FASTQ files for two biological replicates in each condition were trimmed as described above. The reads were aligned to the human genome build hg19 by gsnap aligner v.2017-04-21 with two mismatches allowed (34). The RIP-seq analysis was performed with RIPSeeker R package v.1.18.0 (35) with the parameters as follows: uniqueHit = TRUE, assignMultihits = TRUE, rerunWithDisambiguatedMultihits = TRUE, and automatic bin size selection. Ensembl BioMart build 75 was used for functional annotation of the RIP-seq results. RNA species significantly enriched (adjusted P value threshold < 0.05) above the siE2F1 control RIP are recorded in table S4. RIP sequencing data have been deposited in NCBI’s GEO and are accessible through GEO Series accession number GSE111961.

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