Data from: A comprehensive transcriptome of early development in yellowtail kingfish (Seriola lalandi)

Patel A, Dettleff P, Hernández E, Martinez V

Date Published: September 9, 2015

DOI: http://dx.doi.org/10.5061/dryad.sv31k.2

 

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Title Sequences of S. lalandi transcriptome (fasta file)
Downloaded 11 times
Description Transcriptome contigs assembled from filtered paired end sequencing reads on Illumina HiSeq™ 2000 platform using Trinity. Only non-redundant (cluster in CAP3), more than 300bp contigs with open reading frame were kept
Download S.lalandi_final_transcriptome.fasta (70.79 Mb)
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Title BLAST results, Annotation information, Gene Ontology (.dat file for Blast2GO)
Downloaded 8 times
Description Standard input file for BLAST2GO. This file can be loaded directly into .jnlp executable file downloaded from BLAST2GO website. Includes BLASTX results against NCBI’s non-redundant protein database, InterProScan search result for functional signature of protein domain. Gene Ontology information based on best hit gene matches and KEGG results
Download blast2go_final-S.lalandi.dat (55.60 Mb)
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Title Information on SNPs identified from transcriptome data (vcf file)
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Description The details of SNPs calling are described in Materials and methods
Download Seriola_lalandi_variant_file.vcf (11.34 Mb)
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Title The mapping count table
Downloaded 2 times
Description This count table was used as an input for differential gene expression analysis in edgeR
Download Count_table_S_lalandi.csv (4.374 Mb)
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Title Table containing differential expressed genes (result of edgeR)
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Description This table contains data of list of genes that were < 0.01 FDR value and differed in their expression value at least 2 fold between two groups
Download Final_Results_edgeR.csv (315.7 Kb)
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Title GO term reduction table
Downloaded 3 times
Description Gene Ontology terms were summarized and redundant GO terms were removed by semantic similarity-based approach employed in REViGO .
Download REVIGO_Results.csv (1.014 Kb)
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Title Pathways-K_numbers_contigs-ID
Description This is a text file containing all the pathways reconstructed in KEGG automatic annotation server from this RNA-seq study. All the pathways and the K-numbers (each K number represents an ortholog group of genes, and it is directly linked to an object in the KEGG pathway map or the BRITE functional hierarchy) along with contigs-id associated with corresponding K-number are presented in one file. One can search specific pathways of interest and can note the K numbers and contigs-id therein. There after, these contigs-id can be interrogated in blast2go.dat file to obtain fasta sequences of gene/set of genes from the pathway of interest (in order to design primers or other purpose).
Download Pathways-K_numbers_contigs-ID.txt (785.6 Kb)
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When using this data, please cite the original publication:

Patel A, Dettleff P, Hernández E, Martinez V (2015) A comprehensive transcriptome of early development in yellowtail kingfish (Seriola lalandi). Molecular Ecology Resources 16(1): 364-376. http://dx.doi.org/10.1111/1755-0998.12451

Additionally, please cite the Dryad data package:

Patel A, Dettleff P, Hernández E, Martinez V (2015) Data from: A comprehensive transcriptome of early development in yellowtail kingfish (Seriola lalandi). Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.sv31k.2
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