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The human skeletal muscle transcriptome 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 24 skeletal muscle biopsy samples, 12 individuals and one biopsy per leg per individual. This experiment is linked to E-GEOD-58387.

ORGANISM(S): Homo sapiens

SUBMITTER: Joakim Lundeberg

PROVIDER: E-GEOD-58608 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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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

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The human skeletal muscle transcriptome – sex differences, alternative splicing and tissue homogeneity 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 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.

2014-07-15 | E-GEOD-58387 | 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

Histamine footprint on the human exercise transcriptome

Project description:Transcriptome wide analysis of the skeletal muscle response to exercise in humans. Subjects performed one 60-min bout of moderate-intensity single-leg knee-extension exercise, and samples were obtained by biopsy of the vastus lateralis muscle before, immediately after, and at 3 hr post-exercise. Eight subjects were control (no drug), and eight received combined H1/H2-histamine receptor blockade prior to exercise.

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Demonstration of a day-night rhythm in human skeletal muscle oxidative capacity.

Project description:Five consecutive skeletal muscle biopsies were taken from a young healthy male research volunteer under controlled living conditions consisting of 3 meals and normal sleeping time. Samples were obtained with five hour-intervals, always at least 4 hours after the last meal at 8AM, 1PM, 6PM, 11PM and 4AM the next day. Biopsies were taken according to the Bergström method under local anesthesia from the m. vastus lateralis. The first biopsy was taken from the left leg and each consecutive biopsie was taken from the other leg.

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Contractile activity-specific transcriptome response to acute endurance exercise and training in human skeletal muscle

Project description:In our study, we investigated for contractile activity-specific changes in the transcriptome in untrained and trained (after an aerobic training programme) human skeletal muscle. The second goal was to examine effect of aerobic training on gene expression in muscle at baseline (after long term training). Seven untrained males performed the one-legged knee extension exercise (for 60 min) with the same relative intensity before and after a 2 month aerobic training programme (1 h/day, 5/week). Biopsy samples were taken at rest (baseline condition, 48 h after exercise), 1 and 4 h after the one-legged exercise from m. vastus lateralis of either leg. Comparison of gene expression in exercised leg with that in non-exercised [control] leg allowed us to identify contractile activity-specific genes in both untrained and trained skeletal muscle, i.e., genes that play a key role in adapting to acute exercise, regardless of the level of fitness. RNA-sequencing (84 samples in total; ~47 million reads/sample) was performed by NextSeq 500 and HiSeq 2500 (Illumina). Two months aerobic training increased the aerobic capacity of the knee-extensor muscles (power at anaerobic threshold in the incremental one-legged and cycling tests), the maximum rate of ADP-stimulated mitochondrial respiration in permeabilized muscle fibres and amounts of oxidative phosphorylation proteins. Contractile activity-specific changes in the transcriptome in untrained and trained human skeletal muscle were revealed for the first time. After 2 month aerobic training, transcriptome responses specific for contractile activity in trained muscle substantially decreased relative to those in untrained muscle. We found out that adaptation of skeletal muscle to regular exercise is associated not only with a transient change in the transcriptome after each stress (acute exercise), but also with a marked change in baseline expression of many genes after repeated stress (e.g., long term training).

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Microarray analysis of skeletal muscle hypertrophy induced by heat-stress in healthy humans

Project description:This study was aimed at examining the effects of long-term of heat-stress on the gene expression of skeletal muscle hypertrophy. Heat- and stream-generating (HSG) sheets were placed on thigh laterally. The HSG sheets (heat-stress) were applied 8-hrs/day, once a day, 4 days/weeks, for 10 weeks. A muscle biopsy was taken from the vastus lateralis muscle (2 cm depth) of the treated leg before and after the experiment. Oligonucleotide microarray revealed that genes related to ATP-synthesis, protein synthesis and the molecular chaperonic activity were increased by heat stress. These results suggest that heat-stress might be a useful countermeasure for muscular atrophy during aging. Overall design: Five subjects were applied by heat- and stream-generating (HSG) sheets for 10 weeks. Total RNAs obtained from the skeletal muscle before and after the experiment were used for the analysis.

2011-07-30 | E-GEOD-12474 | biostudies-arrayexpress

Microarray analysis of skeletal muscle hypertrophy induced by heat-stress in healthy humans

2011-07-31 | GSE12474 | GEO