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Links from GEO DataSets

Items: 20

1.

Gene expression from Prep1-ablated mice

(Submitter supplied) The homeodomain transcription factor Prep1 was previously shown to regulate insulin sensitivity. Our aim was to study the specific role of Prep1 for the regulation of energy metabolism in skeletal muscle. Muscle specific ablation of Prep1 resulted in increased expression of respiratory chain subunits. This finding was consistent with an increase in mitochondrial enzyme activity without affecting mitochondrial volume fraction as assessed by electron microscopy. more...
Organism:
Mus musculus
Type:
Expression profiling by array
Platform:
GPL7202
8 Samples
Download data: TXT
Series
Accession:
GSE52424
ID:
200052424
2.

Progressive loss of PGC-1alpha expression in aging muscle potentiates glucose intolerance and systemic inflammation

(Submitter supplied) Decreased mitochondrial mass and function in muscle of diabetic patients is associated with low PGC-1alpha, a transcriptional coactivator of the mitochondrial gene program. To investigate whether reduced PGC-1alpha and oxidative capacity in muscle directly contributes to age-related glucose intolerance, we compared the genetic signatures and metabolic profiles of aging mice lacking muscle PGC-1alpha. more...
Organism:
Mus musculus
Type:
Expression profiling by array
Dataset:
GDS4904
Platform:
GPL1261
12 Samples
Download data: CEL
Series
Accession:
GSE52550
ID:
200052550
3.
Full record GDS4904

Peroxisome proliferator-γ coactivator-1α deficiency effect on aged gastrocnemius muscle

Analysis of muscle from aged animals with muscle-specific Pgc-1α depletion. PGC-1alpha is a transcriptional coactivator of the mitochondrial gene program. Results provide insight into the role of Pgc-1α in the glucose intolerance and chronic systemic inflammation associated with aging.
Organism:
Mus musculus
Type:
Expression profiling by array, transformed count, 2 age, 2 genotype/variation sets
Platform:
GPL1261
Series:
GSE52550
12 Samples
Download data: CEL
4.

A PGC-1alpha-dependent decrease in mitochondrial oxidative metabolism in muscle of humans with inherited insulin resistance

(Submitter supplied) We used microarrays to assess gene expression profiling of 6 patients with a mutation (Arg1174Gln) in the tyrosine kinase domain of the insulin receptor gene (INSR) and 10 matched healthy controls
Organism:
Homo sapiens
Type:
Expression profiling by array
Dataset:
GDS4897
Platform:
GPL571
16 Samples
Download data: CEL
Series
Accession:
GSE36297
ID:
200036297
5.
Full record GDS4897

Skeletal muscle of patients with inherited insulin resistance

Analysis of muscle from patients with a mutation (Arg1174Gln) in the tyrosine kinase domain of the insulin receptor gene (INSR). This mutation is associated with inherited insulin resistance. Results provide insight into molecular mechanisms underlying insulin resistance in skeletal muscle.
Organism:
Homo sapiens
Type:
Expression profiling by array, count, 2 genotype/variation sets
Platform:
GPL571
Series:
GSE36297
16 Samples
Download data: CEL
DataSet
Accession:
GDS4897
ID:
4897
6.

Effects of a 8-week training on human skeletal muscle

(Submitter supplied) Context: Exercise training is a plausible model for identification of molecular mechanisms that cause metabolic-related changes in human skeletal muscle. Objective: The goal was to explore the molecular basis of the adaptation of skeletal muscle to exercise training. Design and Intervention: Obese male subjects were subjected to an individualized supervised training program targeted in order to optimize lipid oxidation during 8 weeks. more...
Organism:
Homo sapiens
Type:
Expression profiling by array
Platform:
GPL16022
16 Samples
Download data: GPR
Series
Accession:
GSE40551
ID:
200040551
7.

mTOR pathway controls mitochondrial gene expression and respiration through the YY1/PGC-1alpha transcriptional complex

(Submitter supplied) Mitochondrial oxidative function is tightly controlled to maintain energy homeostasis in response to nutrient and hormonal signals. An important cellular component in the energy sensing response is the target of rapamycin (TOR) kinase pathway; however whether and how mTOR controls mitochondrial oxidative activity is unknown. Here, we show that mTOR kinase activity stimulates mitochondrial gene expression and oxidative function. more...
Organism:
Mus musculus
Type:
Expression profiling by array
Platform:
GPL1261
12 Samples
Download data: CEL
Series
Accession:
GSE5332
ID:
200005332
8.

Impact of endurance training in MHC-I over-expressed Mice

(Submitter supplied) Myosine heavy chain I was overexpressed in mouse skeletal muscle. The transgenic mice, as well as the wild type mice, were endurance trained on treadmill for 5 days/week over 8 weeks at 80% peak aerobic capacity in comparison with untrained mice. The gene expression profiles of the skeletal muscles from wild-type trained (WTT) and untrained (WTUT), and transgenic trained (TGT) and untrained (TGUT) were measured using Affymetrix Mouse430A 2.0 GeneChips. more...
Organism:
Mus musculus
Type:
Expression profiling by array
Platform:
GPL1261
20 Samples
Download data
Series
Accession:
GSE5297
ID:
200005297
9.

