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. 2022 Feb 9;2(2):100097. doi: 10.1016/j.xgen.2022.100097
REAGENT or RESOURCE SOURCE IDENTIFIER
Bacterial and virus strains
E. coli K-12 MG1655 ATCC 47076
S. cerevisiae (S288C) ATCC 204508
Chemicals, peptides, and recombinant proteins
1-acetylimidazole Millipore Sigma 157864
N-Methylisatoic Anhydride Invitrogen M25
2-methylnicotinic acid imidazole Millipore Sigma 913839
1,1¢-carbonyldiimidazole Millipore Sigma 115533
YPD Millipore Sigma Y1500
M9 minimal salts, 5X Millipore Sigma M6030
LB Broth (Luria low salt) Millipore Sigma L3397
Critical commercial assays
YeaStar RNA kit Zymo Research R1002
Direct RNA nanopore sequencing kit Oxford Nanopore Technologies SQK-RNA002
MinION flow cell Oxford Nanopore Technologies FLO-MIN106D
Flongle flow cell Oxford Nanopore Technologies FLO-FLG001
HiScribe T7 Quick High Yield RNA Synthesis Kit New England Biolabs E2050S
Deposited data
Raw nanopore sequence data NCBI SRA PRJNA634693, https://www.ncbi.nlm.nih.gov/bioproject/634693
Modification detection output, raw absorbance data, SHAPE-MaP profile data GitHub https://github.com/physnano/rRNA_nanoSHAPE
Oligonucleotides
ec16f_t7p: 5′-TAATACGACTCACTATAGGGAAATTGAA
GAGTTTGATCATGGCTC-3′		 This Paper N/A
ec16r: 5′-TAAGGAGGTGATCCAACCG
CAGG-3′		 This Paper N/A
ec23f_t7p: 5′-TAATACGACTCACTATAGGGGGTTAA
GCGACTAAGCGTACACGGT-3′		 This Paper N/A
ec23r: 5′-AAGGTTAAGCCTCACGGTTC
ATTAG-3′		 This Paper N/A
sc18f_t7p: 5′- TAATACGACTCACTATAGGGTATCT
GGTTGATCCTGCCAGTAGTC-3′		 This Paper N/A
sc18r: 5′- TAATGATCCTTCCGCAGGTTCACCTAC-3′ This Paper N/A
sc25f_t7p: 5′- TAATACGACTCACTATAGGGGTTTGA
CCTCAAATCAGGTAGGAGTA-3′		 This Paper N/A
sc25r: 5′- ACAAATCAGACAACAAAGGCTTAATCTC-3′ This Paper N/A
Software and algorithms
nanopolish v0.11.1 Simpson Lab: https://simpsonlab.github.io/ https://github.com/jts/nanopolish
tombo v1.5.1 Stoiber et al.31 https://github.com/nanoporetech/tombo
Jupyter notebooks Project Jupyter https://jupyter.org/
Analysis and plotting scripts This Paper https://github.com/physnano/rRNA_nanoSHAPE
guppy v3.1.5 Oxford Nanopore Technologies https://nanoporetech.com/
ont_fast5_api Oxford Nanopore Technologies https://github.com/nanoporetech/ont_fast5_api
R-chie Lai et al.50 https://www.e-rna.org/r-chie/
RNAstructure v6.2 Mathews Lab https://rna.urmc.rochester.edu/RNAstructure.html
RNAfold v2.4.13 RNAfold WebServer http://rna.tbi.univie.ac.at//cgi-bin/RNAWebSuite/RNAfold.cgi