De novo assembly of the Brown trout (Salmo trutta m. fario) brain and muscle transcriptome: transcript annotation, tissue differential expression profile and SNP discovery.
Joan FiblaN OromiM Pascual-PonsJ L RoyoA PalauM FiblaPublished in: BMC research notes (2020)
We generate two cDNA libraries from pooled RNA samples, isolated from muscle and brain tissues of adult individuals of Salmo trutta m. fario, which were sequenced by Illumina technology. Raw reads were subjected to de-novo transcriptome assembly using Trinity, and coding regions were predicted by TransDecoder. A final set of 35,049 non-redundant ORF unigenes were annotated. Tissue differential expression analysis was evaluated by Cuffdiff. A False Discovery Rate (FDR) ≤ 0.01 was considered for significant differential expression, allowing to identify key differentially expressed unigenes. Finally, we have identified SNP variants that will be useful tools for population genomic studies.
Keyphrases
- genome wide
- rna seq
- copy number
- single cell
- gene expression
- resting state
- small molecule
- white matter
- skeletal muscle
- dna methylation
- high throughput
- functional connectivity
- high density
- cerebral ischemia
- multiple sclerosis
- clinical trial
- genetic diversity
- brain injury
- genome wide identification
- phase iii
- nucleic acid
- case control
- open label
- subarachnoid hemorrhage
- high throughput sequencing