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. Author manuscript; available in PMC: 2023 Jan 20.
Published in final edited form as: Mol Cell. 2021 Nov 18;82(2):404–419.e9. doi: 10.1016/j.molcel.2021.11.003

KEY RESOURCES TABLE.

REAGENT or RESOURCE SOURCE IDENTIFIER
Antibodies
Mouse monoclonal anti-alpha Tubulin Sigma Cat# T5168;RRID:AB_477579
Mouse monoclonal beta-alpha Tubulin Millipore Cat# MAB3408; RRID:AB_94650
Rabbit polyclonal anti Histone H3 Abcam Cat# ab1791;RRID:AB_302613
Yeast, E. coli and human strains/lines
Fission yeast h- Lab stock yDH94
Fission yeast h- dus1::natR This work yDH1491
Fission yeast h- dus2::kanR This work yDH1456
Fission yeast h- dus3::hphR This work yDH1659
Fission yeast h- dus4::bleR This work yDH1631
Fission yeast h- dus1-4 Δ This work yDH1754
Fission yeast h- nda2noD This work yDH2013
Fission yeast h- nda3noD This work yDH2021
Fission yeast h- nda2noD nda3noD This work yDH2018
Human cell line HCT116 ATCC CCL247
Human cell line HCT116 DUS1-4 Δ This work HsΔ4 −/− (#1)
E. coli Lab stock JC8679
E. coli dusA::cmR dusB-fis::kanR dusC::specR Lab stock PS5107
Chemicals
Dynabeads Oligo(dT)25 Life Technologies 61002
sodium borohydride Sigma 452882
rhodamine 110 chloride Sigma 83695
[Ɣ-32P]-ATP Perkin Elmer NEG002A250UC
35S labeled methionine Perkin Elmer NEG709A500UC
Critical commercial assays
wheat germ extracts Promega L4380
Ribodepletion kit Thermo A15020 – K155005
Deposited data
Rho-seq, Ribo-seq and RNA-seq raw and processed data This work GEO: GSE145686; https://doi.org/10.17632/m6v9rcprz6.1
Raw data (Mendeley data) This work
Oligonucleotides
tRNAiMet primer extension ACCTACGGGTTATGAGCCCGTCGG This work 2540
tRNAAspGUC (SPCTRNAASP.06) primer extension GGGCTGCAAGCGTGAC This work 2743
SPMITTRNAARG.02 primer extension CTAACAATTTCGAAGATTGTTAC This work 2746
gBLOCK for synthetic RNA TAATACGACTCACTATAGGGGAGGCGAGAACACACCACAACGAAAACGAGCAAAACCCGGTACGCAACACAAAAGC GAACAACGCGAAAAAGGACACCGAAGCGGAAGCAAAGACAACCAACAGAAAACAACCGCAAACAAACGGGACCAGACAACGCACCAGCAAAA This work N/A
gBLOCK for synthetic RNA with 3 D TAATACGACTCACTATAGGGGAGGCGAGAACACACCACAACGAAAACGAGCAAAACCCTTTACGCACCACAAAAGC GAACAACGCGAAAAAGGACACCGAAGCGGAAGCAAAGACAACCAACAGAAAACAACCGCAAACAAACGGGACCAGA CAACGCACCAGCAAAA This work N/A
synthetic RNA primer extension GTCTTTGCTTCCGCTTCGGTGTCC This work 2567
synthetic RNA with 3 D primer extension CGCGTTGTTCGCTTTTGTGG This work 3079
RNA adaptor (Rho-seq) 5′-P-AGATCGGAAGAGCGTCGTG-ddC 2661
DNA adaptor (Rho-seq) 5′-P-AGATCGGAAGAGCACACGTCTG-ddC 2674
Software and algorithms
AnGeLi Bitton et al., 2015 N/A
WebLogo Crooks et al., 2004 N/A
RNAfold Lorenz et al., 2011 N/A