Two samples of control, K14-Vegfa and K14-Vegfa/Nrp1 cKO, and one sample of K14-Vegfa/Flt1 cKO were sequenced. ATAC-seq paired-end reads of 50 bp were trimmed for adaptor sequences using Trimmomatic. ATAC-seq paired-end reads were then aligned to the mouse GRCm38 genome using Bowtie2 (version 2.2.6) using options “-X 2000 --fr --very- sensitive --no-discordant --no-unal --no-mixed --non-deterministic.” More than 18 million reads were mapped to mouse genomic DNA in each condition (between 18 and 86 millions). Mitochondrial reads and reads aligned to scaffolds and undefined chromosomes were excluded from downstream analysis.

Reads with a mapping quality lower than 20 were eliminated with samtools, and duplicated reads were removed by Picard tools (http://broadinstitute.github.io/picard/). Read start sites were adjusted to represent the center of the transposon binding event as described in (38). Peak calling was performed on each individual sample using Macs2 (version 2.1.0.20151222) with parameter setting of “callpeak -f BAMPE -g mm -q 0.05 –nomodel –call-summits -B – SPMR.” Peaks from all ATAC-seq samples were merged for downstream analysis using bedtools. Pileup bedgraph files generated by MACS2 were transformed to tdf files with Integrative Genomics Viewer (IGV) tools, allowing the visualization of alignment data tracks by IGV. Read counts of each merged peaks for each individual sample were calculated by HTSeq-count using options “-s no -m intersection-nonempty.” These counts were normalized for 1 million of mapped reads in merged peaks, and fold of change was computed for all pairwise comparisons on the means of read counts (for control, K14-Vegfa, and K14-Vegfa/Nrp1 cKO) or on the read count (for K14-Vegfa/Flt1 cKO). Peaks up-regulated were defined as those having at least a twofold change, and merged peaks nonintersecting a peak called with a q value of 0.05 in the up-regulated condition were removed. Peaks were associated to genes with the GREAT software with the following association rules: “basal plus extension” with parameters 5.0 kb in proximal upstream, 1.0 kb in proximal downstream, and 100.0 kb in distal.

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