jchen2025/zga-replication-analysis

Analysis code: DNA replication and transcriptional activation in early Drosophila embryos

分析代码：果蝇早期胚胎发育中 DNA 复制与转录激活的协同机制

Bioinformatics pipelines from the master's thesis A synergistic mechanism between DNA replication and transcriptional activation during early embryonic development in Drosophila (Jiale Chen, Central South University, 2023; supervisor Prof. Kai Yuan).

本仓库整理自中南大学硕士学位论文《果蝇早期胚胎发育过程中 DNA 复制与转录激活之间的协同机制研究》（陈佳乐，2023；导师袁凯教授）第 4 章“生物信息学分析方法和流程”。

The study integrates public ChIP-seq, ATAC-seq, Hi-C and single-embryo RNA-seq data with single-embryo whole-genome sequencing (Cycles 11–13) to ask how the origin recognition complex subunit ORC2 and the pioneer factor Zelda relate to early-replicating regions and zygotic genome activation (ZGA).

This repository contains code and a list of public accessions only. No raw or processed sequencing data are included. 本仓库只包含代码和公共数据编号，不含任何原始或处理后的测序数据。

Repository layout / 目录结构

config/config.sh                      shared paths (reference genome, indices, threads)
environment.yml                       conda environment (tool versions from the thesis)
data/accessions.csv                   public datasets used (GEO / ArrayExpress)
scripts/
  00_download/download_fastq.sh       download + SRA -> FASTQ
  01_chipseq/
    chipseq_pipeline.sh               trim, Bowtie2, MarkDuplicates, input-subtracted RPM bigWig, MACS2, repeat overlap
    plot_signal_heatmaps.sh           deepTools computeMatrix / plotHeatmap / plotProfile
    chipseeker_annotation.R           peak annotation, distance to TSS
    homer_motif.sh                    HOMER motif enrichment
  02_atacseq/
    atacseq_pipeline.sh               QC, trim, Bowtie2, MACS2 (BAMPE), gene overlap, CPM bigWig
    atac_differential.R               DESeq2 differential accessibility
  03_wgs_cnv/
    read_depth.sh                     sequencing depth per FASTQ
    wgs_align.sh                      BWA-MEM, sort, MarkDuplicates
    cnvkit_copy_number.sh             CNVkit S phase vs previous M phase, segment, scatter
    early_replication_regions.sh      log2 ratio >= 1 regions, overlap with Zelda/Clamp, Cycle 12 vs 13 conservation
    overlap_hypergeom.R               hypergeometric test for region overlaps
    cn_expression_correlation.R       Spearman correlation: copy number vs zygotic gene expression
  04_hic/
    juicer_run.sh                     BBMap repair + Juicer contact maps
    hicexplorer_tads.sh               .hic -> .cool -> .h5, contact maps, hicFindTADs, hicPlotTADs
    tracks.ini                        multi-track config (Hi-C, TADs, ORC2, Zelda, genes)
  05_rnaseq/
    rnaseq_pipeline.sh                trim, HISAT2, featureCounts
    deseq2_cpm_pca.R                  CPM export, PCA, Cycle 14 vs Cycle 12 DE
  06_enrichment/go_kegg_enrichment.R  clusterProfiler GO + KEGG (dme)
  07_plots/venn_peaks.py              interval-based Venn diagram
CHANGES_FROM_THESIS.md                fixes made relative to the printed thesis code

Analysis flow / 分析流程

public FASTQ (GEO / ArrayExpress)          single-embryo WGS (C11 M ... C13 M)
      |                                                 |
ChIP-seq / ATAC-seq / RNA-seq / Hi-C          BWA-MEM -> MarkDuplicates
      |                                                 |
peaks, bigWig, CPM, contact maps, TADs        CNVkit log2 ratio vs previous M phase
      \                                                /
       +---- early-replicating regions (log2 >= 1) --+
                         |
   overlap with ORC2 / Zelda / Clamp peaks, signal profiles,
   hypergeometric tests, copy number vs expression correlation,
   GO / KEGG enrichment, Venn diagrams

Quick start / 快速开始

conda env create -f environment.yml
conda activate zga-replication
# edit reference paths
vim config/config.sh

# ChIP-seq example: Zelda Cycle 13 vs its input
bash scripts/01_chipseq/chipseq_pipeline.sh zld_c13 zld_c13_input

# ORC2 / Zelda overlap
python scripts/07_plots/venn_peaks.py peaks/ORC2_peaks.bed peaks/zld_c13_peaks.bed \
  --labels ORC2 Zelda -o orc2_zelda_venn.pdf

Reference genome: dm6 (BDGP Release 6 + ISO1 MT); annotation from FlyBase, UCSC and Ensembl release 109.

Public datasets / 公共数据

See data/accessions.csv: Zelda (GSE30757), Clamp (GSE152598), histone modifications (GSE58935), Pol II (GSE62925), H4K16ac (GSE130335), GAF (GSE152773), ORC2 (GSE38293), ATAC-seq (GSE83851), Hi-C (E-MTAB-4918), single-embryo RNA-seq (GSE154502).

Notes / 说明

• The printed thesis code was cleaned up into runnable scripts; a few bugs were fixed (wrong MACS2 control, human annotation databases, hypergeometric tail, etc.). See CHANGES_FROM_THESIS.md.
• Scripts were syntax-checked but have not been re-run end to end on the original data in this form.
• 论文中的代码片段已整理为可运行脚本，并修正了若干问题（详见 CHANGES_FROM_THESIS.md）。脚本已通过语法检查，但尚未用原始数据以当前形式完整重跑。

Citation

@mastersthesis{chen2023zga,
  author = {Chen, Jiale},
  title  = {A synergistic mechanism between DNA replication and transcriptional activation during early embryonic development in Drosophila},
  school = {Central South University},
  year   = {2023}
}

Contact

Jiale Chen · GitHub @jlchen5