Original paired-end transcriptome outputs from the RNAseq analyses of the deep-sea zoanthid Zibrowius primnoidus
Description
This dataset contains outputs generated from the original paired-end transcriptomic analyses of the deep-sea zoanthid Zibrowius primnoidus. The dataset includes the following files: • 155835_ID3533_1-1_S111_L004_R1_001.fastq.gz.P.qtrim.gz: Preprocessed forward reads used for the de novo assembly, obtained from paired-end RNA-Seq data of Zibrowius primnoidus, containing high-quality sequences that passed quality trimming and filtering with Trimmomatic. • 155835_ID3533_1-1_S111_L004_R2_001.fastq.gz.P.qtrim.gz: Preprocessed reverse reads used for the de novo assembly, obtained from paired-end RNA-Seq data of Zibrowius primnoidus, containing high-quality sequences that passed quality trimming and filtering with Trimmomatic. • Zibrowius_primnoidus_RF_assembly.Trinity.fasta: Original, non-filtered de novo paired-end transcriptome assembly of Zibrowius primnoidus, generated from ~90 million PE reads using the Trinity assembler. • Zibrowius_primnoidus_RF_assembly.Trinity.fasta_stats.txt: Statistical summary of the paired-end transcriptome assembly of Zibrowius primnoidus (e.g. number of transcripts, N50, GC content). • Zibrowius_primnoidus_RF_assembly.Trinity.fasta.gene_trans_map: Transcript-to-gene mapping file generated during the Trinity paired-end transcriptome assembly of Zibrowius primnoidus. • quant_Zp.sf: Salmon output file containing expression estimates (transcript-level abundance) for the assembled transcripts from the paired-end RNA-Seq data of Zibrowius primnoidus. Additionally, the dataset includes the following files from DIAMOND BLASTx analyses, which used the original de novo paired-end transcriptome assembly of Zibrowius primnoidus: • Zibrowius_primnoidus_assembly.Trinity.blastx.outfmt6: BLASTx output file against the UniRef90 database, reporting the top alignment for each query (assembled transcript) from the paired-end assembly of Zibrowius primnoidus. • Zibrowius_primnoidus_assembly.Trinity.blastx.outfmt6.grouped: Grouped BLASTx hits from the paired-end assembly of Zibrowius primnoidus, designed to improve sequence coverage by combining multiple high-scoring segment pairs (HSPs). • Zibrowius_primnoidus_assembly.Trinity.blastx.outfmt6.hist: Histogram summarizing the distribution of BLASTx hit lengths obtained from the paired-end assembly of Zibrowius primnoidus. • Zibrowius_primnoidus_assembly.Trinity.blastx.outfmt6.w_pct_hit_length: File providing percentages of hit lengths from BLASTx analyses of the paired-end assembly of Zibrowius primnoidus, including each top hit’s length and the percentage of that length covered in the alignment.
Files
Steps to reproduce
The paired-end transcriptome of the deep-sea zoanthid Zibrowius primnoidus (Zibrowius_primnoidus_RF_assembly.Trinity.fasta) was assembled with Trinity v2.15.1 using a single k-mer in forward mode. The associated output files (assembly statistics, gene–transcript mapping, and expression quantification) were generated as part of the Trinity RNA-Seq pipeline (see Trinity documentation: https://github.com/trinityrnaseq/trinityrnaseq/wiki ). Raw Illumina paired-end reads were quality-filtered and trimmed using Trimmomatic v0.39, removing low-quality bases and adapter contamination. Only the high-quality paired reads (155835_ID3533_1-1_S111_L004_R1_001.fastq.gz.P.qtrim.gz and 155835_ID3533_1-1_S111_L004_R2_001.fastq.gz.P.qtrim.gz) were retained for the de novo assembly. Transcript abundance estimates (quant_Zp.sf) were obtained with Salmon, using quasi-mapping against the Trinity assembly. Functional annotation of the assembled transcripts was carried out with DIAMOND BLASTx searches against the UniRef90 database, producing the files Zibrowius_primnoidus_assembly.Trinity.blastx.outfmt6, .grouped, .hist, and .w_pct_hit_length.
Institutions
- Stazione Zoologica Anton Dohrn
Categories
Funders
- This work was supported by Centro Ricerche ed Infrastrutture Marine Avanzate in Calabria (CRIMAC) - Fondo FSC 2014-2020 - Piano Stralcio «Ricerca e Innovazione 2015-2017» – Programma Nazionale Infrastrutture di Ricerca (PNIR), CUP C64I20000320001.