Stapled phage-displayed peptide library selections of D-MDM2 and D-CHIP

The data set describes NGS raw sequencing data for a panel of phage display experiments conducted with synthetic mirror-image (all-D amino acid) D-MDM2 and D-CHIP proteins. The goal of the study is to discover novel stapled peptide-based ligands to the two fully synthetic D-proteins. Stapled phage-displayed peptide libraries were constructed using the previously described methods in Proceedings of the National Academy of Sciences, 119, e2210435119 (2022). To conduct phage library screening, the procedures described in the reference above were also followed. Next Generation Sequencing is performed according to the reference above. Briefly, phage particles are denatured from magnetic beads with an added spike-in sequence (not a library member that is used to enable cross-well normalization of sequence reads), followed by a two-step low-cycled PCR to introduce Illumina adaptors and 10bp TruSeq DNA UD Indexes (Illumina, San Diego, CA) according to an Illumina's 16S Metagenomic Sequencing Library Preparation protocol. The NGS library is sequenced by an Illumina NovaSeq platform using a 2x150 bp high-output kit (Illumina, San Diego, CA). Hit ID and clustering is performed as described. Briefly, NGS reads are trimmed for quality and filtered for sequences that matched the design of the phage library. Counts for each unique sequence are tallied, and then normalized by the counts of the spike-in sequence added to each sample. A metric called Hit Strength is computed for each sequence as the fold change between the normalized counts in the highest target concentration sample and the normalized counts in the blank samples (averaged across experimental replicates). When 0 counts are observed for a sequence in blank samples, a count of 0.5 is used to prevent dividing by zero.