Round goby transcript count data

This file was generated using Corset software to process BAM files of RNAseq reads mapped to a de novo assembled transcriptome for nine round goby and enumerate counts of reads per transcript as a proxy for transcript abundance

R code for round goby differential expression analysis

R code for round goby differential expression analysi

R code for analysis of shared orthologs

This R code uses information about the reciprocal best BLAST matches between round and tubenose goby transcripts to combine and analyze the count datasets for shared orthologs

Tubenose goby transcript count data

This file was generated using Corset software to process BAM files of RNAseq reads mapped to a de novo assembled transcriptome for nine tubenose goby and enumerate counts of reads per transcript as a proxy for transcript abundance

Reciprocal best hits between round and tubenose goby transcripts

This file was generated by reciprocally BLASTing the translated longest open reading frame of one species on the other. Pairs of round and tubenose goby transcripts retained in this file are where the pair represent each others best match. This file is required for the analysis of shared orthologs

Unix shell script for transcriptome assembly and read mapping

This script was used to perform de novo transcriptome assembly and read mapping for both round and tubenose goby. Its inclusion is primarily to document specific parameters used for these analysis steps

qPCR data

Raw and normalized starting cDNA concentrations from gill tissue for expression of 4 immune genes and 4 metabolic genes at rest and in response to challenges. Treatments are contained in separate tabs where "C" under the treatment column reflects control or resting state transcription and "T" or "P" indicates response to temperature or vaccine challenge

raw_data

Raw qPCR data for all analyzed genes (Detectors) for all individuals (Samples). Values are cycle relative threshold (Cq) output by QuantStudio 12K Flex instrument including technical replicates for each gene

pcr_efficiencies

PCR efficiencies calculated for each gene using LinRegPC

sample_annotation

Data file containing family, rearing environment, stress treatment and tank associations for each individual