Transcriptome datasets of the deep-sea amphipod Eurythenes maldoror and the surface amphipod Eogammarus possjeticus

Transcriptomic profiling was conducted on four biological replicates of the deep-sea amphipod group. Libraries were prepared and sequenced on an Illumina NovaSeq 6000 platform to generate 150 bp paired-end reads. The resulting raw sequencing data for the deep-sea amphipods have been deposited in CNGB. For comparative analysis, publicly available raw sequencing data from a surface-dwelling amphipod population were downloaded from the NCBI Sequence Read Archive (SRA) under accession number PRJNA472406. Raw sequencing reads were quality-controlled using fastp to remove adapter sequences and low-quality bases. A de novo transcriptome was assembled from the high-quality reads of all samples using Trinity (v2.15.2). The resulting transcripts were clustered to reduce redundancy with CD-HIT (v4.8.1) using a sequence identity threshold of 0.95. Transcript abundance for each sample was quantified against this assembled transcriptome using kallisto (v0.51.0). Assembled unigenes were functionally annotated by performing BLASTx searches against the NCBI non-redundant (nr) protein database with an E-value cutoff of 1e-10. This dataset file includes the complete transcriptome files from the de novo assembly of deep-sea and shallow-sea amphipods (deep-sea amphipod trinity.fasta and surface amphipod trinity.fasta), as well as the annotated files (deep-sea amphipod annotation.tblastx and surface amphipod annotation.tblastx), and the folder for quantitative gene expression (deep-sea amphipod quantify-1/2/3/4 and surface amphipod quantify-1/2/3). Each quantitative expression folder contains three types of quantitative files in tsv, h5, and json formats.