|
| Status |
Public on Mar 20, 2024 |
| Title |
Cardiac ventricle, wt sibling, replicate 3 |
| Sample type |
SRA |
| |
|
| Source name |
Cardiac Ventricle
|
| Organism |
Danio rerio |
| Characteristics |
tissue: Cardiac Ventricle
genotype: WT
treatment: 7days_post_cryoinjury
|
| Extracted molecule |
total RNA |
| Extraction protocol |
4 pools each comprising 5 ventricles were sequenced per condition.
Libraries for RNA-seq were prepared using the "NEBNext Ultra II Directional RNA library prep Kit for Illumina" following manufacturer´s protocol
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 2000 |
| |
|
| Description |
NextSeq P2 100 cycles Flowcell (400 M)
WT_3
|
| Data processing |
Data were quality checked with Fastqc and Multiqc
Sequences were trimmed with fastp
2 pass alignment was performed with STAR Aligner
reads were dounted using featurecounts
Normalization and downstream analysis including differential expression analysis was performed in R
Assembly: GRCz11 v109 Ensembl
Supplementary files format and content: feature counts, tab seprated values
|
| |
|
| Submission date |
Jan 29, 2024 |
| Last update date |
Mar 20, 2024 |
| Contact name |
Nadia Mercader |
| E-mail(s) |
nmercader@cnic.es, nadia.mercader@unibe.ch
|
| Organization name |
University of Bern
|
| Street address |
Baltzerstrasse 2
|
| City |
Bern |
| ZIP/Postal code |
3012 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL30614 |
| Series (1) |
| GSE254466 |
Cox7a1 mediated CIV dimerization impacts skeletal muscle physiology and cardiac injury response |
|
| Relations |
| BioSample |
SAMN39657680 |
| SRA |
SRX23429742 |
