|
| Status |
Public on Sep 17, 2019 |
| Title |
SC.crtl.1 |
| Sample type |
SRA |
| |
|
| Source name |
Gastrocnemius muscle
|
| Organism |
Mus musculus |
| Characteristics |
strain: mdxITGAM-DTR
tissue: Hind-limb skeletal muscle
cell type: satellite cells (SCs)
agent: control
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extracted with Qiagen RNeasy micro kit (Qiagen Cat#: 74004)
Generation of libraries by Smart-Seq2 protocol (Picelli et al., 2014), with minor modifications
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Freshly sorted cells
|
| Data processing |
Read filtering with fastx toolkit version 0.0.13.2: fastq_quality_trimmer -Q33 -t 20 -l 10 -v -i ; fastq_masker -Q33 -q 20 -r -N -v -i
Reads were aligned on the mouse reference genome (NCBI 37, MM9) with tophat version 2.0.8: tophat -r 170 -p 8 --no-novel-juncs --no-novel-inds --library-type fr-unstranded
Transcript abundance was quantified through ‘Reads Per Kilobase exon model per Million mapped reads’ (RPKM)
Genome_build: mm9
Supplementary_files_format_and_content: RPKMs
|
| |
|
| Submission date |
Jul 24, 2019 |
| Last update date |
Sep 17, 2019 |
| Contact name |
Stefano de Pretis |
| E-mail(s) |
[email protected]
|
| Organization name |
IRCCS San Raffaele Institute
|
| Department |
Center for Omics Sciences
|
| Street address |
Via Olgettina, 58
|
| City |
Milano |
| ZIP/Postal code |
20132 |
| Country |
Italy |
| |
|
| Platform ID |
GPL13112 |
| Series (1) |
| GSE134770 |
Expression profiles of satellite cells and alpha7Sca1 cells in mdxITGAM-DTR mice |
|
| Relations |
| BioSample |
SAMN12349188 |
| SRA |
SRX6579268 |
