REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Goat polyclonal anti-eIF3b (for CoIP)	Santa Cruz	sc16377 (discontinued)
Rabbit polyclonal anti-eIF3a	Cell signaling	2538
Mouse polyclonal anti-eIF3b (for western blot)	Thermo Fisher	PA5-23278
Rabbit polyclonal anti-eIF3c	Santa Cruz	sc28858
Rabbit polyclonal anti-eIF3e	Abcam	ab36766
Rabbit polyclonal anti-eIF3i	Sigma	HPA029939
Rabbit polyclonal anti-eIF3l	Bethyl	A304-753A-T
Mouse Monoclonal anti-eIF2alpha	Santa Cruz	sc133132
Rabbit polyclonal anti-eIF5	Santa Cruz	sc282
Rabbit polyclonal anti-RPS14	Santa Cruz	sc68873
Rabbit polyclonal anti-TIF32	Dr. Jiří Hašek	N/A
Rabbit polyclonal anti-PRT1	Cigan et al., 1991	N/A
Rabbit polyclonal anti-GCD11	Dr. Ernie Hanning	N/A
Rabbit polyclonal anti-SUI5	Dr. Alan Hinnebusch	N/A
Rabbit polyclonal anti-ASC1	Dr. Chris Browne	N/A
Chemicals, Peptides, and Recombinant Proteins
DMEM	Sigma	D6429
FBS	Sigma	F7524
Cycloheximide	Merck	01810
Formaldehyde solution	Sigma	F8775
Glycine	Serva	23395.03
protease inhibitor cocktail cOmplete mini EDTA-free	Roche	11836170001
protease inhibitor cocktail cOmplete EDTA-free	Roche	11873580001
RNase I	Invitrogen	AM2294
SUPERaseIN	Invitrogen	AM2694
Protein A/G Agarose	Pierce	20421
ANTI-FLAG M2 affinity gel	Sigma	A2220
FLAG peptide solution	Sigma	F3290
Glycogen	Thermo Fisher	AM5910
RNA fragmentation reagent	Thermo Fisher	AM8740
T4 Polynucleotide kinase PNK	NEB	M0201L
Universal miRNA cloning linker	NEB	S1315S
T4 RNA ligase 2	NEB	M0242L
SuperScript III	Thermo Fisher	18080044
CircLigase ssDNA Ligase	Epicenter	CL4115K
Dynabeads MyOne Streptavidin C1	Thermo Fisher	65001
Phusion Polymerase HF	NEB	M0530S
10 bp DNA ladder	Thermo Fisher	10821-015
Sybr Gold	Thermo Fisher	S11494
Critical Commercial Assays
RNeasy Mini Kit	QIAGEN	74104
Poly(A)Purist MAG Kit	Thermo Fisher	AM1922
Deposited Data
Raw and analyzed data	this paper	GEO: GSE139132
Experimental Models: Cell Lines
HEK293T	ATCC	CRL-3216
Experimental Models: Organisms/Strains
S. cerevisiae SY182	this paper	N/A
S. cerevisiae SY183	this paper	N/A
S. cerevisiae SY194	this paper	N/A
S. cerevisiae H25	this paper	N/A
Oligonucleotides
CAAGCAGAAGACGGCATACGAGATTGAAG CGTGACTGGAGTTCAGACGTGTGCTCTTCCG	This paper	reverse primer, index: GCTTCA, barcode A
CAAGCAGAAGACGGCATACGAGATCTACTA GTGACTGGAGTTCAGACGTGTGCTCTTCCG	This paper	reverse primer, index: TAGTAG, barcode B
CAAGCAGAAGACGGCATACGAGATAGTCGT GTGACTGGAGTTCAGACGTGTGCTCTTCCG	Ingolia et al., 2012	reverse primer, index: ACGACT, NI-NI-3
CAAGCAGAAGACGGCATACGAGATACTGATG TGACTGGAGTTCAGACGTGTGCTCTTCCG	Ingolia et al., 2012	reverse primer, index: ATCAGT, NI-NI-5
CAAGCAGAAGACGGCATACGAGATATGCTG GTGACTGGAGTTCAGACGTGTGCTCTTCCG	Ingolia et al., 2012	reverse primer, index: CAGCAT, NI-NI-6
CAAGCAGAAGACGGCATACGAGATACGTCG GTGACTGGAGTTCAGACGTGTGCTCTTCCG	Ingolia et al., 2012	reverse primer, index: CGACGT, NI-NI-7
CAAGCAGAAGACGGCATACGAGATAGCTGC GTGACTGGAGTTCAGACGTGTGCTCTTCCG	Ingolia et al., 2012	reverse primer, index: GCAGCT, NI-NI-11
CAAGCAGAAGACGGCATACGAGATATCGTA GTGACTGGAGTTCAGACGTGTGCTCTTCCG	Ingolia et al., 2012	reverse primer, index: TACGAT, NI-NI-13
CAAGCAGAAGACGGCATACGAGATGACTA CGTGACTGGAGTTCAGACGTGTGCTCTTCCG	Ingolia et al., 2012	reverse primer, index: GTAGTC, NI-NI-22