Expression data from mouse skeletal muscle

(Submitter supplied) We generated skeletal muscle-specific knockout mice lacking the transcription factor Yin Yang 1 (YY1) and analyzed expression patterns in the skeletal muscle these mice. We used microarrays to detail the global programme of gene expression regulated by YY1.
Organism:
Mus musculus
Type:
Expression profiling by array
Dataset:
GDS4856
Platform:
GPL8321
7 Samples
Download data: CEL
Series
Accession:
GSE39009
ID:
200039009
10.
Full record GDS4856

Transcription factor Yin Yang 1 deficiency effect on the skeletal muscle

Analysis of the soleus muscles of transcription factor Yin Yang 1 (YY1) deficient animals. Many nuclear genes encoding mitochondrial proteins contain binding sites for YY1 in their proximal promoters. Results provide insight into the role of YY1 in mitochondrial function.
Organism:
Mus musculus
Type:
Expression profiling by array, count, 2 genotype/variation sets
Platform:
GPL8321
Series:
GSE39009
7 Samples
Download data: CEL
11.

Gene expression in human healthy control and ISCU myopathy patient muscle biopsies

(Submitter supplied) We performed microarray analysis on ISCU myopathy patient muscle biopsies to identify transcriptional modulation of pathways involved in the cellular response to Fe-S cluster deficiency.
Organism:
Homo sapiens
Type:
Expression profiling by array
Dataset:
GDS4960
Platform:
GPL570
8 Samples
Download data: CEL
Series
Accession:
GSE48574
ID:
200048574
12.
Full record GDS4960

ISCU myopathy

Analyis of vastus lateralis muscles of patients with iron-sulfur cluster scaffold homolog (ISCU) myopathy. ISCU is a rare autosomal recessive Fe-S cluster deficiency syndrome characterized by life-long exercise intolerance. Results provide insight into the molecular pathophysiology of ISCU myopathy.
Organism:
Homo sapiens
Type:
Expression profiling by array, transformed count, 2 disease state sets
Platform:
GPL570
Series:
GSE48574
8 Samples
Download data: CEL
13.

Whole cell mRNA expression profiling in control and complex I deficient patient fibroblasts incubated with DMSO, AICAR, chloramphenicol, and resveratrol

(Submitter supplied) Background: Transcription control of mitochondrial metabolism is essential for cellular function. A better understanding of this process will aid the elucidation of mitochondrial disorders, in particular of the many genetically unsolved cases of oxidative phosphorylation (OXPHOS) deficiency. Yet, to date only few studies have investigated nuclear gene regulation in the context of OXPHOS deficiency. In this study, we combined RNA sequencing of human complex I-deficient patient cells across 32 conditions of perturbed mitochondrial metabolism, with a comprehensive analysis of gene expression patterns, co-expression calculations and transcription factor binding sites. Results: Our analysis shows that OXPHOS genes have a significantly higher co-expression with each other than with other genes, including mitochondrial genes. We found no evidence for complex-specific mRNA expression regulation in the tested cell types and conditions: subunits of different OXPHOS complexes are similarly (co-)expressed and regulated by a common set of transcription factors. However, we did observe significant differences between the expression of OXPHOS complex subunits compared to assembly factors, suggesting divergent transcription programs. Furthermore, complex I co-expression calculations identified 684 genes with a likely role in OXPHOS biogenesis and function. Analysis of evolutionarily conserved transcription factor binding sites in the promoters of these genes revealed almost all known OXPHOS regulators (including GABP, NRF1/2, SP1, YY1, E-box factors) and a set of six yet uncharacterized candidate transcription factors (ELK1, KLF7, SP4, EHF, ZNF143, and EL2). Conclusions: OXPHOS genes share an expression program distinct from other mitochondrial genes, indicative of targeted regulation of this mitochondrial sub-process. Within the subset of OXPHOS genes we established a difference in expression between subunits and assembly factors. Most transcription regulators of genes that co-express with complex I are well-established factors for OXPHOS biogenesis. For the remaining six factors we here suggest for the first time a link with transcription regulation in OXPHOS deficiency.
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platform:
GPL11154
32 Samples
Download data: RPKM
Series
Accession:
GSE65634
ID:
200065634
14.

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
15.

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
16.

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
17.

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
18.

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
19.

ChIP-seq and RNA-seq analyses identify Wnt and Fgf signaling pathways as Prep1 targets in mouse embryonic stem cells

(Submitter supplied) The Prep1 (Pknox1) homeodomain transcription factor is essential at multiple stages of embryo development. In the E11.5 embryo trunk, we previously estimated that Prep1 binds about 3,300 genomic sites at a highly specific decameric consensus sequence, mainly governing basal cellular functions. We now show that in embryonic stem (ES) cells Prep1 binding pattern only partly overlaps that of the embryo trunk, with about 2,000 novel sites, highlighting a change of targets between embryonic differentiated v. more...
Organism:
Mus musculus
Type:
Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platform:
GPL9250
4 Samples
Download data: BED, RPKM
Series
Accession:
GSE63282
ID:
200063282
20.

Skeletal muscle transcriptome in ICU patients suffering from sepsis induced multiple organ failure

(Submitter supplied) Septic patients treated in the intensive care unit (ICU) often develop multiple organ failure including persistent skeletal muscle dysfunction which results in the patient’s protracted recovery process. We have demonstrated that muscle mitochondrial enzyme activities are impaired in septic ICU patients resulting in decreased cellular energy which will interfere with muscle function and metabolism. Here we use detailed phenotyping and genomics to elucidate mechanisms leading to these impairments. more...
Organism:
Homo sapiens
Type:
Expression profiling by array
Dataset:
GDS3463
Platform:
GPL570
21 Samples
Download data: CEL
Series
Accession:
GSE13205
ID:
200013205
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