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SRP043108
Homo sapiens
79 Downloadable Samples
IlluminaHiSeq2000
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. Overall design: 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).
Publication Title
The human skeletal muscle transcriptome: sex differences, alternative splicing, and tissue homogeneity assessed with RNA sequencing.
Sample Metadata Fields
No sample metadata fields
View Samples- Hordeum vulgare
- 12 Downloadable Samples
Affymetrix Barley Genome Array (barley1)
Description
Caryopses of barley (Hordeum vulgare), like all other cereal seeds, are complex sink organs optimized for storage starch accumulation and embryo development. Their development from early stages after pollination to late stages of seed ripening has been studied in great detail. However, information on the caryopses diurnal adaptation to changes in light, temperature and alterations in phloem-supplied carbon and nitrogen remained unknown.
Publication Title
Significance of light, sugar, and amino acid supply for diurnal gene regulation in developing barley caryopses.
Sample Metadata Fields
Age, Specimen part
View Samples- Hordeum vulgare
- 12 Downloadable Samples
- Affymetrix Barley Genome Array (barley1)
Description
High temperature stress, like any abiotic stress, impairs the physiology and development of plants, including the stages of seed setting and ripening.
Publication Title
Transcriptome analysis of high-temperature stress in developing barley caryopses: early stress responses and effects on storage compound biosynthesis.
Sample Metadata Fields
Age, Specimen part
View Samples- Mus musculus
- 23 Downloadable Samples
- Affymetrix Mouse Gene 1.0 ST Array (mogene10st)
Description
Rhomboid family protein RHBDF2, an upstream regulator of the epidermal growth factor (EGF) receptor signaling, has been implicated in cutaneous wound healing. However, the underlying molecular mechanisms are still emerging. Using a gain-of-function mutation in the mouse Rhbdf2 gene (Rhbdf2cub/cub), which shows a regenerative phenotype, we sought to identify the underlying mechanism.
Publication Title
Early induction of NRF2 antioxidant pathway by RHBDF2 mediates rapid cutaneous wound healing.
Sample Metadata Fields
Specimen part, Treatment, Time
View Samples- Mus musculus
- 383 Downloadable Samples
- NextSeq 500
Description
Two 96-well plates per genotype wild type and Myd88 knockout, 4 hour time series in 0.5 hr increments Overall design: Myd88 BMDM transcriptional profiling to complement TF-seq data
Publication Title
Simultaneous Pathway Activity Inference and Gene Expression Analysis Using RNA Sequencing.
Sample Metadata Fields
Sex, Age, Specimen part, Cell line, Treatment, Subject, Time
View Samples- Mus musculus
- 120 Downloadable Samples
- NextSeq 500
Description
Bone marrow derived macrophages treated with small molecules and stimulated with LPS Overall design: Wild-type BMDMs pretreated with small molecules for 30 minutes prior to stimulation with LPS
Publication Title
Simultaneous Pathway Activity Inference and Gene Expression Analysis Using RNA Sequencing.
Sample Metadata Fields
Sex, Age, Specimen part, Cell line, Treatment, Subject, Time
View Samples- Mus musculus
- 96 Downloadable Samples
- NextSeq 500
Description
Bone marrow derived macrophages treated with small molecules and stimulated with LPS Overall design: Wild-type BMDMs pretreated with small molecules for 30 minutes prior to stimulation with LPS
Publication Title
Simultaneous Pathway Activity Inference and Gene Expression Analysis Using RNA Sequencing.
Sample Metadata Fields
Sex, Age, Specimen part, Cell line, Treatment, Subject
View Samples- Homo sapiens
- 81 Downloadable Samples
- IlluminaHiSeq2000
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). Overall design: 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.
Publication Title
The Impact of Endurance Training on Human Skeletal Muscle Memory, Global Isoform Expression and Novel Transcripts.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 40 Downloadable Samples
- IlluminaHiSeq2000
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). Overall design: 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.
Publication Title
The Impact of Endurance Training on Human Skeletal Muscle Memory, Global Isoform Expression and Novel Transcripts.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 26 Downloadable Samples
- IlluminaHiSeq2000
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. Overall design: Analyze of transcriptome in 24 skeletal muscle biopsy samples, 12 individuals and one biopsy per leg per individual
Publication Title
The Impact of Endurance Training on Human Skeletal Muscle Memory, Global Isoform Expression and Novel Transcripts.
Sample Metadata Fields
No sample metadata fields
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