Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

41 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

The human skeletal muscle transcriptome – sex differences, alternative splicing and tissue homogeneity assessed with RNA sequencing

ABSTRACT: The amount of RNA sequencing data on skeletal muscle is very limited. We have analyzed a large set of human muscle biopsy samples and provide extensive information on the baseline skeletal muscle transcriptome, including completely novel protein-coding transcripts. Analyze of transcriptome in 23 skeletal muscle biopsy samples from six individuals. Four biopsies from each subject, two biopsies from each leg (except subject 6 which has only three biopsies in total). This experiment is linked to E-GEOD-58608.

ORGANISM(S): Homo sapiens

SUBMITTER: Joakim Lundeberg

PROVIDER: E-GEOD-58387 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

The human skeletal muscle transcriptome: sex differences, alternative splicing, and tissue homogeneity assessed with RNA sequencing.

Lindholm Malene E ME Huss Mikael M Solnestam Beata W BW Kjellqvist Sanela S Lundeberg Joakim J Sundberg Carl J CJ

FASEB journal : official publication of the Federation of American Societies for Experimental Biology 20140711 10

Human skeletal muscle health is important for quality of life and several chronic diseases, including type II diabetes, heart disease, and cancer. Skeletal muscle is a tissue widely used to study mechanisms behind different diseases and adaptive effects of controlled interventions. For such mechanistic studies, knowledge about the gene expression profiles in different states is essential. Since the baseline transcriptome has not been analyzed systematically, the purpose of this study was to prov ...[more]

PMID: 25016029

Similar Datasets

The human skeletal muscle transcriptome assessed with RNA sequencing

Project description:The amount of RNA sequencing data on skeletal muscle is very limited. We have analyzed a large set of human muscle biopsy samples and provide extensive information on the baseline skeletal muscle transcriptome, including completely novel protein-coding transcripts. Analyze of transcriptome in 24 skeletal muscle biopsy samples, 12 individuals and one biopsy per leg per individual. This experiment is linked to E-GEOD-58387.

2014-07-15 | E-GEOD-58608 | biostudies-arrayexpress

Dynamics of the human skeletal muscle transcriptome in response to exercise training - part 1

Project description:A total of 23 participants (data available in present submission and in GSE58608) completed three months of supervised aerobic exercise training of one leg. Skeletal muscle biopsies have been collected before and after the training period. We have investigated differences between trained and untrained leg and before and after training by studying the gene and isoform expression. Additional samples present in this study has been previously published (GEO accession number GSE58608). Analysis of transcriptome in skeletal muscle biopsy samples in response to exercise training in 22 participants (of the total 23 participants). One biopsy is collected from each leg before and after training period.

2015-01-21 | E-GEOD-60590 | biostudies-arrayexpress

Dynamics of the human skeletal muscle transcriptome in response to exercise training - part 2

Project description:In the present study 23 participants completed three months of supervised aerobic exercise training of one leg (training period 1) followed by 9 months of rest before 12 of the participants completed a second exercise training period (training period 2) of three months of both legs. Skeletal muscle biopsies have been collected before and after the training periods. We have compared trained leg with untrained leg and studied gene and isoform expression. Additional samples included in this study has been previously submitted (GEO accession number GSE58387 and GSE60590). Analyze of transcriptome in skeletal muscle biopsy samples in response to exercise training in 23 participants in total (in addition to data previously submitted GEO accession number GSE58387 and GSE60590). Biopsy is collected from skeletal muscle before and after training period.

2016-08-14 | E-GEOD-60833 | biostudies-arrayexpress

The human skeletal muscle transcriptome assessed with RNA sequencing

2014-07-15 | GSE58608 | GEO

The human skeletal muscle transcriptome – sex differences, alternative splicing and tissue homogeneity assessed with RNA sequencing

2014-07-15 | GSE58387 | GEO

The Heritage family study - skeletal muscle gene expression

Project description:Gene expression profiles generated from skeletal muscle biopsies taken from participants of the HERITAGE family study. Participants completed an endurance training regime in which a skeletal muscle biopsy was taken prior to the start and after the final session of the program. Biopsies were used to generate Affymetrix gene expression microarrays.

