ChIP assays were performed as previously described17 (link),18 (link),63 (link),64 (link) for the following histone marks: H3K4me3 (Abcam, #ab8580), H3K4me1 (Active Motif, #39297), H3K36me3 (Abcam, #ab9050), H3K27ac (Active Motif, #39133), H2AZac (Abcam, #ab18262), H3K9ac (Millipore, #06-599) and H3K27me3 (Millipore, #07-449). ChIP of H3K9me3 (Diagenode, #C15500003) was performed as previously described65 (link). We performed lamin ChIP assays in PrEC and LNCaP as previously described66 (link) for both Lamin B1 (Abcam, #ab16048) and Lamin A/C (Santa Cruz, #sc7292). Each ChIP assay was validated by qPCR against an IgG control and enrichment above input. Libraries were prepared with the Illumina TruSeq Chip Library Prep Kit and sequenced on an Illumina HiSeq 2500.
Sequencing data was processed as previously described17 (link),63 (link). Briefly, ChIP-seq reads were aligned to hg19 using bowtie58 (link) (v1.1.0) allowing up to 3 mismatches, discarding ambiguous and clonal reads. All histone ChIP-seq peaks were called using PeakRanger67 (v1.16). Broad domains of lamins (LADs), H3K9me3 and H3K27me3 were called using the enriched domain detector (EDD) for identification of wide genomic enrichment domains68 (link).
Sequencing data was processed as previously described17 (link),63 (link). Briefly, ChIP-seq reads were aligned to hg19 using bowtie58 (link) (v1.1.0) allowing up to 3 mismatches, discarding ambiguous and clonal reads. All histone ChIP-seq peaks were called using PeakRanger67 (v1.16). Broad domains of lamins (LADs), H3K9me3 and H3K27me3 were called using the enriched domain detector (EDD) for identification of wide genomic enrichment domains68 (link).
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