trinitytranscripts_basedongenemodel_ver3_20181009.fasta (79.96 MB)
trinitytranscripts_basedongenemodel_ver3_20181009.fasta
Version 2 2020-10-08, 14:26
Version 1 2020-10-08, 14:24
dataset
posted on 2020-10-08, 14:24 authored by Xiaokang ZhangXiaokang Zhang, Tomasz Furmanek, Inge Jonassen, Anders GoksøyrThe 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 expression
NCBI project : PRJNA277848
https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA277848
Developmental 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=GSE106968
Samples: 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
Funding
DL: dCod 1.0 -decoding systems toxicology of cod (Gadus morhua) -environmental genomics for ecosystem quality monitoring and risk assessment
The Research Council of Norway
Find out more...