Next-Generation Sequencing of sgRNA spacer sequences from a CRISPRi library screen of the Salmonella enterica serovar Typhimurium 14028s genome in response to repeated monoclonal IgA treatment

For this study, we implemented the anti-lipopolysaccharide monoclonal IgA Sal4 in a genome-wide CRISPR interference (CRISPRi) screen to identify genes that modulate the extent of agglutination of Salmonella enterica serovar Typhimurium (STm) in response to antibody exposure. We leveraged our recently-developed \"snow globe assay\" method to enrich for cells containing sgRNAs that silence the expression of genes that contribute to the process of antibody-mediated agglutination. A high density (~10^8 CFU/mL) culture of an STm strain containing a library of 36,651 sgRNA-encoded plasmids was treated with Sal4 IgA (15 µg/mL) in PBS for five hours at room temperature. The remaining portion of the culture present at the top of the supernatant after antibody treatment was passaged and grown overnight to repeat the enrichment the following day. We then purified the sgRNA-containing plasmids from this agglutinating-evading population using a DNA extraction kit, amplified the spacer sequence via PCR, purified the PCR products using AMPure magnetic beads, and pooled the resulting DNA for Next Generation Sequencing. The files included here represent the raw .fastq files obtained from the Illumina NextSeq platform. For more information of this study, please see https://doi.org/10.1101/2024.12.16.628777.