GSM1423061: GAF-RNAi replicate 2 (MNase-seq); Drosophila melanogaster; MNase-Seq
Ten million cross-linked nuclei were digested with MNase until about 80% of the material has mononucleosome-sized. For H2AvD nucleosomes, immunoprecipitated with 4ul Anti-H2AvD antisera (Glaser lab stock) from 75ul of digested material. Cross-links were reversed at 65°C and the DNA was extracted with phenol:chloroform and precipitated. 50ng of non-immunoprecipitated (MNase-seq) or immunoprecipitated (H2AvD) DNA was ligated to Tru-seq paired-end adapters. The resulting DNA was PCR amplified for 5 cycles and 200-400bp fragments were selected and PCR amplified for 12-15 cycles. The cDNA was then paired-end sequencing was performed (50 bases)  on the Illumina HiSeq 2500.