Drosophila Micro-C ZGA Analysis

Overview

This repository contains analysis code and figures for studying chromatin organization during the Drosophila zygotic genome activation (ZGA) using Micro-C.

Figure Locations

The figures and analysis are spread across several Jupyter notebooks:

Main Figures

Most of the main figures are in one notebook, but some are split into other notebooks for clarity.

• main_analysis/cleaned_up_figures.ipynb.gz: Contains the majority of the main figure plots and analysis
• main_analysis/Make Figure 5.ipynb: Contains the plots for Figure 5
• main_analysis/Make Figures 2C-E.ipynb.gz: Contains the plots for Figures 2C-E
• main_analysis/Make Figures 3B.ipynb: Contains the plots for Figure 3B
• main_analysis/Make Figures 4C, E.ipynb: Contains the plots for Figures 4C and 4E
• main_analysis/Make Figures 5E.ipynb: Contains the plots for Figure 5E
• main_analysis/Make Figures 6E.ipynb: Contains the plots for Figure 6E

D. virilis Analysis

• cleaned_dvir_browser_view.ipynb.gz: Contains comparative analysis and plots for D. virilis

Supplementary plots

• cleaned_up_figures.ipynb.gz: Contains most of the supplementary plots
• supplementary_analysis/Make Figures S2, S3.ipynb: Contains the plots for Figures S2 and S3
• supplementary_analysis/Make Figures S8.ipynb: Contains the plots for Figure S8
• supplementary_analysis/2_Make_Insulation_Correlation_Figures.ipynb.gz: Contains reproducibility plots for the insulation scores

Loop Analysis

The loop-associated analysis is split across three notebooks:

• supplementary_analysis/0_Process_loops.ipynb: Initial processing and analysis of chromatin loops
• supplementary_analysis/1_Make_Loop_Supp_Figures.ipynb: Supplementary figures related to loop analysis
• supplementary_analysis/2_Make_Insulation_Correlation_Figures.ipynb.gz: Analysis of insulation and correlation with loops
• supplementary_analysis/loop_DESEQ2/: Contains the DESEQ2 analysis for loop counts
• supplementary_analysis/loop_DESEQ2/COUNT/Make_DESeq2_Counts.ipynb: Contains the DESEQ2 analysis for loop counts

Data Access

The raw data and processed files associated with this analysis are available through GEO (accession number pending). ChIP-seq data aggregated over loops and boundaries is available in CSE_adata.h5ad, including metadata for each ChIP-seq sample, as well as annotations of loop anchors and clusters for each CSE.

Contact

For questions about the code or analysis, please open an issue in this repository or email gdolsten@princeton.edu.