Chromium chip e single cell kit

Male hemizygous Dlx6a-cre mice (Jax stock #008199) were crossed with female homozygous INTACT mice (flox-Sun1-eGFP, Jax stock #021039) to yield Dlx6a-cre::INTACT offspring for scATAC-seq experiments. Brains from P28 Dlx6a-cre::Sun1-eGFP mice were harvested, sectioned coronally on a mouse brain slicer (Zivic Instruments), and the primary visual cortex was dissected in ice-cold ACSF. Tissue was then transferred to a dounce homogenizer containing Lysis Buffer (10 mM Tris-HCl, 10 mM NaCl, 3 mM MgCl2, 0.01% Tween-20, and 0.01% IGEPAL CA-630, 0.001% Digitonin). Tissue was homogenized with 10 strokes of pestle A, 10 strokes of pestle B, and incubated for 5 min on ice before being filtered through a 30 μm filter and centrifuged at 500xg for 10 min at 4μc. The pellet was resuspended in 1% BSA for sorting GFP+ nuclei on a Sony SH800S cell sorter. Nuclei were sorted into Diluted Nuclei Buffer (10X Genomics). The scATAC library was prepared using the 10x Genomics platform with the Chromium Single Cell ATAC Library & Gel Bead Kit v1.0 (PN-1000111), Chromium Chip E Single Cell kit (PN-1000156) and Chromium i7 Multiplex Kit N, Set A (PN-1000084) as instructed by the manufacturer. High quality data was recovered from approximately 60% of the input nuclei. Libraries were sequenced using a Nova-Seq S2 100 cycle kit (Illumina).