Precise modulation of transcription factor levels identifies features underlying dosage sensitivity

<strong>Processed data and code for "Precise modulation of transcription factor levels reveals drivers of dosage sensitivity," Naqvi et al 2022.</strong> <strong>Count/expression data</strong> all.sub.150bpclust.greater2.500bp.merge.ATAC.counts.fulldep.3h.24h.txt.gz - ATAC-seq counts from all samples (SOX9 titration and depletion) over all reproducible ATAC-seq peak regions all.sub.150bpclust.greater2.500bp.merge.k27ac.txt.gz - H3K27ac ChIP-seq counts from SOX9 depletion samples over all reproducible peak regions all.sub.150bpclust.greater2.500bp.merge.SOX9titr.V5.counts.txt.gz - V5 (SOX9) ChIP-seq counts from partial SOX9 titration (100%, 60%, 30%, 0%) over all reproducible peak regions all.sub.150bpclust.greater2.500bp.merge.SOX9titr.TWIST1.in.counts.tab.txt.gz - TWIST1 and input ChIP-seq counts from partial SOX9 titration (100%, 60%, 30%, 0%) over all reproducible peak regions rna.salmon.7rep.txi.counts.txt.gz - RNA-seq counts from SOX9 titration samples rna.salmon.7rep.txi.abundance.txt.gz - RNA-seq TPM values from SOX9 titration samples slam.tcreadcount.txt.gz - SLAM-seq T-C conversion-containing read counts (representing newly transcribed mRNAs) from SOX9 depletion samples slam.readcount.txt.gz - SLAM-seq read counts (representing all mRNAs) from SOX9 depletion samples <strong>Metadata</strong> all.protcod.gene.features.txt.gz - Features of interest for all protein-coding genes all.sub.150bpclust.greater2.500bp.merge.features.txt.gz - Features of interest for all reproducible peak regions atac_depletion_3h_24h_design.txt - design matrix for ATAC-seq SOX9 depletion samples atac_titration_48h_design.txt - design matrix for ATAC-seq SOX9 titration samples Homo_sapiens.GRCh38.cdna.all.txid2gene.id.symbol.type.txt.gz - Ensembl transcript types (for filtering to protein-coding genes in various analyses) k27_depletion_3h_24h_design.txt - design matrix for H3K27ac ChIP-seq SOX9 depletion samples v5_sox9titration_design.txt - design matrix for V5 (SOX9) ChIP-seq SOX9 partial titration samples twist1_sox9titration_design.txt - design matrix for TWIST1 ChIP-seq SOX9 partial titration samples rna_titration_48h_design.txt - design matrix for RNA-seq SOX9 titration samples slam_depletion_3h_24h_design.txt - design matrix for SLAM-seq SOX9 depletion samples <strong>Scripts</strong> atac_deseq_fitmodels_bs_parallel.R - R code for fitting bootstrapped Hill equations to all SOX9-dependent REs (computationally intensive, so has been coded for parallelization over multiple cores) Input: all.sub.150bpclust.greater2.500bp.merge.ATAC.counts.fulldep.3h.24h.txt.gz, atac_titration_48h_design.txt Output: enh_linear_sig_aic_bsmat.txt, enh_linear_sig_aic_bsmat_enhind.txt atac_deseq_fitmodels.R - R code for fitting Hill equations (no bootstrap) to all SOX9-dependent REs Input: all.sub.150bpclust.greater2.500bp.merge.ATAC.counts.fulldep.3h.24h.txt.gz, atac_titration_48h_design.txt Output: enh_linear_sig_aic.rds atac_k27_depletion_deseq.R - R code for DESeq2 analysis of ATAC and H3K27ac ChIP SOX9 depletion (3h and 24h) Input: all.sub.150bpclust.greater2.500bp.merge.ATAC.counts.fulldep.3h.24h.txt.gz, all.sub.150bpclust.greater2.500bp.merge.k27ac.txt.gz, atac_depletion_3h_24h_design.txt Output: atac_depletion_3h_24h_deseq.txt, k27_depletion_3h_24h_deseq.txt v5_twist1_sox9titration_deseq.R - R code for DESeq2 analysis of V5 (SOX9) and TWIST1 ChIP in partial SOX9 titration (100%, 60%, 30%, 0%) Input: all.sub.150bpclust.greater2.500bp.merge.SOX9titr.V5.counts.txt.gz, all.sub.150bpclust.greater2.500bp.merge.SOX9titr.TWIST1.in.counts.tab.txt.gz, v5_sox9titration_design.txt, twist1_sox9titration_design.txt Output: v5_sox9titration_deseq.txt, twist1_sox9titration_deseq.txt drm.R - Modified version of code from drc() package to prevent errors, install drc() with this version to avoid errors group_comparisons.Rmd - R code to compare computed parameters (i.e. ED50, Hill) between sets of REs/genes utilizing bootstrap information Input: