Pixel-seqV2 mouse kidney: source selection, tissue preparation and assay v1

Pixel-seqV2 profiles whole-transcriptome RNA in mouse kidney sections using spatially barcoded polony gels. The assay builds on the Pixel-seq framework described by Fu et al. (2022). In V2, an adapter-bearing degenerate second-strand primer replaces template switching during library construction. The second-strand priming strategy is analogous to that used in Seq-Scope. [1, 2] This protocol describes source selection, tissue preparation and assay methods for the P1 mouse-kidney submission. The original ten-record frozen reference cohort is listed below. The kidneys were prepared by Mariya Sweetwyne’s laboratory and originated from NIA-supplied mice. The analyte is RNA, and the assay uses whole-transcriptome capture.