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Transcriptome sequencing data for the heater tissue of Mediterranean Swordfish, Xiphias gladius
Citation
Carnevali, O.; Castro, L.F.; Marisaldi, L.; Machado, A.; Università Politecnica delle Marche: Italy; Interdisciplinary Centre of Marine and Environmental Research (CIIMAR). University of Porto: Portugal; (2019): Transcriptome sequencing data for the heater tissue of Mediterranean Swordfish, Xiphias gladius. http://www.assembleplus.eu/information-system?module=dataset&dasid=6347

Availability: Unrestricted after moratorium period
Data are initially restricted, but the access condition relaxes to academic or unrestricted once a specified period of time after an event (such as collection, publication, completion of QC procedures or project cessation) has elapsed

Description
Swordfish heater tissue transcriptome: raw data and the final heater tissue transcriptome and relative statistics. Samples were collected between May and June in Carloforte (Sardinia, Italy, sampled in a tuna trap, right outside the town) and around Aeolian islands (Sicily, Italy, aboard a commercial longliner fishing vessel). more

The dataset consists of two parts: 1. The raw data cleaned and filtered according to requirements for NCBI submission. The raw data are .fastq files and represent the output from the Illumina NovaSeq 6000 sequencing. For each sample (16, 55, 60, 21 are the ID number of samples in the file name) there are F1 and F2 since the sequencing was 100 bp paired-end. 2. The final heater tissue transcriptome and relative statistics. The raw reads were treated as follows: sequencing raw reads were submitted to a conservative pipeline of quality control (Fastqc, Trimmomatic, Rcorrector and Centrifuge). In the end of pre-processing stage, only raw reads with phred score ≥ 28 were kept for downstream analysis. The de-novo transcriptome assembly was built with the Trinity assembler (default parameters) and decontaminated using previously stablished methods (Machado et al., 2019). The transcriptome assessment was done with Transrate and BUSCO (benchmarking universal single-copy orthologs) tools.

Scope
Themes:
Biology > Fish
Keywords:
Marine/Coastal, de novo transcriptome, heater tissue, Transcriptomics, MED, Central Mediterranean, MED, Italy, Sardinia, MED, Italy, Sicily: Aeolian I, MED, Tyrrhenian Sea, Xiphias gladius Linnaeus, 1758

Geographical coverage
MED, Central Mediterranean [Marine Regions]
MED, Italy, Sardinia [Marine Regions]
MED, Italy, Sicily: Aeolian I
MED, Tyrrhenian Sea [Marine Regions]

Temporal coverage
27 May 2019 - 9 June 2019

Taxonomic coverage
Xiphias gladius Linnaeus, 1758 [WoRMS]

Contributors
Polytechnic University of Marche; Faculty of Sciences; Department of Life and Environmental Sciences (DiSVA), moredata creator
University of Porto; Interdisciplinary Centre for Marine and Environmental Research (Porto) (CIIMAR), moredata creator

Project
ASSEMBLE+: Association of European Marine Biological Laboratories Expanded, more

Dataset status: In Progress
Data type: Data
Data origin: Research: lab experiment
Metadatarecord created: 2019-10-22
Information last updated: 2020-04-16
All data in the Integrated Marine Information System (IMIS) is subject to the VLIZ privacy policy