Annotating and quantifying pri-miRNA transcripts using RNA-Seq data of wild type and serrate-1 globular stage embryos of Arabidopsis thaliana
The genome annotation for the model plant Arabidopsis thaliana does not include the primary transcripts from which MIRNAs are processed. Here we present and analyze the raw mRNA sequencing data from wild type and serrate-1 globular stage embryos of A. thaliana, ecotype Columbia. Because SERRATE is r...
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
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Elsevier
2017-12-01
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| Series: | Data in Brief |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S235234091730536X |
| _version_ | 1811259152400384000 |
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| author | Daniel Lepe-Soltero Alma Armenta-Medina Daoquan Xiang Raju Datla C. Stewart Gillmor Cei Abreu-Goodger |
| author_facet | Daniel Lepe-Soltero Alma Armenta-Medina Daoquan Xiang Raju Datla C. Stewart Gillmor Cei Abreu-Goodger |
| author_sort | Daniel Lepe-Soltero |
| collection | DOAJ |
| description | The genome annotation for the model plant Arabidopsis thaliana does not include the primary transcripts from which MIRNAs are processed. Here we present and analyze the raw mRNA sequencing data from wild type and serrate-1 globular stage embryos of A. thaliana, ecotype Columbia. Because SERRATE is required for pri-miRNA processing, these precursors accumulate in serrate-1 mutants, facilitating their detection using standard RNA-Seq protocols. We first use the mapping of the RNA-Seq reads to the reference genome to annotate the potential primary transcripts of MIRNAs expressed in the embryo. We then quantify these pri-miRNAs in wild type and serrate-1 mutants. Finally, we use differential expression analysis to determine which are up-regulated in serrate-1 compared to wild type, to select the best candidates for bona fide pri-miRNAs expressed in the globular stage embryos. In addition, we analyze a previously published RNA-Seq dataset of wild type and dicer-like 1 mutant embryos at the globular stage [1]. Our data are interpreted and discussed in a separate article [2]. |
| first_indexed | 2024-04-12T18:26:10Z |
| format | Article |
| id | doaj.art-44b929af9cad4de58d12147b67963319 |
| institution | Directory Open Access Journal |
| issn | 2352-3409 |
| language | English |
| last_indexed | 2024-04-12T18:26:10Z |
| publishDate | 2017-12-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Data in Brief |
| spelling | doaj.art-44b929af9cad4de58d12147b679633192022-12-22T03:21:14ZengElsevierData in Brief2352-34092017-12-0115642647Annotating and quantifying pri-miRNA transcripts using RNA-Seq data of wild type and serrate-1 globular stage embryos of Arabidopsis thalianaDaniel Lepe-Soltero0Alma Armenta-Medina1Daoquan Xiang2Raju Datla3C. Stewart Gillmor4Cei Abreu-Goodger5Laboratorio Nacional de Genómica para la Biodiversidad (Langebio), Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados (CINVESTAV), Irapuato, Guanajuato, MexicoLaboratorio Nacional de Genómica para la Biodiversidad (Langebio), Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados (CINVESTAV), Irapuato, Guanajuato, MexicoPlant Biotechnology Institute, National Research Council, Saskatoon, Saskatchewan, CanadaPlant Biotechnology Institute, National Research Council, Saskatoon, Saskatchewan, CanadaLaboratorio Nacional de Genómica para la Biodiversidad (Langebio), Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados (CINVESTAV), Irapuato, Guanajuato, MexicoLaboratorio Nacional de Genómica para la Biodiversidad (Langebio), Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados (CINVESTAV), Irapuato, Guanajuato, Mexico; Corresponding author.The genome annotation for the model plant Arabidopsis thaliana does not include the primary transcripts from which MIRNAs are processed. Here we present and analyze the raw mRNA sequencing data from wild type and serrate-1 globular stage embryos of A. thaliana, ecotype Columbia. Because SERRATE is required for pri-miRNA processing, these precursors accumulate in serrate-1 mutants, facilitating their detection using standard RNA-Seq protocols. We first use the mapping of the RNA-Seq reads to the reference genome to annotate the potential primary transcripts of MIRNAs expressed in the embryo. We then quantify these pri-miRNAs in wild type and serrate-1 mutants. Finally, we use differential expression analysis to determine which are up-regulated in serrate-1 compared to wild type, to select the best candidates for bona fide pri-miRNAs expressed in the globular stage embryos. In addition, we analyze a previously published RNA-Seq dataset of wild type and dicer-like 1 mutant embryos at the globular stage [1]. Our data are interpreted and discussed in a separate article [2].http://www.sciencedirect.com/science/article/pii/S235234091730536X |
| spellingShingle | Daniel Lepe-Soltero Alma Armenta-Medina Daoquan Xiang Raju Datla C. Stewart Gillmor Cei Abreu-Goodger Annotating and quantifying pri-miRNA transcripts using RNA-Seq data of wild type and serrate-1 globular stage embryos of Arabidopsis thaliana Data in Brief |
| title | Annotating and quantifying pri-miRNA transcripts using RNA-Seq data of wild type and serrate-1 globular stage embryos of Arabidopsis thaliana |
| title_full | Annotating and quantifying pri-miRNA transcripts using RNA-Seq data of wild type and serrate-1 globular stage embryos of Arabidopsis thaliana |
| title_fullStr | Annotating and quantifying pri-miRNA transcripts using RNA-Seq data of wild type and serrate-1 globular stage embryos of Arabidopsis thaliana |
| title_full_unstemmed | Annotating and quantifying pri-miRNA transcripts using RNA-Seq data of wild type and serrate-1 globular stage embryos of Arabidopsis thaliana |
| title_short | Annotating and quantifying pri-miRNA transcripts using RNA-Seq data of wild type and serrate-1 globular stage embryos of Arabidopsis thaliana |
| title_sort | annotating and quantifying pri mirna transcripts using rna seq data of wild type and serrate 1 globular stage embryos of arabidopsis thaliana |
| url | http://www.sciencedirect.com/science/article/pii/S235234091730536X |
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