De novo Trinity transcript assembly of Atlantic cod

• Main Authors: Xiaokang Zhang, Furmanek, Tomasz, Jonassen, Inge, Goksøyr, Anders
• Format: Dataset
• Language: unknown
• Published: figshare 2020
• Subjects: 60102 Bioinformatics; FOS Computer and information sciences; atlantic cod; Gadus morhua
• Online Access: https://dx.doi.org/10.6084/m9.figshare.13067324.v2; https://figshare.com/articles/dataset/trinitytranscripts_basedongenemodel_ver3_20181009_fasta/13067324/2

The reference is based on a de novo Trinity [1,2] assembly because the official gene models versions did not contain full length sequences for all genes. The assembly consists of sequences from the following RNA-Seq data: Gadus morhua Transcriptome or Gene expressionNCBI project : PRJNA277848https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA277848Developmental stages: 10-dph, 20-dph, 30-dph, 45-dph, 60-dph, 90-dph SRR2045416 brain ,SRR2045417 gills, SRR2045418 heart, SRR2045419 muscle, SRR2045420 liver, SRR2045421 kidney, SRR2045422 bones, SRR2045423 intestine, SRR2045425 embryo, SRR2045415 ovary Three cod liver samples:GEO accession: GSE106968 [3] https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE106968Samples: dcod_12_S3, dcod_1_S1, dcod_25_S25 Reads were assembled using Trinity through the Agalma pipeline version 0.5.0 [4]. The transcript assemblies from different stages and tissue samples were mapped to both cod genomes (gadMor 1 and 2) [5,6]. Transcripts were mapped to both genomes as each genome is missing some genes. 1 Grabherr, M.G. et al. (2011) Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat. Biotechnol. 29, 644–652 2 Haas, B.J. et al. (2013) De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis. Nat. Protoc. 8, 1494–1512 3 Yadetie, F. et al. (2018) RNA-Seq analysis of transcriptome responses in Atlantic cod (Gadus morhua) precision-cut liver slices exposed to benzo[a]pyrene and 17α-ethynylestradiol. Aquat. Toxicol. 201, 174–186 4 Dunn, C.W. et al. (2013) Agalma: an automated phylogenomics workflow. BMC Bioinformatics 14, 330 5 Star, B. et al. (2011) The genome sequence of Atlantic cod reveals a unique immune system. Nature 477, 207–210 6 Tørresen, O.K. et al. (2017) An improved genome assembly uncovers prolific tandem repeats in Atlantic cod. BMC Genomics 18, 95