Single nucleus gene expression profile of the rodent brains response to systemic innate immune system challenges

The mammalian brain consists of heterogeneous cell populations with distinct responses to innate immune system challenges. Here we used single nucleus RNA sequencing (snRNAseq) to analyze cell type and stimulus dependent transcriptional responses of the rodent brain to peripheral LPS and Poly(I:C) challenges. Innate immune system challenges were induced by the intra peritoneal (i.p.) application of lipopolysaccharide (LPS), polyinosinic:polycytidylic acid (poly(I:C)), or saline (sham control) treatment. Four animals were pooled per treatment-group, generating 3 single nucleus RNA sequenced (snRNAseq) datasets: Saline treated = RN_brain_Saline, LPS treated = RN_brain_LPS, Poly(I:C) treated = RN_brain_PIC. Seven hours after i.p. injection of LPS (5mg/kg bodyweight), poly(I:C) (12 mg/kg bodyweight), or saline brains were harvested for nuclei purification. Nuclei were isolated using nuclei extraction buffer (Miltenyi) and standard discontinuous iodixanol gradient separation, followed by library preparation using standard 10x Genomics workflows and snRNAseq (NovaSeq 6000, Illumina). Details on the study design and sample processing can be found in: Bormann, D., D. Copic, K. Klas, M. Direder, C. J. Riedl, G. Testa, H. Kühtreiber, E. Poreba, S. Hametner, B. Golabi, M. Salek, C. Haider, V. Endmayr, L. E. Shaw, R. Höftberger, H. J. Ankersmit and M. Mildner (2023). "Exploring the heterogeneous transcriptional response of the CNS to systemic LPS and Poly(I:C)." Neurobiology of Disease 188: 106339. https://doi.org/10.1016/j.nbd.2023.106339.