|
| Status |
Public on Mar 04, 2024 |
| Title |
Muscle stem cells (MuSCs), DEN, rep 2 |
| Sample type |
SRA |
| |
|
| Source name |
Muscle stem cells
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Muscle stem cells
genotype: C57BL/6
treatment: DEN
|
| Treatment protocol |
Sham/ DEN for 21 days
|
| Extracted molecule |
total RNA |
| Extraction protocol |
MuSCs were FACS-isolated and sorted directly into lysis buffer containing β-mercaptoethanol from the RNeasy Micro Kit (Qiagen).
Library preparation was performed with a two-step approach: 1) introducing 4 ng of total RNA to the SMART-Seq® v4 Ultra® Low Input RNA Kit for Sequencing (Takara) for full-length cDNA synthesis was followed by 2) introducing 300 pg of full-length cDNA to the Nextera XT DNA Library Preparation Kit (Illumina).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
MuSC_10
|
| 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 0).
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) |
dnaseq@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 |
GPL19057 |
| Series (1) |
| GSE217929 |
Gene expression analysis in murine muscle stem cells after denervation |
|
| Relations |
| BioSample |
SAMN31712680 |
| SRA |
SRX18250159 |
