GSM7291132: WT_ovaries_1_8st_rep1_Hi-C; Drosophila melanogaster; Hi-C
For the ChIP-Seq experiments ovaries were collected in PBS buffer (50 pairs per ChIP), cross-linked with 1% of formaldehyde for 5 min and then incubated for 5 min with 125 mM Glycine. After that ovaries were washed with PBS buffer for three times. The remaining ChIP protocol was performed as described previously (Vorobyeva et al (2013) NAR, 41:11, 5717–5730). For the in situ Hi-C experiments, ovaries were collected in PBS buffer (200 pairs per Hi-C), cross-linked with 1% of formaldehyde for 5 min and then incubated for 5 min with 125 mM Glycine. Then ovaries were washed with 1xPBS buffer for three times. The remaining in situ Hi-C protocol was performed as described previously (Rao et al (2014) Cell, 159:1665-1680). For extraction of RNA the ovaries of 15 hour old wild-type (oregon) and su(Hw)v/E8 females were collected in PBS buffer (50 pairs per sample), in two biological repeats. Total RNA was extracted with the TRI reagent (Ambion). PolyA comprising RNA fraction was isolated and prepared for sequencing with the NEBNext UltraTM II Directional RNA Library Prep Kit. ChIP-Seq, Hi-C and RNA-Seq libraries were prepared for sequencing using standard Illumina protocols