Table 2 Sources of alternative ORI positions used in this study

OK-seq

[42]

BAM files for hg19 were downloaded from the SRA database, under accession number PRJEB25180. Replication origins were identified using our algorithm described below.

[31]

BED files with ORI positions for hg19 were provided by the authors of the publication.

SNS-seq

[23]

Genomic coordinates of ORI positions for hg38 were downloaded from the manuscript supplement (Table S1). The coordinates were converted to hg19 using the liftOver function from the rtracklayer Bioconductor library [68]. ORI from Q1 and Q2 were combined into the “core” group, while the remaining Q3–10 into “stochastic”

[35]

BED files with ORI positions for hg19, for Hela, IMR90, and K562 cell lines were downloaded from http://pbil.univ-lyon1.fr/members/fpicard/oriseq/

[38]

hg19 ORI positions were downloaded from the DeOri database [8] for both HCT116 and K562 cell lines

Repli-seq

[7]

ENCODE Repli-seq data were downloaded from the GEO dataset GSE34399.

We used the peak locations of the wavelet-smoothed signal available as the BED files with the Pk suffix.

Ini-seq

[39]

Genomic coordinates of ORI positions for hg19 were downloaded from the manuscript supplement (Table S3) (determination by SICER at E = 10e−5).

Bubble-seq

[40]

ORI positions for hg18 were downloaded in a bedGraph format from GEO dataset GSE38809 (GM_combined_RD_bubbles file). The coordinates were converted to hg19 using the liftOver function from the rtracklayer Bioconductor library [68].

ORC1-ChIP-seq

[43]

ORI positions for hg18 were downloaded in a BED format from GEO dataset GSM922790 (ChIPseq_Orc1_GradientHela_enrichRegions file). The coordinates were converted to hg19 using the liftOver function from the rtracklayer Bioconductor library [68].

ORC2-ChIP-seq

[44]

Genomic coordinates for hg19 were downloaded from the manuscript supplement (Table S1).

MCM7-ChIP-seq

[45]

Genomic coordinates for hg19 were downloaded from GEO dataset GSE107248 (MCM7ChIP_exp1/2.txt files).

Nucleotide comp. skew

[21]

ORI positions for hg17 were downloaded from the manuscript supplement (N-domain_positions.xls file). The coordinates were converted to hg19 using the liftOver function from the rtracklayer Bioconductor library [68].