DOI: 10.34636/dmportal/9qm0f7
title: Gonadal transcriptome assembly, functional annotation and open reading frames of the edible sea urchin, Paracentrotus lividus. Support dataset of the article https://doi.org/10.1016/j.aqrep.2021.100936

description: Gonadal transcriptome assembly, functional annotation and open reading frames of the edible sea urchin, Paracentrotus lividus - Support dataset of the article. 1 - Data Description: Compressed transcriptome assemblies (versions 0 and 1) of Paracentrotus lividus (RNA sequence ;EDAM:data_3495 ; FASTA;EDAM:format_1929 ; GZIP format ;EDAM:format_3989). P.lividus_Transcriptome_V0.fasta.gz P.lividus_Transcriptome_V1.fasta.gz Compressed functional annotation reports of versions 0 and 1 of transcriptome assembly of Paracentrotus lividus (xlsx;EDAM:format_3620 ; GZIP format;EDAM:format_3989). P.lividus_Transcriptome_V0_Annotation_Report.xlsx.gz P.lividus_Transcriptome_V1_Annotation_Report.xlsx.gz Compressed open reading frames predicted in version 0 transcriptome assembly of Paracentrotus lividus (Protein sequence;EDAM:data_2976 ; FASTA;EDAM:format_1929 ; GZIP format ;EDAM:format_3989). P.lividus_Transcriptome_V0_Transdecoder_orfs.fasta.gz 2 - Data Processing: Transcriptome assemblies of Paracentrotus lividus. Version 0 - The initial version of the Paracentrotus lividus gonadal transcriptome assembly (V0) was performed using the raw RNASeq reads of 6 specimens (3 males, 3 females ; BioProject:PRJNA625933) and the Trinity (RRID:SCR_013048) (version 2.8.4) assembler, with the specific parameter (SS_lib_type RF). The detailed process can be consulted in the Material and methods - Section 2.3 of the original publication. Version 1 - The V1 version of the Paracentrotus lividus gonadal transcriptome assembly was obtained by the filtering and redundancy removal of V0 version, based on three criteria, codifying status, functional annotation, and read coverage of the transcripts. The detailed process can be consulted in the Material and methods - Section 2.5 of the original publication. Functional annotation report of versions 0 and 1 of the transcriptome assembly of Paracentrotus lividus. The annotation report of the Paracentrotus lividus gonadal transcriptome assembly (V0) was performed using the Trinotate (RRID:SCR_018930) pipeline (version 3.0.2). The V1 annotation report corresponds to a sub-dataset of V0 transcriptome assembly version. The detailed process can be consulted in the Material and methods - Section 2.4 of the original publication. Open reading frames predicted in version 0 transcriptome assembly of Paracentrotus lividus. The open reading frames of Paracentrotus lividus gonadal transcriptome assembly (V0) were predicted using the TransDecoder (RRID:SCR_017647) pipeline (version 5.3.0). The detailed process can be consulted in the Material and methods - Section 2.4 of the original publication. 3 - Data ontology and nomenclature : Data type: Species : Paracentrotus lividus;NCBI:txid7656 Tissue: gonad;UBERON:0000991 Experiment Type: RNA-seq assay;OBI:0001271 Developmental stage: adult organism;UBERON:0007023 Raw Data: Sequence Read Archive BioProject:PRJNA625933 Custom nucleotide sequence headers follow the nomenclature: &gt;Name.OfSpecies_TrinityCode (e.g. &gt;P.lividus_DN0_c10_g1_i2) Custom protein sequence headers follow the nomenclature: &gt;Name.OfSpecies_TrinityCode.NumberofOrfDetected (e.g.&gt;P.lividus_DN0_c10_g1_i2.p1)