GSM5024885: E13_MGE_Dlx6neg_2_ATAC; Mus musculus; ATAC-seq
For embryonic timepoints, male hemizygous Dlx6a-Cre mice (Jax stock #008199) were crossed with female homozygous Ai9 or Ai14 mice (Rosa-LSL-tdtomato, Jax stock # 007909 or 007914) and checked daily for the presence of a vaginal plug, with the morning a plug was found being considered embryonic day 0. Embryos were screened using a fluorescent microscope for the presence of tdTomato. For embryonic timepoints using wild-type mice, timed pregnant CD-1 mice were used (Charles River #022). For postnatal timepoints, male hemizygous Dlx6a-Cre mice were crossed with female homozygous INTACT mice (flox-Sun1-eGFP, Jax stock #021039) to yield Dlx6a-Cre;INTACT offspring. For the P2 Mef2c conditional knockout (Mef2c_cKO), mice with the Lhx6-iCre (Jax stock #026555) and Mef2c-Fl/+ (Jax stock #025556) alleles were crossed with mice with the Mef2c-Fl/Fl and INTACT alleles to yield Lhx6-iCre;INTACT;Mef2c-Fl/Fl offspring. ﻿For embryonic timepoints, embryos were harvested from pregnant dams and relevant brain regions were dissected in ice-cold Leibovitz's L-15 medium. Pooled tissue from several embryos were dissociated using the Neural Tissue Dissociation Kit (T) (Miltyeni Biotec, PN-130-093-231) according to the manufacturer's instructions. Dissociated cells were then filtered through a 70 um filter, centrifuged at 300xg for 5 min at 4C, and, where cell-sorting was required, resuspended in 1% BSA in PBS for cell sorting of tdTomato+ cells. For postnatal timepoints, brains were harvested, sectioned coronally on a stainless-steel mouse brain slicer (Zivic Instruments), and regions of interest were 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 minutes on ice before being filtered through a 30 μm filter and centrifuged at 500xg for 10 minutes at 4C. The pellet was resuspended in 1% BSA in PBS for sorting for GFP+ nuclei. For all timepoints, cells or nuclei were sorted into Diluted Nuclei Buffer (10x Genomics) on a Sony SH800S cell sorter with a 100 µm chip. scATAC-seq libraries were prepared using the Chromium Single Cell ATAC Solution v1 (10X Genomics). Libraries were sequenced using a Nova-Seq 100 cycle kit (Illumina).