This repository contains the code used to design and optimize the transcription factor activity reporters in the following studies:

• Trauernicht M, et al. (2023) Optimisation of TP53 reporters by systematic dissection of synthetic TP53 response elements. Nucleic Acids Research 51(18):9690-9702 (https://academic.oup.com/nar/article/51/18/9690/7256891)
• Trauernicht M, et al. Optimized reporters for multiplexed detection of transcription factor activity (submitted)

• p53_GR_initial_predictions.R Uses the RapidScore library and the associated sequence optimization code to build a set of sequences with varying affinity and number of mutations
• response_element_scorer.R Uses the RapidScore library to compute affinities for the designed response elements
• Images/ contains plots made by p53_GR_initial_predictions.R
• RData/ contains the p53/GR models used to make predictions/score
• data/ contains input files necessary for the two R scripts to run
  • mt20191119_TFs_list_updated.csv Second follow-up list to Initial list of TFs considered to design reporters to study in mouse ES cells, updated list of TFs with corresponding motif and CIS-BP Motif ID
  • mt20210208_oligo_pool_deep_RE_only.fasta contains all unique response elements (excluding primer adapters, minimal promoters, barcodes, etc.) for the designed P53 and GR reporter sequences used in the assay
  • mt20200619_oligo_pool_deep.fasta same sequences as in mt20210208_oligo_pool_deep_RE_only.fasta, but including the whole reporter (inclusive of the upstream adapter sequence, downstream minimal promoter, barcode and adapter)
  • fit.Zhang2017.GR.7297.json ProBound GR fit 7297 used to create optimized sequences. This fit is derived from data generated as part of the Zhang 2017 paper.
• out/ contains files created by the R scripts
  • factor_info.xlsx contains manually-modified motifs from mt20191119_TFs_list_updated.csv that are designed to eliminate binding for a given transcription factor. Used to design the reporters in Trauernicht M, et al. Optimized reporters for multiplexed detection of transcription factor activity (submitted).
  • GR/p53scores_RE/_full.tsv files output by response_element_scorer.R that contain the GR/p53 affinity scores for sequences in mt20210208_oligo_pool_deep_RE_only.fasta/mt20200619_oligo_pool_deep.fasta
  • p53_GR_initial_predictions.RData RData files containing the outputs of the sequence optimization runs

R $\geq $ 4.2.1

The RapidScore library must be manually installed first - tarball is under ScoringTools

R packages:

• abind
• dplyr
• ggplot2
• reshape2