single cell mRNA from intestinal epithelial cells of Cryptosporidium parvum infected mice rep2
The ileum was isolated and peyers patches removed. The epithelial cell layer was isolated as a single cell suspension generated. Single cell suspensions were processed according to 10x Genomics and Biolegend protocols to create Cellular Indexing of Transcriptomes and Epitomes (CITE-seq) libraries. In brief, cells were stained with the TotalSeq B Mouse Universal Cocktail V1.0, which includes oligo-conjugated antibodies for ~100 surface proteins (Biolegend). Cells and 10x Genomics barcoded gel beads were then encapsulated using GEM-X 3 chips and a Chromium Controller device. Standard library amplification and indexing were performed with either 10x Genomics GEM-X single cell 3 v3 or v4 chemistry. All paired-end libraries were sequenced on a NextSeq 2000.