ChIP-qPCR was used to validate target genes derived from the ATAC-seq analysis. Three independent clonal isolates from LNCaP cells stably over-expressing HIST1H1A or control vector were used for ChIP assays as previously described [45 (link)]. Briefly, 1% formaldehyde was used to fixed cells, followed by cell lysis. Cell lysates were pre-cleared with Protein G Sepharose beads (GE Healthcare), then incubated with HIST1H1A (HPA043753, Sigma Life Science) or IgG (12-370, Millipore), and Protein G Sepharose beads were added for overnight incubation at 4° C. NaCl was used for reverse cross-linking, and DNA was extracted using Qiaquick PCR purification kit (Qiagen). The DNA product was used for ChIP-qPCR analysis, and samples were amplified in duplicates using ABI Fast SYBR Green Master Mix (Life Technologies, Grand Island, NY USA). Student’s T-tests was used to calculate statistical significance, and data are presented as mean ± SD with P < 0.05 being considered significant.
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