Single-embryo RNA sequencing for continuous and sex-specific gene expression analysis on Drosophila
Summary: Exploring early embryonic gene expression is challenging due to the rate of development and the limited material available. Here, we present a protocol for ordering Drosophila embryos along a developmental pseudo-time trajectory and determining the sex of the embryos using RNA-seq data. We...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
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Elsevier
2023-09-01
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| Series: | STAR Protocols |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2666166723005026 |
| _version_ | 1797690202709295104 |
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| author | J. Eduardo Pérez-Mojica Lennart Enders Kin H. Lau Adelheid Lempradl |
| author_facet | J. Eduardo Pérez-Mojica Lennart Enders Kin H. Lau Adelheid Lempradl |
| author_sort | J. Eduardo Pérez-Mojica |
| collection | DOAJ |
| description | Summary: Exploring early embryonic gene expression is challenging due to the rate of development and the limited material available. Here, we present a protocol for ordering Drosophila embryos along a developmental pseudo-time trajectory and determining the sex of the embryos using RNA-seq data. We describe steps for sample collection, RNA isolation, RNA-seq, and RNA-seq data processing. We then detail the establishment of a continuous transcriptome dataset for assessing gene expression throughout early development and in a sex-specific manner.For complete details on the use and execution of this protocol, please refer to Pérez-Mojica et al.1 : Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics. |
| first_indexed | 2024-03-12T01:56:10Z |
| format | Article |
| id | doaj.art-6a306c8ecfa848088955588b05661fd3 |
| institution | Directory Open Access Journal |
| issn | 2666-1667 |
| language | English |
| last_indexed | 2024-03-12T01:56:10Z |
| publishDate | 2023-09-01 |
| publisher | Elsevier |
| record_format | Article |
| series | STAR Protocols |
| spelling | doaj.art-6a306c8ecfa848088955588b05661fd32023-09-08T04:33:54ZengElsevierSTAR Protocols2666-16672023-09-0143102535Single-embryo RNA sequencing for continuous and sex-specific gene expression analysis on DrosophilaJ. Eduardo Pérez-Mojica0Lennart Enders1Kin H. Lau2Adelheid Lempradl3Department of Metabolism and Nutritional Programming, Van Andel Institute, Grand Rapids, MI 49503, USA; Corresponding authorDepartment of Epigenetics, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg im Breisgau, GermanyBioinformatics and Biostatistics Core, Van Andel Institute, Grand Rapids, MI 49503, USADepartment of Metabolism and Nutritional Programming, Van Andel Institute, Grand Rapids, MI 49503, USA; Corresponding authorSummary: Exploring early embryonic gene expression is challenging due to the rate of development and the limited material available. Here, we present a protocol for ordering Drosophila embryos along a developmental pseudo-time trajectory and determining the sex of the embryos using RNA-seq data. We describe steps for sample collection, RNA isolation, RNA-seq, and RNA-seq data processing. We then detail the establishment of a continuous transcriptome dataset for assessing gene expression throughout early development and in a sex-specific manner.For complete details on the use and execution of this protocol, please refer to Pérez-Mojica et al.1 : Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics.http://www.sciencedirect.com/science/article/pii/S2666166723005026Developmental BiologyRNAseqGene Expression |
| spellingShingle | J. Eduardo Pérez-Mojica Lennart Enders Kin H. Lau Adelheid Lempradl Single-embryo RNA sequencing for continuous and sex-specific gene expression analysis on Drosophila STAR Protocols Developmental Biology RNAseq Gene Expression |
| title | Single-embryo RNA sequencing for continuous and sex-specific gene expression analysis on Drosophila |
| title_full | Single-embryo RNA sequencing for continuous and sex-specific gene expression analysis on Drosophila |
| title_fullStr | Single-embryo RNA sequencing for continuous and sex-specific gene expression analysis on Drosophila |
| title_full_unstemmed | Single-embryo RNA sequencing for continuous and sex-specific gene expression analysis on Drosophila |
| title_short | Single-embryo RNA sequencing for continuous and sex-specific gene expression analysis on Drosophila |
| title_sort | single embryo rna sequencing for continuous and sex specific gene expression analysis on drosophila |
| topic | Developmental Biology RNAseq Gene Expression |
| url | http://www.sciencedirect.com/science/article/pii/S2666166723005026 |
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