Precise modulation of transcription factor levels reveals drivers of dosage sensitivity

Processed data and code for "Precise modulation of transcription factor levels reveals drivers of dosage sensitivity," Naqvi et al 2022.

Count/expression data

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

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

Metadata

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

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

Scripts

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 

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

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)

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)

chromatin_predictions.tar.gz (self-contained folder for chromatin-based predictions of gene expression change) contains:

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

 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