Reduction of embryonic E93 expression as a key factor for the evolution of insect metamorphosis

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• Article "Reduction of embryonic E93 expression as a key factor for the evolution of insect metamorphosis"
• Link to preprint in bioRxiv: https://www.biorxiv.org/content/10.1101/2022.10.04.510826v1
• Scripts author: Gabriela Machaj, 2022
• Laboratory of Bioinformatics and Genome Biology, Jagiellonian University

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This repository contains the scripts written by Dr. Machaj for analyzing the data and obtaining the results publsihed at "Reduction of embryonic E93 expression as a key factor for the evolution of insect metamorphosis".

Scripts are organized in two main analysis:

1. RNA-seq analysis of B. germanica libraries under E93 knockdown compared to control
   1. Prepare data, QC, and mapping
   2. Table of counts, DEA, GSEA, etc.
2. Comparison of E93 expression in embryo vs pre-adult across hexapods
   1. Identify appropriate datasets in NCBI-SRA
   2. Download genomes form NCBI
   3. Download and map RNA-seq data from NCBI-SRA
   4. Generate tables of counts
   5. Calculate E93 expression ratio in pre-adult vs embryo