Per chromatin immunoprecipitation experiment, 5× 106dH1f cells were used. ChIP-seq assays were performed in triplicate as described
previously at the same timepoints as RNA-seq experiments23 (link). Briefly, for quantitative ChIP experiments, 4 ×
106 SF9 cells were spiked into the pool at 1:5 ratio. The cells
were then cross-linked by formaldehyde treatment, and chromatin was fragmented
to 200–300 bp by sonication using a Biorupter® Pico (Diagenode).
Each lysate was immunoprecipitated with 5 μg of primary antibody.
Purified DNA was used for library preparation using a NEBNext Ultra DNA sample
preparation kit (NEB) according to the manufacturer's recommendations.
The samples were multiplexed, quantified on Tapestation (Agilent), and sequenced
on a NextSeq 500 (Illumina) platform (paired-end, 2 × 41 bp). Sequencing
depth was in excess of 20 million reads/sample, suggesting sufficient coverage.
Antibodies for the ChIP-seq experiments were: Anti-H3K27Ac (Active Motif,
39133), Anti-H3K18Ac (Abcam ab1191), Anti-H3K4me3(Merck Millipore 07-473),
Anti-H3K4me1 (Diagenode C15410194).
previously at the same timepoints as RNA-seq experiments23 (link). Briefly, for quantitative ChIP experiments, 4 ×
106 SF9 cells were spiked into the pool at 1:5 ratio. The cells
were then cross-linked by formaldehyde treatment, and chromatin was fragmented
to 200–300 bp by sonication using a Biorupter® Pico (Diagenode).
Each lysate was immunoprecipitated with 5 μg of primary antibody.
Purified DNA was used for library preparation using a NEBNext Ultra DNA sample
preparation kit (NEB) according to the manufacturer's recommendations.
The samples were multiplexed, quantified on Tapestation (Agilent), and sequenced
on a NextSeq 500 (Illumina) platform (paired-end, 2 × 41 bp). Sequencing
depth was in excess of 20 million reads/sample, suggesting sufficient coverage.
Antibodies for the ChIP-seq experiments were: Anti-H3K27Ac (Active Motif,
39133), Anti-H3K18Ac (Abcam ab1191), Anti-H3K4me3(Merck Millipore 07-473),
Anti-H3K4me1 (Diagenode C15410194).
