Midbrain E11.5 ATAC-seq, biological replicate 1
Mouse embryos (E11.5 and E14.5) were dissected in PBS to obtain samples from limbs (E11.5), midbrain (E11.5), whole eye (E11.5), and lens and retina (E14.5). Tissue samples were pooled from at least 10 embryos, and frozen in liquid nitrogen after dissection. ATAC was performed on each tissue in at least two biological replicates, following protocol from Buenrostro et al. 2013. In short, we ground approximately 4mg of tissue/sample on lysis buffer, spun for 10min at 400g, discarded supernatant, resuspended nuclei in ATAC mix (Illumina Nextera), and incubated for 30min at 37oC. Library amplification was done for 10 PCR cycles, using Illumina Nextera reagents. Libraries were quantified with Fragment Analyzer (Advanced Analytical) and KAPA (KAPA Biosystems) and equimolar pooled for sequencing. All libraries were sequenced on Illumina HiSeq 2500/NextSeq, to obtain 2x75 bp reads.