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| Status |
Public on Sep 08, 2020 |
| Title |
Y_sCMB_79: Young_Subject-sCMB79 |
| Sample type |
SRA |
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| Source name |
Vastus lateralis muscle
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| Organism |
Homo sapiens |
| Characteristics |
tissue: Vastus lateralis muscle
study arm: Young
biopsy: 0
batch: 1
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| Extracted molecule |
total RNA |
| Extraction protocol |
Approximately 35 mg of muscle was subjected to bead homogenization in Qiazol and RNA purified using miRNeasy Mini Kits and stored at -80 C.
RNA libraries were prepared for sequencing using standard Illumina protocols
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
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| Data processing |
Total RNA was sequenced on an Illumina HiSeq 4000 system, using a standard paired-end 150 bp dual indexing protocol. The two sets of samples (University of Kentucky and University of Alabama), each containing samples from all timepoints of both placebo and metformin arm as well as young, were sequenced in different batches that were corrected for in the downstream analyses (see batch).
Raw fastq sequence reads were passed through quality control using FastQC (0.11.4) and the QC results were compiled for all samples using MultiQC (1.7).
Raw fastq files were trimmed for adapter sequences, filtered for low quality reads and short reads, using the default parameters in fastp (0.19.4)
After checking for QC, RNA-Sequencing by Expectation Maximization- RSEM (1.3.0) in conjunction with the STAR aligner (2.6.1b) was used to align the raw reads to the hg38 primary assembly build of the reference human genome, with transcript annotations (gencode.v29.annotation.gtf) downloaded from GENCODE
All statistical analysis for the gene expression data were carried out using the R statistical software (R-3.6.0)
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited text file containing raw counts for each sample (generated using RSEM)
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| Submission date |
Sep 07, 2020 |
| Last update date |
Sep 08, 2020 |
| Contact name |
Ameya S Kulkarni |
| E-mail(s) |
ameyak225@gmail.com
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| Phone |
9195618761
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| Organization name |
AbbVie
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| Department |
Genomics Research Center
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| Street address |
1 N Waukegan Road
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| City |
North Chicago |
| State/province |
Illinois |
| ZIP/Postal code |
60064 |
| Country |
USA |
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| Platform ID |
GPL20301 |
| Series (1) |
| GSE157585 |
Metformin Alters Skeletal Muscle Transcriptome Adaptations to Resistance Training in Older Adults |
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| Relations |
| BioSample |
SAMN16073872 |
| SRA |
SRX9087934 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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