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Sample GSM6730062 Query DataSets for GSM6730062
Status Public on Mar 04, 2024
Title Whole muscle (TA), sham, rep 4
Sample type SRA
 
Source name Whole muscle
Organism Mus musculus
Characteristics tissue: Whole muscle
genotype: C57BL/6
treatment: sham
Treatment protocol Sham/ DEN for 21 days
Extracted molecule total RNA
Extraction protocol TA muscles or EDL myofibers were homogenized in TRIzol reagent and RNA was isolated according to the manufacturer`s protocol (VWR, 30-2010)
Library preparation was performed using the NEBNext Ultra II directional RNA kit with polyA molecule selection and unique dual indexing.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Description TA_08
Data processing Sequence information was converted to FASTQ format using bcl2fastq v2.20.0.422
Adapter trimming was performed with CutAdapt v2.1 (-m 30 –a ADAPER-SEQUENCE).
FastQ files were mapped using Tophat v.2.1.0 (parameters: -x 1 -g 1 --no-coverage-search –no-convert-bam).
Reads per gene were counted with featureCounts v1.6.5 (-s 2).
RPKMs were calculated based on the gene length given by featureCounts.
Assembly: Ensembl: GRCm38.100
Supplementary files format and content: Excel sheet (xlsx) containing counts, RPMs and RPKMs
 
Submission date Nov 14, 2022
Last update date Mar 04, 2024
Contact name Marco Groth
E-mail(s) cfngs@leibniz-fli.de
Organization name Leibniz Institute on Aging - FLI
Department Core Facility - Next Generation Sequencing
Street address Beutenbergstraße 11
City Jena
ZIP/Postal code 07747
Country Germany
 
Platform ID GPL24247
Series (1)
GSE217928 Gene expression analysis in murine muscle fibers and whole muscle after denervation
Relations
BioSample SAMN31712556
SRA SRX18249981

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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