Neural DV ATAC

Scripts for genomic data analysis in Delás et al (2022) Dev Cell

Developmental cell fate choice in neural tube progenitors employs two distinct cis-regulatory strategies

M. Joaquina Delás, Christos M. Kalaitzis, Tamara Fawzi, Madeleine Demuth, Isabel Zhang, Hannah T Stuart, Elena Costantini, Kenzo Ivanovitch, Elly M.Tanaka and James Briscoe

Analysis and code: M. Joaquina Delás

• Email
• Web

Data download

• How to download (using nf-core/fetchngs) for datasets produced in this paper:
  • CaTS-ATAC
  • Fixed RNA-seq
  • Inducibled Foxa2 bulk ATAC-seq

Sequencing processing

• CaTS-ATAC sequencing processing (using nf-core/atacseq):
  • pipeline script
  • fdr interval filtering
• RNA-seq processing (using nf-core/rnaseq):
  • pipeline script
  • removal of PCR duplicates
• Published ChIP-seq processing (using nf-core/chipseq) :
  • summary and scripts
• Bulk ATAC-seq processing (using nf-core/atacseq):
  • pipeline script

CaTS-ATAC analysis

• Comparison of accessibility across conditions (using Deseq2)
  • Differential accessibility between SAG concentrations
• Global accessibility analysis (using Deseq2):
  • PCA and correlation heatmaps
  • Differentially accessible elements
  • kmeans clustering
• Heatmap visualization of ATAC-seq and ChIP-seq (using deeptools):
  • CaTS-ATAC and ChIP
  • FOXA2 ChIP
• Metaplot of ChIPseq over ATAC peaks, and ATAC clusters over ChIPseq peaks

RNA-seq analysis

• Normalized counts export and key genes (using Deseq2)
  • Analysis and plot

Footprinting analysis

• Footprinting score calculations (using TOBIAS)
  • Scripts
• Most variable footprints across p0-M
  • Analysis and plots
• Most variable footprints across all: plot of p3-specific FOX
  • Analysis and plots

Inducible Foxa2 ATACseq

• Differential accessibility in inducible Foxa2 (using Deseq2)
  • Analysis and plots
• Intersect opened regions with CaTS-ATAC clusters
  • script
• Plotting intersects
  • Plots of intersect