title: GSM9013269: wildtype, blastoderm stage, ATAC-seq replicate 5; Drosophila melanogaster; ATAC-seq
library_construction_protocol: For ChIP experiments, embryos were crosslinked (Heptane/PBS/formaldehyde, 15 minutes) and sorted by stage prior to homogenization in RIPA buffer and sonication. Sonicated chromatin samples were subjected to immunoprecipiation with the indicated antibodies. For ATAC seq, individual embryos were staged in mid cellular blastoderm stages and homogenized in ATAC lysis buffer (Buenrostro, 2013). Nuclear pellets were isolated by low-speed centrifugation prior to library preparation. ChIP libraries: following IP but prior to washes, antibody-chromatin complexes were tagmented by incubation with Illumina Tn5 (Nextera) reagent for 40 minutes at 37 degrees C. Following tagmentation, beads were washed and subjected to PCR with barcoding primers (Buenrostro, 2013). ATAC libraries: nuclear pellets were tagmented by incubation with Illumina Tn5 (Nextera) reagent for 30 minutes at 37 degrees C. DNA was cleaned up using a Qiagen MinElute kit. Tagmented library fragments were subjected to PCR with barcoding primers (Buenrostro, 2013).