GSM8887843: Female WT MGE, mouse E13.5; Mus musculus; ATAC-seq
Embryonic brain dissections: Pregnant dams were anesthetized with an i.p. injection of Euthasol, E13.5 embryos were removed and placed in ice-cold carbogenated artificial cerebral spinal fluid (ACSF, in mM: 87 NaCl, 26 NaHCO3, 2.5 KCl, 1.25 NaH2PO4, 0.5 CaCl2, 7 MgCl2, 10 glucose, 75 sucrose, saturated with 95% O2, 5% CO2, pH 7.4). Embryonic tails were cut for genotyping. MGE and hypothalamus were dissected from individual brains in ice-cold ACSF, transferred to individual 0.5 mL Eppendorf tubes, then flash frozen on dry ice and stored at -80°C. Adult brain dissections:  The somatosensory cortex and hypothalamus were dissected, transferred to 1.5 mL Eppendorf tubes, then flash frozen on dry ice and stored at -80°C. Frozen E13.5 and P60 tissue from Nkx2.1-Cre;H3.3K4M;sun1-GFP mice were mechanically lysed, washed and filtered to generate single nuclei suspensions for the 10x Genomics Multiome assay as previously described. These suspensions were then sorted via flow cytometry to harvest ~100,000 GFP+ nuclei. Nuclei solutions were centrifuged in a bucket centrifuge at 500 g for 5 minutes at 4 degree. Supernatant was removed and nuclei reconstituted in 1x Nuclei buffer at a density of 3,000 nuclei/μL. 5 μL of this solution was then used for the 10x Genomics Single Cell Multiome Assay per manufacturer's protocol. Joint libraries for scRNA-seq and scATAC-seq were created using 10X Genomics Single Cell Multiome ATAC + Gene Expression kit (1000285) by following manufacturer's protocols.