GEO DataSets

(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) Skeletal muscle atrophy is a debilitating condition associated with weakness, fatigue, and reduced functional capacity. Nuclear factor-kappaB (NF-κB) transcription factors play a critical role in atrophy. Knockout of genes encoding p50 or the NF-κB co-transactivator, Bcl-3, abolish disuse atrophy and thus they are NF-κB factors required for disuse atrophy. We do not know however, the genes targeted by NF-κB that produce the atrophied phenotype. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL8321

24 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

Platform:

GPL18480

12 Samples

Download data: BEDGRAPH

(Submitter supplied) We analyzed effects of dexamethasone (Dex) on primary satellite cells (SCs) purified from control and MCK-Cre:Klf5f/f mice.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18480

8 Samples

Download data: BEDGRAPH

(Submitter supplied) We analyzed the accessible chromatin regions globally in response to dexamethasone in primary mouse satellite cells (SCs)

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL18480

4 Samples

Download data: BEDGRAPH

(Submitter supplied) Deletion of Klf5 in satellite cells impaired muscle regeneration due to a failure of differentiation. Mechanistically, Klf5 controls transcription of muscle genes by interacting with MyoD and Mef2. These findings provide a potential intervention into the process of muscle regeneration through modulation of Klf5.

Organism:

Mus musculus

Type:

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

Platforms:

GPL13112 GPL18480

14 Samples

Download data: BEDGRAPH, TXT, XLS

(Submitter supplied) The goal of this study was to identify changes in muscle gene expression that may contribute to loss of adaptability of old muscle. Muscle atrophy was induced in young adult (6-month) and old (32-month) male Brown Norway/F344 rats by two weeks of hind limb suspension (HS) and soleus muscles were analyzed by cDNA microarrays. We conclude that a cold shock response may be part of a compensatory mechanism in muscles undergoing atrophy to preserve remaining muscle mass and that RBM3 may be a therapeutic target to prevent muscle loss.

Organism:

Rattus norvegicus

Type:

Expression profiling by array

Platform:

GPL7045

18 Samples

Download data: CSV

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

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL6105

48 Samples

Download data

(Submitter supplied) Analysis of dexamethasone-regulation of muscle mass at gene expression level. The hypothesis tested in the present study was that the presence of MuRF1 contributes to the extent of gene expression changes observed in specific sets of genes during a challenge leading to muscle atrophy. Results provide important information on the response of triceps surae muscle to synthetic glucocorticoid treatment, such as specific cell signaling and metabolic enzyme genes, that may be influenced by MuRF1 during atrophy.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL6105

24 Samples

Download data: TXT

(Submitter supplied) Analysis of denervation induced regulation of muscle mass at gene expression level. The hypothesis tested in the present study was that the presence of MuRF1 contributes to the extent of gene expression changes observed in specific sets of genes during a challenge leading to muscle atrophy. Results provide important information on the response of triceps surae muscle to sciatic nerve resection (denervation), such as specific structural, metabolic, and neuromuscular junction associated genes, that may be influenced by MuRF1 during atrophy.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL6105

24 Samples

Download data: TXT

(Submitter supplied) To determine the role of cardiomyocyte muscle ring finger-1 (MuRF1) in vivo, we employed whole genome microarray expression profiling as a discovery platform to identify genes differentially regulated by MuRF1 using MuRF1-/- and alphaMHC (cardiomyocyte-specific) MuRF1 transgenic mice in a model of pulmonary hypertension-induced right sided heart failure. Mice were placed in hypoxia chambers set at 10.0% oxygen (partial pressure of oxygen roughly 65 mmHg in Albuquerque) and monitored both by the digital feedback control system (Biospherix, Colorado) as well as by a secondary O2/CO2 monitor (O2Cap, OxiGraf, Inc.; Mountain View, CA). more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL4134

17 Samples

Download data: TXT

(Submitter supplied) Existing data suggest that NF-kappaB signaling is a key regulator of cancer-induced skeletal muscle wasting. However, identification of the components of this signaling pathway and of the NF-κB transcription factors that regulate wasting is far from complete. In muscles of C26 tumor bearing mice, overexpression of d.n. IKKβ blocked muscle wasting by 69%, the IκBα-super repressor blocked wasting by 41%. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL11078

6 Samples

Download data: CEL

(Submitter supplied) We investigated the impact of EDA-A2-EDA2R signaling in gene expression profiles of mouse primary myotubes. Cells were treated with recombinant EDA-A2 for 24hrs and transcriptional changes were studied by RNA-sequencing.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

4 Samples

Download data: TXT

(Submitter supplied) p53 regulates a distinct subset of skeletal muscle mRNAs during immobilization-induced skeletal muscle atrophy For additional details see Fox et al, p53 and ATF4 mediate distinct and additive pathways to skeletal muscle atrophy during limb immobilization. Am J Physiol Endocrinol Metab. 2014 Aug 1;307(3):E245-61.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL6885

17 Samples

Download data: IDAT

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

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL24247 GPL21103

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