BioSample

Protocols: BT474 cells were obtained from American Type Culture Collection (ATCC) and cultured according to their recommended conditions. Cells were treated at 5 μM SAHA (suberoylanilide hydroxamic acid) or 500 nM FLAVO (flavopiridol) for 4 hours. Chromatin was prepared and immunoprecipitated as previously described (Kim, Y.J., Cecchini, K.R. & Kim, T.H. Conserved, developmentally regulated mechanism couples chromosomal looping and heterochromatin barrier activity at the homeobox gene A locus. Proc Natl Acad Sci U S A 108, 7391-6 (2011)), except that 25% of the amount of chromatin was used for RNAP2 and acetyl ChIPs to reduce oversaturation of bead binding. ThruPLEX® DNA-seq Kit from Rubicon Genomics was used for multiplexed ChIP-seq library prep of BT474 chromatin. Indexed samples were quantitated with qPCR and mixed in equimolar amounts. Input sample was prepared with an Illumina DNA-seq kit.