GEO DataSets

(Submitter supplied) Male and female 2- and 3-years old brown bear from the region of Tackasen (Sweden) were captured in summer and winter. Muscle biopsies from vastus lateralis were collected in february (hibernation state) and june (active period). Total RNA were extracted from muscle tissue and full transcriptome analysis (RNA Seq) were performed. Statistical analysis were performed to winter versus summer comparison from matched paired samples

Organism:

Ursus arctos

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28129

12 Samples

Download data: TXT

(Submitter supplied) Hibernation is energy saving adaptation involving suppression of activity to survive in highly seasonal environments. Immobility and disuse generate muscle loss in most mammalian species. In contrast to other mammals, bears and ground squirrels demonstrate limited muscle atrophy over the physical inactivity of winter hibernation. This suggests that hibernating mammals have adaptive mechanisms to prevent disuse muscle atrophy. more...

Organism:

Urocitellus parryii

Type:

Expression profiling by array

Platform:

GPL15674

19 Samples

Download data: TXT

(Submitter supplied) Hibernation is energy saving adaptation involving suppression of activity to survive in highly seasonal environments. Immobility and disuse generate muscle loss in most mammalian species. In contrast to other mammals, bears and ground squirrels demonstrate limited muscle atrophy over the physical inactivity of winter hibernation. This suggests that hibernating mammals have adaptive mechanisms to prevent disuse muscle atrophy. more...

Organism:

Ursus americanus

Type:

Expression profiling by array

Platform:

GPL13263

12 Samples

Download data: TXT

(Submitter supplied) Physical inactivity reduces mechanical load on the skeleton, which leads to losses of bone mass and strength in non hibernating mammalian species. Although bears are largely inactive during hibernation, they show no loss in bone mass and strength. To obtain insight into molecular mechanisms preventing disuse bone loss, we conducted a large-scale screen of transcriptional changes in trabecular bone comparing winter hibernating and summer non hibernating black bears using a custom 12,800 probe cDNA microarray. more...

Organism:

Ursus americanus

Type:

Expression profiling by array

Platforms:

GPL8249 GPL13263

24 Samples

Download data: TXT

(Submitter supplied) To identify atrophy genes directly targeted by Bcl-3 transactivator at a genome wide level, we performed whole transcript expression array and ChIP-seq for muscles from weight bearing or 5-day hind limb unloaded mice. Genes that showed increased expression with unloading and a Bcl-3 peak in the promoter (from ChIP-seq data) were considered as Bcl-3 direct targets during disuse atrophy. Using ChIP array, we identified 241 direct targets for Bcl-3. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL11078

8 Samples

Download data: CEL

(Submitter supplied) We conducted a large-scale gene expression screen using the 3,200 cDNA probe microarray developed specifically for Ursus americanus to detect expression differences in liver and skeletal muscle that occur during winter hibernation in comparison to animals sampled during summer. The expression of 12 genes, including RNA binding protein motif 3 (Rbm3), that are mostly involved in protein biosynthesis, was induced during hibernation in both liver and muscle. more...

Organism:

Ursus americanus

Type:

Expression profiling by array

Platform:

GPL8249

27 Samples

Download data: TXT

(Submitter supplied) A porcine aortic coarctation model was used to examine regulation of gene expression in early hypertensive vascular remodeling. Aortic segments were collected proximal (high pressure) and distal (low pressure) to the coarctation after 2 weeks of sustained hypertension (mean arterial pressure>150mmHg). Porcine 10K oligoarrays used for gene expression profiling of the two regions of aorta revealed downregulation of cytoskeletal and upregulation of extracellular region genes relative to the whole genome. more...

Organism:

Sus scrofa

Type:

Expression profiling by array

Platform:

GPL4872

6 Samples

Download data: TXT

(Submitter supplied) The patterning and ossification of the mammalian skeleton requires the coordinated actions of both intrinsic bone morphogens and extrinsic neurovascular signals, which function in a temporal and spatial fashion to control mesenchymal progenitor cell (MPC) fate. Here we show genetic inhibition of Tropomyosin receptor kinase A (TrkA) sensory nerve innervation of the developing cranium results in premature calvarial suture closure, associated with a decrease in suture MPC proliferation. more...

