FOXG1, NFIB, SOX5, and TBR1 ChIP-seq Analysis

Chromatin immunoprecipation was performed as previously described [24 (link)]. Antibodies used were Rabbit anti FOXG1 (Cell Signaling), Rabbit anti NFIB (Active Motif), Rabbit anti SOX5 (Abcam), and Rabbit anti TBR1 (Abcam). Sequencing libraries were generated using the Illumina TruSeq kit according to the manufacturer’s protocol. Sequencing was performed on an Illumina Hiseq 2000 at the UCSC Genome Technology Center. Input DNA was sequenced as control. Sequencing reads were mapped to the mouse genome (mm9) using the Bowtie mapping algorithm. Non-overlapping reads and PCR duplicates were removed. Peaks were called using the MACS algorithm [48 (link)].