Transcriptome of Xenopus andrei, an octoploid frog, during embryonic development.

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However, transcriptomic information is currently available for only one of these species, the tetraploid Xenopus laevis. Xenopus andrei, an octoploid species within the Xenopus genus, offers an opportunity for assessing a novel polyploid transcriptome during vertebrate development. RNA-Seq data was generated at nine different developmental stages ranging from unfertilized eggs through swimming tadpole stages and raw FASTQ files were deposited in the NCBI SRA database (accession number SRP134281). Additionally, RNA-seq data from all nine stages were pooled to create a de novo assembly of the transcriptome using Trinity and has been deposited in the NCBI GEO database (accession number GSE111639). To our knowledge, this represents the first published assembly of an octoploid vertebrate transcriptome. In total, 849 Mb were assembled, which led to the identification of 1,650,048 transcripts in the assembly with a contig N50 of 630 bases. This RNA-Seq and transcriptome data will be valuable for comparing polyploid transcriptomes across Xenopus species, as well as understanding evolutionary implications of whole-genome duplication and polyploidy in vertebrates.", "claims": [{"id": "claim-data-access", "statement": "The data presented here can be accessed at SRA: SRP134281 for raw FASTQ files of all sequencing, and GEO: GSE111639 for assembly of the transcriptome.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:29900348", "locator": "sections[3] \"Data\" paragraph 2", "quote": "The data presented here can be accessed at SRA: SRP134281 for raw FASTQ files of all sequencing, and GEO: GSE111639 for assembly of the transcriptome."}], "state": "complete"}, {"id": "claim-target-result", "statement": "RNA-Seq data from nine developmental stages were assembled de novo with Trinity to produce the first published assembly of an octoploid vertebrate transcriptome, totaling 849 Mb and 1,650,048 transcripts with a contig N50 of 630 bases; raw FASTQ files are available through NCBI SRA under accession SRP134281, and the transcriptome assembly is available through NCBI GEO under accession GSE111639.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:29900348", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "RNA-Seq data was generated at nine different developmental stages ranging from unfertilized eggs through swimming tadpole stages and raw FASTQ files were deposited in the NCBI SRA database (accession number SRP134281)."}, {"asset": "source:pmid:29900348", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Additionally, RNA-seq data from all nine stages were pooled to create a de novo assembly of the transcriptome using Trinity and has been deposited in the NCBI GEO database (accession number GSE111639)."}, {"asset": "source:pmid:29900348", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "To our knowledge, this represents the first published assembly of an octoploid vertebrate transcriptome."}, {"asset": "source:pmid:29900348", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "In total, 849 Mb were assembled, which led to the identification of 1,650,048 transcripts in the assembly with a contig N50 of 630 bases."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "RNA-Seq data from nine developmental stages were assembled de novo with Trinity to produce the first published assembly of an octoploid vertebrate transcriptome, totaling 849 Mb and 1,650,048 transcripts with a contig N50 of 630 bases; raw FASTQ files are available through NCBI SRA under accession SRP134281, and the transcriptome assembly is available through NCBI GEO under accession GSE111639.", "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:29900348"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "complete", "blocked_on": null, "description": "The GEO series accession resolves and its sample accessions are listed. 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