Organism:

Mus musculus

Type:

Other

Platform:

GPL13112

4 Samples

Download data: CSV, H5, JPG, JSON, PNG, TXT

(Submitter supplied) Loss of muscle mass occurs in a variety of diseases including cancer, chronic heart failure, AIDS, diabetes and renal failure, often aggravating pathological progression. Preventing muscle wasting by promoting muscle growth has been proposed as a possible therapeutic approach. Myostatin is an important negative modulator of muscle growth during myogenesis and myostatin inhibitors are attractive drug targets. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL1261

3 Samples

Download data: CEL, CHP

(Submitter supplied) AQM shows acute muscle wasting and weakness. Key aspects of AQM include muscle atrophy and myofilament loss. Gene expression profiling, using muscle biopsies from AQM, neurogenic atrophy and normal controls, showed that both myogenic and neurogenic atrophy share induction of myofiber-specific ubiquitin/proteosome pathways while only the AQM shows a specific strong induction of transforming growth factor (TGF)-beta/MAPK pathways. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platforms:

GPL96 GPL8300

10 Samples

Download data: CEL

(Submitter supplied) Hibernating American black bears have significantly different clotting parameters than their active summer counterparts, affording them innate protection against venous thromboembolism (VTE) despite prolonged periods of immobility. Physiologic changes that occur during hibernation are thought to result from differential gene expression, rather than novel genes, and there is increasing evidence miRNAs may play an important role this regulation. more...

Organism:

Ursus americanus

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL25987

21 Samples

Download data: CSV, TSV

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

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL21103 GPL24247

10 Samples

Download data: BED, BW, MTX, TSV

(Submitter supplied) To investigate the possible changes of genes expression during muscle atrophy, we performed bulk RNA-seq of skeletal muscle from C57 BL/6 mice with or without denervation (2 weeks).

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

6 Samples

Download data: BW, XLSX

(Submitter supplied) Current atlas of regulatory sequences controlling skeletal muscle atrophy are still incomplete and lack cell type resolution. We applied single-cell chromatin accessibility assays (snATAC) to normal and denervated skeletal muscle from mice. We integrated these snATAC datasets with our single-nucleus RNA-sequence dataset to reveal the status of open chromatin. Using these datasets, we delineated chromatin accessibility maps in both normal and atrophic muscles and identified cis-regulatory elements (CREs) in all type of cell in skeletal muscle that may regulating muscle protein metabolism, energy metabolism and transcription activities, thus, provided a rich resource for understanding gene regulatory programs in skeletal muscle and related disorders.

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL21103

6 Samples

Download data: BED, MTX, TSV

(Submitter supplied) The epigenomic regulation is a part of Gene Regulatory Network (GRN). During we study the reprogramming of GRN adaptive to atrophic stimulation in skeletal muscle, we performed Histone 3 lysine 27 (H3K27) acetylation (H3K27ac) ChIP-seq assay using mouse skeletal muscle with or without denervation. This dataset combining with our snATAC datasets enable us to infer the candidate enhancer that could regulate muscle protein metabolism and energy metabolism during atrophy.

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24247

4 Samples

Download data: BW

(Submitter supplied) Skeletal muscle exhibits remarkably plasticity under both physiological and pathological conditions. We used adult mice with sciatic denervation as model of muscle atrophy. SnRNA-seq was performed to generate single-nucleus transcriptome profiles of gastrocnemius from normal and denervation mice. Our results define the myonuclear transition, metabolic remodeling and gene regulation networks associated with muscle atrophy induced by denervation and illustrated the molecular basis of heterogeneity and plasticity of muscle cells in response to muscle atrophy, thus providing a resource for exploring molecular mechanisms leading to muscle atrophy

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21103

6 Samples

Download data: RDS, TAR

(Submitter supplied) Obesity impairs the developmental progress and metabolism of the skeletal muscle. Using scRNA-seq, the initial impacts caused by maternal obesity were revealed at the embryonic stage.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

4 Samples

Download data: MTX, TSV