Single-nucleus RNA-seq (10x Genomics Flex) of wild-type C57BL/6J mouse spleen following Plasmodium berghei ANKA infection, generated as a transcriptome-wide reference for the SpatialBench spatial transcriptomics benchmark
Single-nucleus RNA-seq (10x Genomics Flex) of wild-type C57BL/6J mouse spleen following Plasmodium berghei ANKA infection, generated as a transcriptome-wide reference for the SpatialBench spatial transcriptomics benchmark
Spleens were collected from 8-week-old wild-type female C57BL/6J mice infected intravenously with 1×10^5 Plasmodium berghei ANKA-infected red blood cells to induce splenic germinal-center formation. After onset of clinical symptoms, infection was cleared by treatment with chloroquine and pyrimethamine. Mice were euthanised 12 days post-infection and spleens were fixed in 10% neutral buffered formalin and processed into formalin-fixed paraffin-embedded (FFPE) blocks by standard histological procedures. All animal procedures were approved by the WEHI Animal Ethics Committee. Five 25 µm scrolls were taken from each FFPE spleen block and dissociated into single nuclei following the 10x Genomics pestle dissociation demonstrated protocol (CG000632, Rev A). Following trituration, 1.5 million nuclei per sample were taken immediately into probe hybridization. Single-nucleus libraries were prepared using the probe-based 10x Genomics Chromium Fixed RNA Profiling (Flex) assay. Nuclei were subjected to overnight probe hybridization and processed according to the NextGEM Chromium Fixed RNA Profiling Singleplexed Samples User Guide (CG000691, Rev A), targeting capture of 10,000 nuclei per sample.