sFANS ATACseq profiling of cortical cell types from human control samples

To reveal gene expression programs altered in the deep layer neuron cell classes of Huntington's Disease samples, we first filtered the cell-type specific differential gene expression lists from our DESeq2 analyses based on the cell-type specific accessible promotor peaks revealed through ATACseq of control deep layer nuclei. This step allowed us to focus our gene lists for the following GO analyses to those genes that were truly accessible in the specific cell-types. Overall design: We have employed serial fluorescence activated nuclear sorting (sFANS) protocols to isulate nuclei from deep layer cortical cell types, followed by ATACseq profiling.