Reagent/Resource	Reference or source	Identifier or catalog number
Chemicals, enzymes, and other reagents
Antarctic phosphatase	New England BioLabs	Cat#M0289
T4 Polynucleotide Kinase	New England BioLabs	Cat#M0201
ProtoScript II Reverse Transcriptase	New England BioLabs	Cat#M0368
miRNeasy Mini kit	Qiagen	Cat#217004
15% TBE–urea gels	NOBEX, Invitrogen	Cat#EC6885BOX
RNeasy MinElute Cleanup Kit	Qiagen	Cat#74204
QIAquick PCR Purification Kit	Qiagen	Cat#28106
Experimental models
BJ/hTERT	Gift from Anders H. Lund laboratory (Disa Tehler).	N/A
HeLa	ATCC	CCL‐2
HEK293	ATCC	CRL‐1573
HCT116	ATCC	CCL‐247
MDA‐MB‐231	ATCC	HTB‐26
Software
BBMap [v38.22]	Bushnell B.	https://sourceforge.net/projects/bbmap/
FastQC [v0.11.4]	Andrews S.	https://www.bioinformatics.babraham.ac.uk/projects/fastqc
SAMtools [v1.3.1]	(Li et al, 2009)	http://samtools.sourceforge.net
tRNAscan‐SE [v2.0]	(Chan & Lowe, 2019)	http://lowelab.ucsc.edu/tRNAscan-SE
BEDtools [v2.27.1]	(Quinlan & Hall, 2010)	https://bedtools.readthedocs.io/en/latest
Segemehl [v0.3.1]	(Hoffmann et al, 2009)	https://www.bioinf.uni-leipzig.de/Software/segemehl
Picard [v2.18.17]	Broad Institute	https://github.com/broadinstitute/picard
GATK [v3.8]	(McKenna et al, 2010)	https://software.broadinstitute.org/gatk
GSEA [v3.0]	(Subramanian et al, 2005)	https://software.broadinstitute.org/gsea
BLAST [v2.9.0]	(Altschul et al, 1990)	https://blast.ncbi.nlm.nih.gov