AATGATACGGCGACCACCGAGATCTACAC	Ingolia et al., 2012	forward primer, NI-NI-2
5′-(Phos)-AGATCGGAAGAGCGTCGTGTAGGGAAAGAGT GTAGATCTCGGTGGTCGC-(SpC18)-CACTCA- (SpC18)-TTCAGACGTGTGCTCTTCCGA TCTATTGATGGTGCCTACAG	Ingolia et al., 2012	split adaptor primer, NI-NI-9
AUGUACACGGAGUCGAG CUCAACCCGCAACGCGA-(Phos)-3′	Ingolia et al., 2012	34nt size marker oligo, RNA
AUGUACACGGAGUCGACCCAACGCGA-(Phos)-3′	Ingolia et al., 2012	26nt size marker oligo, RNA
5′ -biotin-TEG-GGGGGGATGCGTGCATTTATCAGATCA	Ingolia et al., 2012	human rRNA depletion oligos
5′ -biotin-TEG-TTGGTGACTCTAGAT AACCTCGGGCCGATCGCACG	Ingolia et al., 2012	human rRNA depletion oligos
5′ -biotin-TEG-GAGCCGCCTGGATAC CGCAGCTAGGAATAATGGAAT	Ingolia et al., 2012	human rRNA depletion oligos
5′ -biotin-TEG-TCGTGGGGGGCCCA AGTCCTTCTGATCGAGGCCC	Ingolia et al., 2012	human rRNA depletion oligos
5′ -biotin-TEG-GCACTCGCCGAAT CCCGGGGCCGAGGGAGCGA	Ingolia et al., 2012	human rRNA depletion oligos
5′ -biotin-TEG-GGGGCCGGGCCG CCCCTCCCACGGCGCG	Ingolia et al., 2012	human rRNA depletion oligos
5′ -biotin-TEG-GGGGCCGGGC CACCCCTCCCACGGCGCG	(Ingolia et al., 2012)	human rRNA depletion oligos
5′ -biotin-TEG-CCCAGTGCGCCCCGGGCGTCG TCGCGCCGTCGGGTCCCGGG	Ingolia et al., 2012	human rRNA depletion oligos
5′ -biotin-TEG-TCCGCCGAGGGC GCACCACCGGCCCGTCTCGCC	Ingolia et al., 2012	human rRNA depletion oligos
5′ -biotin-TEG-AGGGGCTCTCGCTTCTGGCGCCAAGCGT	Ingolia et al., 2012	human rRNA depletion oligos
5′ -biotin-TEG-GAGCCTCGGTTGGCCCCGGATAGCCGGGTCCCCGT	Ingolia et al., 2012	human rRNA depletion oligos
5′ -biotin-TEG-GAGCCTCGGTTGGCCTCGGATAGCCGGTCCCCCGC	Ingolia et al., 2012	human rRNA depletion oligos
5′ -biotin-TEG-TCGCTGCGATCTATTGAAAGTCAGCCCTCGACACA	Ingolia et al., 2012	human rRNA depletion oligos
5′ -biotin-TEG-TCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCT	Ingolia et al., 2012	human rRNA depletion oligos
5′ -biotin-TEG-GGTGCACAATCGACCGATC	Ingolia et al., 2012	yeast rRNA depletion oligo
5′ -biotin-TEG-GTTTCTTTACTTATTCAATGAAGCGG	Ingolia et al., 2012	yeast rRNA depletion oligo
5′ -biotin-TEG-TATAGATGGATACGAATAAGGCGTC	Ingolia et al., 2012	yeast rRNA depletion oligo
5′ -biotin-TEG-TTGCTCGAATATATTAGCATGGAATAATAGAATA	This paper	yeast rRNA deple-tion oligo, y sub 5
5′ -biotin-TEG-GAGATGTATTTATTAGATAAA	This paper	yeast rRNA deple-tion oligo, y sub 6
5′ -biotin-TEG-TGGTATAACTGTGGTAATTCTAGAGCTAATACAT	This paper	yeast rRNA deple-tion oligo, y sub 7
5′ -biotin-TEG-TTTTACTTTGAAAAAATTAGAGTGTTCAAAGCAGG	This paper	yeast rRNA deple-tion oligo, y sub 8
5′ -biotin-TEG-ATGATTAATAGGGACGGTCGGGGG	This paper	yeast rRNA deple-tion oligo, y sub 9
5′ -biotin-TEG-GCCAAGGACGTTTTCATTAATCAAGAACGAA	This paper	yeast rRNA deple-tion oligo, y sub 10
5′ -biotin-TEG-TTCCAGGGGGCATGCCTGTTTGAGCGTCATT	This paper	yeast rRNA deple-tion oligo, y sub 11
5′ -biotin-TEG-TCCACGTTCTAGCATTCAAGGTCC	This paper	yeast rRNA deple-tion oligo, y sub 12
Software and Algorithms
Bowtie	Langmead et al., 2009	N/A
Bowtie2	Langmead and Salzberg, 2012	N/A
Tophat		N/A
FASTX-Toolkit		N/A
Python 2.7	van Rossum (1995)	N/A
HTSeq	Anders et al., 2015	https://academic.oup.com/bioinformatics/article-lookup/doi/10.1093/bioinformatics/btu638
matplotlib	Hunter (2007)	N/A
R	R Core Team (2018)	https://www.R-project.org/
SAMtools	Li et al., 2009	[PMID: 19505943]