fahrner_kabuki

Code and associated files for analysis of KS2 RNAseq data. Raw and processed data files available at GEO accession number GSE262539.

The RNAseq/final_analysis directory contains scripts and data objects for Fig 4 and Supp Fig 6 and 8.

• RNAseq_final.R: Imports the quant files, summarizes to transcript level using tximeta and performs differential analysis with DESeq2
• Fig4.Rmd: Generates plots displayed in Fig 4 and Supp Fig 6 and 8
• Several data objects MGI.*.rda: Gene lists obtained from MGI used in the Wilcoxon rank sum analyses
• Several other data objects permutation.rank.*.rda: Rank permutations generated in the course of the Wilcoxon rank sum analyses
• quants_final/: Salmon output files for the experiment Kabuki 2 Mut vs Wt cell lines at Day 14
• quants_final_KS1/: Salmon output files for a previously published experiment Kabuki 1 Mut vs Wt at Day 7 (Fahrner et al., JCI Insight 2019), processed identically
• RNAseq_final_KS1.R: Similar to RNAseq_final.R but for the previously published Kabuki 1 experiment

The subdirectory RNAseq/final_analysis/230510_KS1-KS2_NGS contains the script and sample sheet for Fig 5 and Supp Fig 9. This is the combined RNAseq experiment with both KS2 and KS1 cell lines, at Days 7 and 14 of chondrogenic differentiation.

• quants_final_KS1-KS2/: Salmon output files for the combined RNAseq experiment