NextSeq 550 paired end sequencing; Single-cell 5' Gene Expression and V(D)J Amplification (10X Genomics) of splenic CD4+ T cells from Plasmodium chabaudi infected mice
Single-cell 5' Gene Expression and V(D)J Amplification (10X Genomics) of splenic CD4+ T cells from Plasmodium chabaudi infected mice
Mice (n=2) were infected with MT P. chabaudi (AS)-GFP by intra-peritoneal injection of 1x105 parasitised erythrocytes, and euthanised at day 7 post-infection. CD3+ CD4+ splenocytes were were isolated by FACS using a BD FACSAria III instrument and sorted into 100L 0.04% BSA in PBS.  Standard 10x Genomics protocols for the kit were used to load cells into the Chromium chip. Barcoded cDNA libraries were prepared from sorted samples using the 10x Genomics Single Cell 5' Library Kit v2. Full length V(D)J segments were enriched from amplified cDNA with primers specific to the TCR constant region using the Chromium Single Cell V(D)J Enrichment Kit – Mouse T-Cell. Libraries were prepared as per manufacturers' protocol.