REAGENT or RESOURCE	SOURCE	IDENTIFIER
Chemicals, peptides, and recombinant proteins
Ethanol absolute ≥99.8%	VWR	20821.330
Glass beads, acid-washed	Sigma-Aldrich	G8772
Acid-Phenol:Chloroform, pH 4.5 (with IAA, 125:24:1)	Thermo Fisher Scientific	AM9722
dNTP set, 100 mM solution	Thermo Fisher Scientific	R0181
Phenol solution. Saturated with 0.1M citrate buffer, pH 4.3 ± 0.2	Sigma-Aldrich	P4682
Chloroform:isoamyl alcohol 24:1	Sigma-Aldrich	C0549
Sodium acetate buffer solution, pH 5.3	Sigma-Aldrich	S7899
Glycoblue coprecipitant (15 mg/mL)	Thermo Fisher Scientific	AM9515
Nuclease-free water, not DEPC treated	Thermo Fisher Scientific	AM9937
RiboLock RNase inhibitor 40 000U/mL	Thermo Fisher Scientific	EO0382
Turbo DNase kit	Thermo Fisher Scientific	AM1907
T4 RNA ligase 1	NEB	M0204L
SuperScript™ II Reverse Transcriptase	Thermo Fisher Scientific	18064071
Phusion®High-Fidelity PCR Master Mix	NEB	M0531S
AMPure XP	Beckman Coulter	A63881
RNAClean XP	Beckman Coulter	A63987
Duplex-specific nuclease	Evrogen	EA002
Critical commercial assays
High Sensitivity DNA kit	Agilent	5067-4626
Qubit™ dsDNA HS Assay Kit	Thermo Fisher Scientific	Q32854
Qubit™ RNA HS assay kit	Thermo Fisher Scientific	Q32852
Deposited data
The raw and processed sequencing data	This paper	GEO: GSE152375
Experimental models: organisms/strains
Saccharomyces cerevisiae strains: BY4741:(MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0)	NA	NA
Oligonucleotides
See Tables 1 and 2	This paper	N/A
Software and algorithms
Fivepseq package	GitHub	Nersisyan et al., 2020
bcl2fastq v2.20.0	Illumina	https://emea.support.illumina.com/sequencing/sequencing_software/bcl2fastq-conversion-software.html
Cutadapt	GitHub	https://github.com/marcelm/cutadapt/
UMI-tools	GitHub	Smith et al., 2017
STAR 2.7.0	GitHub	Dobin et al., 2013
DESeq2	Bioconductor	Love et al., 2014
Subread package	GitHub	Liao et al., 2014
IGV	https://igv.org	Thorvaldsdóttir et al., 2013
RStudio version 3.5.0	RStudio, Inc., Boston, MA	N/A
Equipment
Refrigerated benchtop centrifuge	N/A	N/A
Thermo-block	N/A	N/A
Agilent Bioanalyzer 2100	Agilent	Bioanalyzer 2100
Chemical hood	N/A	N/A
Qubit Fluorometer	Invitrogen	QuBit 2.0
Magnet stand for PCR tubes	N/A	N/A
Vortex mixer	Scientific Industries	Vortex-Genie 2