077
ID:
200022077
16.

DNA methylation in progenitor cells

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Homo sapiens
Type:
Expression profiling by array; Methylation profiling by genome tiling array
Platforms:
GPL7408 GPL7363
23 Samples
Download data: PAIR
Series
Accession:
GSE19795
ID:
200019795
17.

DNA methylation in progenitor cells: MeDIP study

(Submitter supplied) We surveyed DNA methylation profiles of all human RefSeq promoters in relation to gene expression and differentiation in adipose tissue, bone marrow and muscle mesenchymal progenitors, as well as in bone marrow-derived hematopoietic progenitors. We unravel strongly overlapping DNA methylation profiles between adipose stem cells (ASCs), bone marrow mesenchymal stem cells (BMMSCs) and muscle progenitor cells (MPCs), while hematopoietic progenitor cells (HPCs) are more epigenetically distant from MSCs seen as a whole. more...
Organism:
Homo sapiens
Type:
Methylation profiling by genome tiling array
Platform:
GPL7408
12 Samples
Download data: PAIR
Series
Accession:
GSE19794
ID:
200019794
18.

DNA methylation in progenitor cells: expression study

(Submitter supplied) We surveyed DNA methylation profiles of all human RefSeq promoters in relation to gene expression and differentiation in adipose tissue, bone marrow and muscle mesenchymal progenitors, as well as in bone marrow-derived hematopoietic progenitors. We unravel strongly overlapping DNA methylation profiles between adipose stem cells (ASCs), bone marrow mesenchymal stem cells (BMMSCs) and muscle progenitor cells (MPCs), while hematopoietic progenitor cells (HPCs) are more epigenetically distant from MSCs seen as a whole. more...
Organism:
Homo sapiens
Type:
Expression profiling by array
Platform:
GPL7363
11 Samples
Download data: TXT
Series
Accession:
GSE19773
ID:
200019773
19.

Epigenetic environment of histone H3.3 on promoters revealed by integration of imaging, ChIP-chip, and MeDIP-chip data

(Submitter supplied) Epigenetic environment of histone H3.3 on promoters revealed by integration of imaging and genome-scale chromatin and methyl-DNA immunoprecipitation information. Chromatin regions with different transcriptional outputs are distinguished by the deposition of histone variants. Histone H3.3 is incorporated into chromatin in a replication-independent manner; yet the relationship between H3.3 deposition, chromatin environment is incompletely understood. more...
Organism:
Homo sapiens
Type:
Genome binding/occupancy profiling by genome tiling array; Methylation profiling by genome tiling array; Expression profiling by array
Platforms:
GPL7408 GPL7363
18 Samples
Download data: PAIR, TXT
Series
Accession:
GSE17053
ID:
200017053
20.

Analysis of the common and respective roles of CBP and p300 co-activators in human primary myoblast differentiation.

(Submitter supplied) We used Affymetrix microarrays to detail the global programme of gene expression regulated by CBP and/or p300 during human primary myoblast differentiation.
Organism:
Homo sapiens
Type:
Expression profiling by array
Platform:
GPL16686
21 Samples
Download data: CEL
Series
Accession:
GSE94006
ID:
200094006
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