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Sample GSM4771048 Query DataSets for GSM4771048
Status Public on Sep 08, 2020
Title P_012_1: plaPRT_Subject-012_Biopsy-1
Sample type SRA
 
Source name Vastus lateralis muscle
Organism Homo sapiens
Characteristics tissue: Vastus lateralis muscle
study arm: plaPRT
biopsy: 1
batch: 1
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
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 4000
 
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)
 
Submission date Sep 07, 2020
Last update date Dec 17, 2020
Contact name Ameya S Kulkarni
E-mail(s) [email protected]
Phone 9195618761
Organization name AbbVie
Department Genomics Research Center
Street address 1 N Waukegan Road
City North Chicago
State/province Illinois
ZIP/Postal code 60064
Country USA
 
Platform ID GPL20301
Series (1)
GSE157585 Metformin Alters Skeletal Muscle Transcriptome Adaptations to Resistance Training in Older Adults
Relations
Reanalyzed by GSE163434
BioSample SAMN16073787
SRA SRX9087807

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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