Adnp_Chd4_scRNAseq_v2.h5ad

Embryos were harvested and the dorsal telencephalon was microdissected. Cells were dissociated with papain (Worthington) in the presence of DNAse I, washed, and then barcoded. Briefly, 250 000 dissociated cells per replicate were incubated with ‘anchor’ and ‘co-anchor’ lipid-modified oligonucleotides generously provided by the Gartner lab⁴⁰. Each replicate was then co-incubated with barcode oligonucleotides for 10 minutes and then washed 3 times with PBS. Replicates were then pooled in equivalent ratios, and approximately 20 000 pooled cells were combined in individual Chromium™ runs (3’ Library &amp; Gel Bead Kit v2, PN-120237, 10X Genomics). Expression library FASTQs were processed using CellRanger (10X Genomics). The deMULTIplex workflow⁴⁰ was used to remove doublets and exclude cells lacking barcodes. Output files were filtered and analyzed using Scanpy version 1.9.1⁹¹ in Python(Python Core Team n.d.). Genes detected in less than 3 cells were removed from the analysis. Contaminant or low-quality cells (less than 5000 genes detected, less than 20 000 reads/counts detected or more than 0.05% of mitochondrial genes detected) were also excluded.<br>