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De novo transcriptome assembly of loggerhead sea turtle nesting of the Colombian Caribbean
Loggerhead sea turtle Caretta caretta is widely distributed in the oceans of tropical and subtropical latitude. This turtle is an endangered species due to anthropic and natural factors that have decreased their population levels. In this study, RNA sequencing and de-novo assembly of genes expressed...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Elsevier
2017
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5472237/ https://www.ncbi.nlm.nih.gov/pubmed/28649496 http://dx.doi.org/10.1016/j.gdata.2017.06.005 |
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author | Hernández-Fernández, Javier Pinzón, Andrés Mariño-Ramírez, Leonardo |
author_facet | Hernández-Fernández, Javier Pinzón, Andrés Mariño-Ramírez, Leonardo |
author_sort | Hernández-Fernández, Javier |
collection | PubMed |
description | Loggerhead sea turtle Caretta caretta is widely distributed in the oceans of tropical and subtropical latitude. This turtle is an endangered species due to anthropic and natural factors that have decreased their population levels. In this study, RNA sequencing and de-novo assembly of genes expressed in blood were performed. The raw FASTQ files have been deposited on NCBI's SRA database with accession number SRX2629512. A total of 5.4 Gb raw sequence data were obtained, corresponding to 48,257,019 raw reads. Trinity pipeline was used to perform a de-novo assembly, we were able to identify 64,930 transcripts for female loggerhead turtle transcriptome with an N50 of 1131 bp. The obtained transcriptome data will be useful for further studies of the physiology, biochemistry and evolution in this species. |
format | Online Article Text |
id | pubmed-5472237 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2017 |
publisher | Elsevier |
record_format | MEDLINE/PubMed |
spelling | pubmed-54722372017-06-23 De novo transcriptome assembly of loggerhead sea turtle nesting of the Colombian Caribbean Hernández-Fernández, Javier Pinzón, Andrés Mariño-Ramírez, Leonardo Genom Data Data in Brief Loggerhead sea turtle Caretta caretta is widely distributed in the oceans of tropical and subtropical latitude. This turtle is an endangered species due to anthropic and natural factors that have decreased their population levels. In this study, RNA sequencing and de-novo assembly of genes expressed in blood were performed. The raw FASTQ files have been deposited on NCBI's SRA database with accession number SRX2629512. A total of 5.4 Gb raw sequence data were obtained, corresponding to 48,257,019 raw reads. Trinity pipeline was used to perform a de-novo assembly, we were able to identify 64,930 transcripts for female loggerhead turtle transcriptome with an N50 of 1131 bp. The obtained transcriptome data will be useful for further studies of the physiology, biochemistry and evolution in this species. Elsevier 2017-06-08 /pmc/articles/PMC5472237/ /pubmed/28649496 http://dx.doi.org/10.1016/j.gdata.2017.06.005 Text en © 2017 The Authors http://creativecommons.org/licenses/by-nc-nd/4.0/ This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/). |
spellingShingle | Data in Brief Hernández-Fernández, Javier Pinzón, Andrés Mariño-Ramírez, Leonardo De novo transcriptome assembly of loggerhead sea turtle nesting of the Colombian Caribbean |
title | De novo transcriptome assembly of loggerhead sea turtle nesting of the Colombian Caribbean |
title_full | De novo transcriptome assembly of loggerhead sea turtle nesting of the Colombian Caribbean |
title_fullStr | De novo transcriptome assembly of loggerhead sea turtle nesting of the Colombian Caribbean |
title_full_unstemmed | De novo transcriptome assembly of loggerhead sea turtle nesting of the Colombian Caribbean |
title_short | De novo transcriptome assembly of loggerhead sea turtle nesting of the Colombian Caribbean |
title_sort | de novo transcriptome assembly of loggerhead sea turtle nesting of the colombian caribbean |
topic | Data in Brief |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5472237/ https://www.ncbi.nlm.nih.gov/pubmed/28649496 http://dx.doi.org/10.1016/j.gdata.2017.06.005 |
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