|
| Status |
Public on Feb 08, 2024 |
| Title |
wt trunk group 1 |
| Sample type |
SRA |
| |
|
| Source name |
trunk muscle
|
| Organism |
Danio rerio |
| Characteristics |
tissue: trunk muscle
age: 5 month old
strain: AB
cell type: Trunk muscle myofibers
genotype: WT
|
| Growth protocol |
WT AB zebrafish used originated from the same line utilized when generating the desma-/-;desmb-/- double mutant. Zebrafish were maintained by standard procedures on a 10/14h dark/light cycle at 28°C
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA-later solution from Sigma and stored at -80C. All collected samples were then treated with TRIZOL according to the manufactors description. 400ng total RNA was used for library construction.
Illumina TruSeq Stranded mRNA, poly-A selection
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Sequence reads were mapped to GRCz11 using STAR (options: --outSAMtype BAM SortedByCoordinate --seedSearchStartLmax 12 --outFilterScoreMinOverLread 0.3 --alignSJoverhangMin 15 --outFilterMismatchNmax 33 --outFilterMatchNminOverLread 0 --outFilterType BySJout --outSAMunmapped Within --outSAMattributes NH HI AS NM MD --outSAMstrandField intronMotif --quantMode GeneCounts)
Read count extraction and normalization were performed using R package DeSEQ2
Assembly: GRCz11
Supplementary files format and content: tab-delimited text files include raw counts
|
| |
|
| Submission date |
Sep 01, 2023 |
| Last update date |
Feb 08, 2024 |
| Contact name |
Nils Dennhag |
| E-mail(s) |
nils.dennhag@umu.se
|
| Organization name |
Umeå Univeristy
|
| Street address |
Linneaus väg 9
|
| City |
Umeå |
| ZIP/Postal code |
901 87 |
| Country |
Sweden |
| |
|
| Platform ID |
GPL24995 |
| Series (2) |
| GSE242136 |
fhl2b expression ameliorates muscular dystrophy [5 months EOM and trunk] |
| GSE242137 |
fhl2b expression ameliorates muscular dystrophy |
|
| Relations |
| BioSample |
SAMN37229913 |
| SRA |
SRX21589471 |
