Analysis, files, and figures for the following publication: "Genome-wide characterization of the Caenorhabditis elegans intestine GATA transcription factor ELT-2"

This repository serves to simplify and supersede the exploratory analysis performed for this publication. Code related to initial exploratory analysis can be found in the following repository: ELT-2-ChIP-revision

Analysis for this publication was performed using the R language. To utilize and explore the code in this repository, clone the repository and open the williams_et_al.Rproj file using RStudio. Relevant package installation commands are listed where necessary. Output files and plots were generated using R version 4.1.0 and RStudio version 1.4.1106.

Below describes the analysis directory structure:

• 01_tissue_specific_genes: Generate a list of "tissue specific genes" based on WormBase Ontology Browser.
• 02_emb_L1_L3_intestine_RNAseq: RNA-seq analysis of FACS isolated intestine samples using the DESeq2 package.
• 03_elt2_RNAseq: RNA-seq analysis of elt-2 (-) vs. wt samples (Dineen and Nishimura et al., 2018) using the DESeq2 package.
• 04_promoters: Analysis of ELT-2 ChIP-seq data downloaded from the modERN resource. Analysis in this directory was performed by David King.
• 05_elt2_target_analysis: Quantification and visualization gene set categories corresponding to intestine enrichment and ELT-2 regulation. Additional analysis includes Gene Ontology (GO) analysis and quantification of microscopy images from translation reporter worm strains.
• 06_intestine_enriched_genes: GO analysis of intestine enriched genes evaluated generated in the intestine FACS RNA-seq dataset.
• 07_expression_heatmaps: generate heatmaps for transcript abundance in the intestine transcriptome and elt-2 (-) RNA-seq datasets.
• 08_elt2_promoter_regulation: evaluate if there is a higher abundance of RNA-seq reads aligning to the elt-2 promoter in elt-2(-) compared to wildtype

Within each directory are three sub-directories:

• 01_input: contains any input data necessary to perform the analysis
• 02_scripts: contains the R markdown scripts that were utilized to perform the analysis. Corresponding HTML and PDF files are associated with each R markdown script to facilitate documentation of the analysis performed.
• 03_output: Contains any output files or figures generated in the R markdown scripts.