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Chunk #57 — STAR Methods — METHOD DETAILS — Characterization of single-cell suspensions — Cell recovery rates from intact tissue

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Molecular Diversity and Specializations among the Cells of the Adult Mouse Brain.
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(lsl) ZsGreen Cre-reporter (Jackson Labs, 007906). ZsGreen aids in the identification of single-cells as it is sequestered in the soma and proximal processes of cells. Specifically, confocal stacks were obtained with a 40× objective using the FV1200 (Olympus). ZsGreen+ and DAPI+ cells were randomly sampled within a grid, using bounding box of 5 μm in the Z dimension to avoid over-counting (Cortex, mouse 1: n=22 stacks, n=181 boxes; mouse 2: n=12 stacks, n=108 boxes; Striatum, mouse 1: n=15 stacks, n=1135 boxes; mouse 2: n=16 stacks, n=144 boxes). In both Frontal Cortex and Striatum, ~66% of DAPI+ cells were ZsGreen+ on average. To estimate cell totals in suspensions of acute 400 μm slabs of Frontal Cortex or Striatum were cut from Nestin-Cre;lsl-ZsGreen mice. We controlled the volume of tissue in each tube by processing only one coronal slice / tube at the appropriate anterior-posterior location. We resuspended the pellet in 1 mL of Dissociation Buffer + BSA and then re-measured the volume to account for extra buffer introduced by filter wetting. 20 μl samples were assayed n=3 times on the haemocytometer. Each sample was randomly imaged at n=5 locations. To estimate the concentrations of all cells and ZsGreen+ cells, images containing