Validation of a murine proteome-wide phage display library for identification of autoantibody specificities

Autoimmunity is characterized by loss of tolerance to tissue-specific as well as systemic antigens, resulting in complex autoantibody landscapes. Here, we introduce and extensively validate the performance characteristics of a murine proteome-wide library for phage display immunoprecipitation and sequencing (PhIP-seq), to profile mouse autoantibodies. This system and library were validated using seven genetic mouse models across a spectrum of autoreactivity. Mice deficient in antibody production (Rag2-/- and mMT) were used to model non-specific peptide enrichments, while cross-reactivity was evaluated using anti-ovalbumin B cell receptor (BCR)-restricted OB1 mice as a proof of principle. The PhIP-seq approach was then utilized to interrogate three distinct autoimmune disease models. First, serum from Lyn-/- IgD+/- mice with lupus-like disease was used to identify nuclear and apoptotic bleb reactivities, lending support to the hypothesis that apoptosis is a shared origin of these antigen..., PhIP-seq library design and validation of the murine proteome., , # Mouse PhIP-seq library design and experimental files

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These files correspond to the publication: [ https://insight.jci.org/articles/view/174976](https://insight.jci.org/articles/view/174976)

## Description of the data and file structure

***Design files for library:***

mouseome_design_files.zip contains:

1. mouseoligo_in_T7-packaged_ER_02212023.dna: SnapGene file of example peptide sequence cloned into T7 genome. This file has helpful annotations of the cloning site and primer sequences
2. mouse_associate_genes_no-nan.csv : a table with fasta header (peptide name), protein (gene) name, and amino acid sequence
3. mouse_T7_display_peps_alternate-header.fasta : Amino acid sequences of peptides to display (linkers trimmed)
4. mouse_T7_display_seqs_alternate-header.fasta : DNA sequences of peptides to display (includes linkers)
5. mouse_T7_display_seqs_pool_1.fasta : Pool 1 DNA sequences sent to Agilent for synthesis
6. mouse_T7_display_seqs_pool_2.fasta : Pool 2 DNA sequence...