♣ Downloaded data
♣ Processed data according to the description of the paper

Methods/ResourceReagentSpeciesCell line / ConditionNumber of bases with scoreData Type
PARS (Nature, 2010)V1 & S1YeastS288C in_vivo3,254,906transcriptome-wide
PARS (Nature, 2014)V1 & S1HumanGM12878 native deproteinized in_vitro240,200transcriptome-wide
GM12878 native deproteinized followed by renatured in_vitro40,879transcriptome-wide
GM12878 renatured in_vitro3,265,933transcriptome-wide
GM12891 renatured in_vitro2,526,825transcriptome-wide
GM12892 renatured in_vitro2,921,326transcriptome-wide
PARTE (Mol Cell, 2012)V1YeastS288C 23℃ in_vitro1,029,095transcriptome-wide
S288C 30℃ in_vitro953,300transcriptome-wide
S288C 37℃ in_vitro983,672transcriptome-wide
S288C 55℃ in_vitro1,084,136transcriptome-wide
S288C 75℃ in_vitro765,720transcriptome-wide
DMS-seq (Nature, 2014)DMSHumanK562 in_vivo7,095,073transcriptome-wide
K652 in_vitro2,722,195transcriptome-wide
K562 denatured4,391,436transcriptome-wide
FBL in_vivo1,336,825transcriptome-wide
FBL in_vitro2,872,416transcriptome-wide
FBL denatured1,435,069transcriptome-wide
DMSYeastBY4741 in_vivo2,120,926transcriptome-wide
BY4741 in_vitro1,501,023transcriptome-wide
BY4741 denatuerd1,472,051transcriptome-wide
DMS-seq & SHAPE (Science, 2016)NoneHumanHEK293T K+ no-reagent509,106transcriptome-wide
HEK293T Na+ no-reagent384,681transcriptome-wide
HeLa K+ no-reagent455,380transcriptome-wide
HeLa Na+ no-reagent713,806transcriptome-wide
DMSMousemES DMS in_vitro 95℃234,705transcriptome-wide
mES DMS in_vitro 0mM K+1,454,858transcriptome-wide
mES DMS in_vitro 150mM K+384,510transcriptome-wide
mES DMS in_vivo PDS1,426,567transcriptome-wide
mES DMS in_vivo1,596,053transcriptome-wide
NAImES NAI in_vitro 0mM K+2,681,830transcriptome-wide
mES NAI in_vitro 150mM K+3,076,217transcriptome-wide
mES NAI in_vivo5,171,130transcriptome-wide
NonemES K+ no-reagent309,922transcriptome-wide
mES Na+ no-reagent86,082transcriptome-wide
mES Li+ no-reagent135,738transcriptome-wide
DMSYeastyRH101 DMS in_vitro 0mMK+2,611,745transcriptome-wide
yRH101 DMS in_vitro 150mMK+2,202,509transcriptome-wide
yRH101 DMS in_vivo2,326,412transcriptome-wide
NoneyRH101 K+ no-reagent1,333,943transcriptome-wide
yRH101 Na+ no-reagent1,645,607transcriptome-wide
DMSE.coliTOP10 DMS in_vitro 0mMK+71,848transcriptome-wide
TOP10 DMS in_vitro 150mMK+57,462transcriptome-wide
TOP10 DMS in_vivo42,686transcriptome-wide
NoneTOP10 K+ no-reagent42,095transcriptome-wide
TOP10 Na+ no-reagent39,846transcriptome-wide
DMSP.putidaKT2440 DMS in_vitro 0mMK+354,429transcriptome-wide
KT2440 DMS in_vitro 150mMK+286,808transcriptome-wide
KT2440 DMS in_vivo317,943transcriptome-wide
NoneKT2440 K+ no-reagent27,906transcriptome-wide
KT2440 Na+ no-reagent26,050transcriptome-wide
DMSSynechococcusWH8102 DMS in_vitro 0mMK+9,752transcriptome-wide
WH8102 DMS in_vitro 150mMK+10,176transcriptome-wide
NoneWH8102 K+ no-reagent5,455transcriptome-wide
WH8102 Na+ no-reagent5,239transcriptome-wide
DMS-seq (NSMB, 2018)DMSZebrafishGRCZ11 DMS in_vivo 64c 5,027,519transcriptome-wide
GRCZ11 DMS in_vivo sphere3,621,907transcriptome-wide
GRCZ11 DMS in_vivo shield3,538,202transcriptome-wide
GRCZ11 DMS in_vitro5,209,188transcriptome-wide
