|
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 |