Single-embryo RNA sequencing for continuous and sex-specific gene expression analysis on Drosophila

J Eduardo Pérez-Mojica; Lennart Enders; Kin H Lau; Adelheid Lempradl

doi:10.1016/j.xpro.2023.102535

Single-embryo RNA sequencing for continuous and sex-specific gene expression analysis on Drosophila

STAR Protoc. 2023 Sep 15;4(3):102535. doi: 10.1016/j.xpro.2023.102535. Epub 2023 Sep 7.

Authors

J Eduardo Pérez-Mojica¹, Lennart Enders², Kin H Lau³, Adelheid Lempradl⁴

Affiliations

¹ Department of Metabolism and Nutritional Programming, Van Andel Institute, Grand Rapids, MI 49503, USA. Electronic address: [email protected].
² Department of Epigenetics, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg im Breisgau, Germany.
³ Bioinformatics and Biostatistics Core, Van Andel Institute, Grand Rapids, MI 49503, USA.
⁴ Department of Metabolism and Nutritional Programming, Van Andel Institute, Grand Rapids, MI 49503, USA. Electronic address: [email protected].

Abstract

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.

Keywords: Developmental Biology; Gene Expression; RNAseq.

MeSH terms

Animals
Drosophila* / genetics
Female
Gene Expression Profiling*
Male
RNA-Seq
Sequence Analysis, RNA
Transcriptome / genetics