Overview
This repository contains the preprocessing and analysis pipelines used to generate the ATAC-seq, ChIP-seq, and single-embryo RNA-seq results in the paper. We profiled chromatin accessibility and transcription factor occupancy across a panel of Drosophila melanogaster genotypes spanning wild type, BOT-background (bcd⁻ osk⁻ tsl⁻), and BOTC-background (BOT + cic⁻) embryos, with and without toll10b-driven ventralization, at nuclear cycle 14 (early and late) and gastrulation stages, alongside matched single-embryo RNA-seq to quantify transcriptional output.
embryo_segmentation_and_expression_analysis_ESEA_V1.m segments embryos from raw microscopy images and extracts intensity profiles for expression analysis.
Version requirements: MATLAB: 2021; Windows 10 Data Format: tif; lif; czi; mat Typical Run time: <1 min Briefly: This code accepts an image file, converts to uint16 and then accepts a user defined threshold to segment the embryo. The user then picks the embryo mask and the intensity profiles are generated. Instructions: Instructions to run the code is available in the Methods section as well as code header. Demo Data: ctrl_122.tif
Contact: imrodrig@caltech.edu