Preliminary single cell sequencing data from "Telocytes and CCL24+ macrophages do not contribute to TSLP responses during high dose <i>Trichuris muris</i> infection."

Infected mice, all age-matched C57BL/6 males, were administered 400 <i>Tm</i> eggs by oral gavage: four mice were infected for harvest at d14 p.i., four mice for harvest at d21 p.i., and four remained uninfected. Caeca were harvested from all mice simultaneously, washed in PBS, and the epithelia stripped <i>via</i> two, 30 minute incubations in 10mL of strip buffer per sample (HBSS -Mg/Ca + 5mM EDTA + 1mM DTT (Sigma), 5% FCS), before vortexing samples and separating lamina propria from suspended epithelial cells through a 100µm filter. Epithelial cell suspensions from mice of the same infection timepoint were combined centrifuged at 400xg at 4ºC for 10 minutes, resuspended in PBS and kept on ice. Lamina propria samples were combined, and each of the three grouped samples digested enzymatically for 30min at 37ºC in a shaking shaking incubator. Digestion buffer was comprised of HBSS +Mg/Ca +1mg/mL of Liberase TL +10mg/mL DNAse. Digested samples were centrifuged at 400xg at 4ºC for 10 minutes, resuspended in chilled PBS buffer. This was repeated to wash samples. Cells were stained using Zombie UV fixable <i>via</i>bility dye and sorted for live cells using the Bigfoot Cell Sorter (Thermo Fisher). The concentrations of cells for the three sorted lamina propria samples, and the three epithelial samples, were determined <i>via</i> CASY counter, and for each group a sample was generated containing 8,000 lamina propria cells and 2,000 epithelial cells in EDTA-free FACS buffer, which was deposited with the Genomics Core Facility for 10x single cell sequencing. FASTQ files generated were subjected to quality control and three resolutions of clustering and annotation by the Bioinformatics Core Facility, who provided the R-scripts used for quality control, .csv files containing cell clustering annotations against cell barcode, and total and log transformed reads for all transcripts against cell barcodes, as well as access to the data loaded onto the Shiny App for examination of data. Data presented here uses Prism-generated graphs of data from quality controlled .csv files at the finest cluster resolution provided by the Bioinformatics Core Facility. The gene list given has been restricted to genes graphed in the related manuscript, with genes for validation of clustering provided, for potential use in subsequent research by authors and collaborators.