ATAC-seq and single-cell mRNA-seq of gata5GFP+ cells in early zebrafish development

This repository contains code used in the analysis of the manuscript: "GATA4/5/6 family transcription factors are conserved determinants of cardiac versus pharyngeal mesoderm fate" https://www.science.org/doi/10.1126/sciadv.abg0834.

06/23/2022

• ATAC-seq of gata5GFP+/- cells in WT and Gata5/6 deficient zebrafish embryos during gastrulation (8 hpf)
• Scripts for ATAC-seq analysis has been added to the repository (from QC, alignment to all downstream analysis)

11/29/2020

• Single-cell mRNA-seq of gata5GFP+ cells in WT and Gata5/6 deficient cells from gastrulation to somitogenesis in zebrafish
• Scripts for making Figure 1-3 and Supplementary Figure 1-3.
• Input matrices can be found at ArrayExpress (E-MTAB-9193) and processed Rdata can be downloaded at figShare (https://figshare.com/s/72704b3218b17b071523).
• rmd folder contains the Rmarkdown files and asscociated Html outputs for Seurat clustering and dynverse trajectory analyses.
• seurat_plots and dynvers_plots folders contains the figures generated from each analysis.
• STITCH folder contains scripts and figures for making the force-directed layout.