Mapping Enhancer Landscapes in Interneurons

ChIP-seq data sets of epigenetic marks associated with active enhancers were analyzed to identify enhancer sequences in H9-ESC that were differentiated into inhibitory interneurons (Eshel et al., unpublished). At day 26 of culture, human MGE progenitors (1 − 2 × 10⁵) were cross-linked using formaldehyde, lyzed with sodium dodecyl sulfate-based reagents, and chromatin was sonicated on a Bioruptor (Diagenode, Denville, NJ, USA) using a modified ChIP-seq protocol (43 (link)). ChIP was performed using antibodies against H3K27ac (Abcam Ab4729) and H3K27me3 (Abcam Ab4729). Prepared libraries from ChIP and input DNA were sequenced on an Illumina HiSeq instrument. For all experiments, reads were mapped to hg19 using BWA (44 (link)) and peaks were called using MACS (45 (link)). The generated ChIP-seq data will be available in a coming manuscript (Eshel et al., unpublished).