Seqcap adapter kit a

The ChIP DNA was fragmented by Picoruptor (Diagenode) for 10 cycles of 30 s on, 30 s off. Then, ChIP library was constructed by KAPA Hyper Prep Kit (KAPA BIOSYSTEMS) and SeqCap Adapter Kit A (Roche) or SMARTER ThruPLEX DNA-seq kit (TAKARA) and SMARTer DNA Unique Dual Index Kit (TAKARA) according to manufacturer instructions. The concentration of the ChIP-seq library was quantified by KAPA Library quantification kit (KAPA BIOSYSTEMS). ChIP-sequencing was performed on a HiSeq X platform (Illumina). We performed two biological replicates for H3K9me2 ChIP-seq and correlation between replicates as described in Supplementary Table 1.

We chose DCIS/IDC samples with distinct degrees of HER2 amplification from 4 patients for WGS analysis. LCM slides consecutive to the Smart-3SEQ LCM slides were cut and matched samples were collected to a CapSure HS LCM Cap. Genomic DNA was isolated from FFPE cells using PicoPure DNA Extraction kit (Thermo Fisher Scientific, US), cleaned up with AMPure XP beads at 3:1 ratio (Beckman Coulter, US), and quantified by Quant-iT PicoGreen dsDNA Assay (Thermo Fisher Scientific, US). DNA Libraries were constructed from 1ng of genomic DNA with KAPA HyperPlus Kit (Roche, US) for FFPE DNA and amplified by 19 PCR cycles. Barcode adapters were used for multiplexed sequencing of libraries with SeqCap Adapter Kit A (Roche, US). Library size distribution was assessed on an Agilent 2100 Bioanalyzer using the DNA 1000 assay (Agilent, US), and its concentration was measured by Qubit® dsDNA HS Assay Kit (Thermo Fisher Scientific, US). Twelve samples were pooled at 18ng/ul and sequenced by Novogene (Sacramento, CA, USA) on 1 lane of the Illumina HiSeq Platform collecting 110G per 275M reads output of paired-end 150 bp read length. The median coverage per base is 2.0.