Fig. 1
CUTseq implementation and reproducibility. a CUTseq workflow. (1) RE, restriction enzyme. T7, T7 phage promoter. IVT, in vitro transcription. RA5, RA3, SP7, and SP9: Illumina’s sequencing adapters. b BT474 cells copy number profiles (100 kb resolution). ρ, Pearson’s correlation. c Pearson’s correlation (ρ) between the copy number profiles (100 kb resolution) of five cancer cell lines digested with HindIII (rows) or NlaIII (columns). d Chr17 copy number profiles (NlaIII, 100 kb resolution) in two HER2-positive (SKBR3 and BT474) and one HER2-negative cell line (MCF7). ERBB2/HER2 is highlighted in red. e Copy number profiles (NlaIII, 100 kb resolution) in five replicates (Rep) from FFPE tumor samples. COAD, colon adenocarcinoma. MELA, melanoma. ρ, Pearson’s correlation. f Pearson’s correlation (ρ) between the replicates shown in e at different resolutions. Each dot represents one pair of replicates. Error bars indicate the median and interquartile range. g Pearson’s correlation (ρ) between the fraction of the genome (100 kb resolution) either amplified or deleted in the replicates (Rep) shown in e. Each dot represents one pair of replicates. Dashed line: linear regression. h, i Length of amplified (AMP) or deleted (DEL) genomic segments in Rep1 (h) and Rep2 (i) samples shown in e, at various resolutions. j Zoom-in view on chr9 q-arm in sample TRN4 shown in e. Arrows indicate focal amplifications detected only at 10 kb resolution in both replicates. Red: centromeric region. The p-arm is not shown. k Copy number profiles (NlaIII, 100 kb resolution) determined using 120 pg of gDNA extracted from one FFPE breast cancer (BRCA) sample and three different numbers of PCR cycles. l Pearson’s correlation (ρ) between copy number profiles (100 kb resolution) determined using different amounts of gDNA extracted from the sample shown in k. In all the profiles, gray dots represent individual genomic windows, whereas black lines indicate segmented genomic intervals after circular binary segmentation37. The numbers below each box indicate chromosomes from chr1 (leftmost) to chr22 (rightmost). In all the cases, TRN refers to the ID of Turin samples, as shown in Supplementary Table 2. All the source data for this figure are provided as a Source Data file
