|
| Status |
Public on May 08, 2023 |
| Title |
200d KO Muscle 5 |
| Sample type |
SRA |
| |
|
| Source name |
Muscle
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Muscle
strain: C57BL/6
genotype: COX10 KO
age (d): 200
Sex: Male
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Liver, calf muscle, and hypothalamus were removed and flash frozen in liquid nitrogen. RNA was harvested using Trizol and the Qiagen RNeasy Mini Kit (Cat# 74104). The Lexogen QuantSeq 3’ mRNA-Seq Library Prep Kit FWD for Illumina was used with 500 ng of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Illumina Casava1.7 software used for basecalling.
Raw sequence reads were processed using the BBDuk program in the BBMap package
Trimmed reads were aligned to the mouse genome assembly GRCm38.p6 using the STAR aligner (version 2.5.0a for Liver and Muscle samples, 2.7.9a for Hypothalamus).
SAM files were converted to BAM to read overlapping reads per gene using HTseq-count (version 0.6.1)
|
| |
|
| Submission date |
Feb 07, 2023 |
| Last update date |
May 09, 2023 |
| Contact name |
Nneka Southwell |
| E-mail(s) |
[email protected]
|
| Organization name |
Weill Cornell Graduate School
|
| Department |
Brain and Mind Research Institute
|
| Street address |
407 E 64th St Fl 5
|
| City |
New York |
| State/province |
New York |
| ZIP/Postal code |
10065 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE224780 |
An integrated multiorgan feed-forward metabolic response exacerbates muscle wasting and lipid accumulation in human mitochondrial myopathies |
|
| Relations |
| BioSample |
SAMN33193399 |
| SRA |
SRX19305338 |
