Role of Bcl3 in Dendritic cell function in the context of Toxoplasma gondii infection

This experiment contains two mice genotypes – WT and Bcl3 flx/flx Zbtb46 cre knockouts (both C57BL/6 background). These mice were either infected with 15 cysts of Toxoplasma gondii (ME49 strain) or kept uninfected. Spleens were harvested from mice 7 days post infection and splenocytes were isolated. With four experimental groups (KO/WT and infected/uninfected) and two biological replicate mice per group, we have a total of 8 biological samples comprising of single cell suspensions of splenocytes enriched for CD11c. Single cell RNA-seq libraries were prepared from CD11c-enriched single cells using the Chromium Single Cell 3' Reagent Kits v3 (10X Genomics; Pleasanton, CA, USA). Eight sample libraries were multiplexed and sequenced 100bp paired end in four different runs of Illumina NextSeq2000, followed by demultiplexing that resulted in multiple raw FASTQ files corresponding to paired reads (R1 and R2), index barcodes (I1) and four sequencing runs (Seq1 - Seq4). The main goal of this project was to define Bcl3-associated transcriptional responses in dendritic cells during T. gondii infection. Overall design: Single-cell mRNA profiles of splenocytes from Bcl3 flx/flx Zbtb46 cre KO and WT mice that were either infected with Toxoplasma gondii or kept uninfected.