Virginia Institute of Marine Science
This dataset contains supplemental materials for Chapter 2: Comparative Transcriptomics of Spotted Seatrout (Cynoscion nebulosus) Populations to Cold and Heat Stress in the associated publication - Search for Selection: Genomic, Transcriptomic, and Phenotypic Investigations of Spotted Seatrout (Cynoscion nebulosus.
Data are contained in a compressed file and include files in FASTA format (.fa), a text-based format representing nucleotide sequences using single-letter codes, Trinotate v3.1.1, an open source annotation suite designed for automatic functional annotation of transcriptomes, (see Bryant et al. 2017, doi: 10.1016/j.celrep.2016.12.063) and data generated by Kallisto v.0.43.1., an open source RNA-seq quantification program. (see Bray et al. 2016, doi: 10.1038/nbt.3519).
File Name | Description:
- SuppInfo_S1_Transcriptome.fa : Spotted seatrout (Cynoscion nebulosus) liver transcriptome in FASTA format
- SuppInfo_S2_Trinotate_Report.xls: Functional annotation report from Trinotate for the liver transcriptome.
- SuppInfo_S3_20_Common_Transcripts.xls: Significant common transcripts responsive to both cold and heat stress and in both the southern and northern populations.
- SuppInfo_S4_DE_contig_names.xlsx: Transcript names showing significant differential expression to temperature stress, separated by populations
- SuppInfo_S5_kallisto_matrix: Transcripts quantification matrix for all samples
- SuppInfo_S6_KEGG_pathways.xlsx: Names of common and unique Kyoto Encyclopedia of Genes and Genomes (KEGG) molecular pathways between and within populations.
- Suppinfo_S7_GO_enrichment.xlsx: Significant biological processes based on Gene Ontology enrichment analysis of differentially expressed genes (DEGs).
Transcriptome, RNA-seq, thermal stress, Cynoscion nebulosus
Song, Jingwie. Search for Selection: Genomic, Transcriptomic, and Phenotypic Investigations of Spotted Seatrout (Cynoscion nebulosus). (2020) PhD Dissertation, School of Marine Science, William & Mary. forthcoming
Jingwei Song ORCID ID: https://orcid.org/0000-0003-3151-543X
Virginia Sea Grant (NOAA Sea Grant Omnibus award NA140AR417009
Song, Jingwei, "Search for Selection: Genomic, Transcriptomic, and Phenotypic Investigations of Spotted Seatrout (Cynoscion nebulosus): Supplemental Data" (2020). Data. William & Mary.