anti-GFP ChIP DNA from Kc167 cells expressing Ubx-GFP (Experiment 1)
cell line source
Female late embryo derived cell line
Sequenced DNA Library
Chromatin was prepared from FACS-sorted Hox-GFP expressing cells, and Hox-DNA complexes were immunopurified using anti-GFP antibody. Detailed protocol is described in associated publication. Samples were processed and sequenced by Source BioScience. The Illumina TruSeq ChIP Sample Preparation Kit was used to generate indexed paired-end sequencing libraries in accordance with the manufacturer’s guide (Rev. A, August 2012) except that no size selection was performed. For the ChIP samples, the entire 10 µl volume of ChIP DNA was used for library preparation and 17 cycles of amplification were performed. For the input sample, 5-10 ng of input DNA were used for library preparation and 12 cycles of amplification were performed. Samples were either sequenced on the Illumina MiSeq (Experiment 1; Ubx, Abd-A, Abd-B and input) or HiSeq 2000 (Experiment 2; Ubx, mutant Ubx and Ubx+Hth) platforms to generate 36 bp or 100 bp reads respectively.