2018-07-14 | GSE117070 | GEO

Effect of fasting on human skeletal muscle mRNA levels

Project description:The goal of these studies was to determine the effects of fasting on skeletal muscle mRNA levels in healthy human subjects. Seven healthy adult human subjects fasted for 40 hours and then a muscle biopsy (fasting sample) was obtained from the vastus lateralis muscle. Immediately after the first muscle biospy, subjects then ate a mixed meal. Six hours after the first muscle biopsy, a second muscle biopsy (fed sample) was obtained from the contralateral vastus lateralis muscle. In each subject, mRNA levels under fasting conditions were normalized to mRNA levels under fed conditions, which were set at 1.

2011-06-08 | E-GEOD-28016 | biostudies-arrayexpress

Effects of resistance exercise and resistance training on the skeletal muscle transcriptome in young and old adults

Project description:Global microarray (HG U133 Plus 2.0) was used to investigate the effects of resistance exercise and resistance training on the skeletal muscle transcriptome profile of 28 young and old adults. Vastus lateralis muscle biopsies were obtained pre and 4hrs post resistance exercise in the beginning (untrained state) and at the end (trained state) of a 12 wk progressive resistance training program. A total of 28 subjects were included in this investigation. The young (n=16, 24±1y) participants included 8 males and 8 females. The old (n=12, 84±1y) participants included 6 males and 6 females. All subjects participated in 12 wks of progressive resistance training consisting of bilateral knee extensions with 3x10 reps at 70% of 1-RM, and 3d/wk for a total of 36 training sessions. Vastus lateralis biopsies were obtained in conjunction with the 1st and 36th (last) training session and included a basal biopsy and another biopsy 4hrs post the resistance exercise session (for a total of 4 biopsies per subject). The RNA integrity for all samples was very good with an average RIN number of 7.6. All 110 samples were analyzed on a separate microarray chip, and samples were not pooled between subjects. The study design allowed us to examine the acute effects of resistance exercise on the skeletal muscle transcriptome in the untrained and trained state. The design also provided information on the effects of resistance training on basal level gene expression and the effects of age on basal level gene expression

2012-02-21 | E-GEOD-28422 | biostudies-arrayexpress

The 24-Hour Time Course of Integrated Molecular Responses to Resistance Exercise in Human Skeletal Muscle Implicates MYC as a Hypertrophic Regulator

Project description:Molecular control of recovery after exercise in muscle is temporally dynamic. A time course of biopsies around resistance exercise (RE) combined with -omics is necessary to better comprehend the molecular choreography of skeletal muscle adaptation in humans. We collected vastus lateralis biopsies before and 30 minutes, 3-, 8-, and 24 hours after acute RE. RNA-sequencing defined the transcriptome and a time-point matched biopsy only group were controls. DNA methylomics and computational approaches complimented the transcriptome data. Moreover, we tested whether cyclic transient overexpression of transcription factor MYC for 4 weeks were sufficient to induce skeletal muscle hypertrophy in female mice.

2024-04-17 | GSE252357 | GEO

Next Generation Sequencing Methylation Profiling in Skeletal Muscle from Lean and Obese Subjects [Bisulfite-Seq]

Project description:Obesity is a metabolic disease caused by environmental, genetic, and epigenetic factors. However, the epigenetic mechanisms of obesity are incompletely understood. The aim of our study was to identify skeletal muscle DNA methylation patterns in obesity. Muscle biopsies were obtained basally from lean (n=11) and obese (n=9) participants in combination with euglycemic hyperinsulinemic clamps to assess insulin sensitivity. We performed reduced representation bisulfite sequencing next generation methylation analysis on DNA isolated from vastus lateralis muscle biopsies.

2015-11-01 | E-GEOD-73303 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data