enh_linear_sig_aic_bsmat_enhind.txt, enh_linear_sig_aic_bsmat.txt.gz, enh_linear_sig_aic.rds, gene_linear_sig_aic_bsmat_enhind.txt, gene_linear_sig_aic_bsmat.txt.gz, gene_linear_sig_aic.rds, all.sub.150bpclust.greater2.500bp.merge.features.txt.gz, all.protcod.gene.features.txt.gz Uses: summarize_bs_helper.R plot_re_gene_fits.Rmd - R code for plotting individual RE/gene counts and Hill/linear fits Input: all.sub.150bpclust.greater2.500bp.merge.ATAC.counts.fulldep.3h.24h.txt.gz, atac_titration_48h_design.txt, rna.salmon.7rep.txi.counts.txt.gz, rna.salmon.7rep.txi.abundance.txt.gz, rna_titration_48h_design.txt rna_deseq_fitmodels_bs_parallel.R - R code for fitting bootstrapped Hill equations to all SOX9-dependent genes (computationally intensive, so has been coded for parallelization over multiple cores) Input: rna.salmon.7rep.txi.counts.txt.gz, rna.salmon.7rep.txi.abundance.txt.gz, rna_titration_48h_design.txt Output: gene_linear_sig_aic_bsmat.txt, gene_linear_sig_aic_bsmat_enhind.txt rna_deseq_fitmodels.R - R code for fitting Hill equations (no bootstrap) to all SOX9-dependent genes Input: rna.salmon.7rep.txi.counts.txt.gz, rna.salmon.7rep.txi.abundance.txt.gz, rna_titration_48h_design.txt Output: gene_linear_sig_aic.rds slam_depletion_deseq.R - R code for DESeq2/sva analysis of SLAM-seq SOX9 depletion (3h and 24h) Input: slam.tcreadcount.txt.gz, slam_depletion_3h_24h_design.txt Output: slam_depletion_3h_24h_deseq.txt summarize_bs_helper.R - Helper functions for group_comparisons.Rmd <strong>Intermediate/output files (some files are gzipped to save space, the Rscripts that output them won't gzip but they expect gzipped input when indicated)</strong> atac_depletion_3h_24h_deseq.txt.gz - DESeq2 output of ATAC SOX9 depletion (3h and 24h) enh_linear_sig_aic_bsmat_enhind.txt - index to name file for SOX9-dependent RE bootstrap output enh_linear_sig_aic_bsmat.txt.gz - SOX9-dependent RE bootstrap output enh_linear_sig_aic.rds - Parameters from Hill equation fit on all SOX9-dependent REs (no bootstrap) (RDS file) gene_linear_sig_aic_bsmat_enhind.txt - index to name file for SOX9-dependent gene bootstrap output gene_linear_sig_aic_bsmat.txt.gz - SOX9-dependent gene bootstrap output gene_linear_sig_aic.rds - Parameters from Hill equation fit on all SOX9-dependent gene (no bootstrap) (RDS file) k27_depletion_3h_24h_deseq.txt.gz - DESeq2 output of H3K27ac ChIP-seq SOX9 depletion (3h and 24h) slam_depletion_3h_24h_deseq.txt.gz - DESeq2 output of SLAM-seq SOX9 depletion (3h and 24h) v5_sox9titration_deseq.txt.gz - DESeq2 output of V5 (SOX9) ChIP-seq in partial SOX9 titration (100%, 60%, 30%, 0%) twist1_sox9titration_deseq.txt.gz - DESeq2 output of TWIS1 ChIP-seq in partial SOX9 titration (100%, 60%, 30%, 0%) <strong>chromatin_predictions.tar.gz (self-contained folder for chromatin-based predictions of gene expression change) contains:</strong> ABC_6conc.sh - Bash script to calculate predicted gene expression change based on ATAC-seq fold-change at each of five SOX9 concentrations (warning: creates a number of very large additional intermediate output files). Requires as input all files in this folder except for all.sub.150bpclust.greater2.500bp.merge.ABC.5Mb.power-0.7.norm.6conc.all.total.txt <strong> </strong>all.sub.150bpclust.greater2.500bp.merge.ABC.5Mb.power-0.7.norm.6conc.all.total.txt - ATAC-based predicted fold-change of all genes each of five SOX9 concentrations (78, 52, 25, 8, 0, in that order), relative to 100% SOX9 all.sub.150bpclust.greater2.500bp.merge.ATAC.DMSO.counts.txt - ATAC-seq counts over all reproducible peak regions in updepleted samples all.sub.150bpclust.greater2.500bp.merge.bed - bed file of all reproducible peak regions all.sub.150bpclust.greater2.500bp.merge.deseq.allconc.lfc.txt - DESeq2 output from ATAC SOX9 titration, comparing each lowered SOX9 concentration to 100% SOX9 all.sub.150bpclust.greater2.500bp.merge.k27ac.dmso.counts.txt - H3K27ac ChIP-seq counts over all reproducible peak regions in updepleted samples hg38_refGene_TSS_collapsed.bed - collapsed TSSs for all genes hg38.genome - genome file