GRCZ11 DMS in_vivo 64c for translation inhibition3,551,200transcriptome-wide
GRCZ11 DMS in_vivo 64c PatA treated for translation inhibition4,398,966transcriptome-wide
GRCZ11 DMS in_vivo 64c CHX treated for translation inhibition3,253,266transcriptome-wide
DMS-seq (eLife, 2017)DMSE.coliMG1655 37℃ in_vitro WT 90,566transcriptome-wide
MG1655 95℃ in_vitro WT247,648transcriptome-wide
MG1655 37℃ in_vivo WT1,058,069transcriptome-wide
MG1655 37℃ in_vivo dusB-M3698,581transcriptome-wide
MG1655 37℃ in_vivo dusB-M3:2561,410transcriptome-wide
MG1655 37℃ in_vivo ∆gcvB679,085transcriptome-wide
MG1655 37℃ in_vivo ∆gcvB+ksg754,811transcriptome-wide
Structure-seq (Nature, 2014)DMSA.thaliana seeding in_vivo717,266transcriptome-wide
Structure-seq2 (NAR, 2017)DMSO.sativashoot_tissue in_vivo BiotinVAR custom_primer27,858transcriptome-wide
shoot_tissue in_vivo BiotinVAR standard_primer19,378transcriptome-wide
shoot_tissue custom_primer78,386transcriptome-wide
shoot_tissue standard_primer42,321transcriptome-wide
CIRS-seq (GenomeBiology, 2014)DMS & CMCTMousemES in_vivo6,587,101transcriptome-wide
Mod-seq (RNA, 2014)DMSYeastrpl26Δ in_vivo1,222transcriptome-wide
BY4741 in_vivo1,258transcriptome-wide
DIM-2P-seq (Cell, 2017)DMSHumanHEK293T in_vivo1,777,482transcriptome-wide
DMS-MaPseq (Nature Methods, 2017)DMSHumanHEK293T in_vivo2,398,505transcriptome-wide
DMSYeastBY4741 DMS in_vivo TGIRT 5,407,062transcriptome-wide
BY4741 DMS in_vivo SSii/Mn+ 3,507,962transcriptome-wide
BY4741 2.5% DMS in_vivo1,169,814transcriptome-wide
BY4741 5% DMS in_vivo1,519,676transcriptome-wide
NoneBY4741 TGIRT no-reagent1,491,993transcriptome-wide
BY4741 SSii/Mn+ no-reagent2,316,911transcriptome-wide
DMS-MaPseq (Nature, 2018)DMSYeastBY4741 Ded1p_Mutate in_vivo3,035,616transcriptome-wide
BY4741 WT in_vivo3,620,439transcriptome-wide
RAPiD-MaPseq (NAR, 2019)DMSIAVA/Puerto Rico/8/1934(H1N1) in_vivo6,989transcriptome-wide
A/Puerto Rico/8/1934(H1N1) in_vitro6,991transcriptome-wide
SHAPE-MaP (Biochemistry, 2015)1M7Mousetrophoblast stem cells incell30,944transcriptome-wide
trophoblast stem cells exvivo534transcriptome-wide
SHAPE-MaP (Cell, 2018)1M7E.coliMG1655 cell_free368,290transcriptome-wide
MG1655 in_cell384,796transcriptome-wide
MG1655 Kasugamycin in_cell244,826transcriptome-wide
SHAPE-MaP (PNAS, 2015)1M7HCV HCV in_vitro28,426transcriptome-wide
SHAPE (Nature, 2009)1M7HIVHIV-1 in_vivo9,120transcriptome-wide
SHAPE-MaP (Nature Methods, 2014)1M6HIVHIV-1 1M6 in_vivo9,159transcriptome-wide
1M7HIV-1 1M7 in_vivo9,150transcriptome-wide
NMIAHIV-1 NMIA in_vivo9,157transcriptome-wide
SHAPE-MaP (PLOS CompBio, 2015)1M7HIVHIV in_vivo27,837transcriptome-wide
SHAPE-MaP (Mol. Cell, 2021)NAISARS-CoV-2Wuhan-Hu-1 in_vivo29,848transcriptome-wide
SHAPE-MaP (PNAS, 2018)1M6Denguestrain S16803 exviron_1M610,628transcriptome-wide
strain S16803 inviron_1M610,443transcriptome-wide
1M7strain S16803 exviron_1M710,628transcriptome-wide
strain S16803 inviron_1M710,583transcriptome-wide
NMIAstrain S16803 exviron_NMIA10,633transcriptome-wide
strain S16803 inviron_NMIA10,637transcriptome-wide
NAI-MaP (Nature Communication, 2019)NAIDengueDengue in_vivo42,545transcriptome-wide
NAI-MaP (Nature Communication, 2019)NAIZikaZIKV in_vivo42,932transcriptome-wide
SHAPE (Mol Cell, 2016)NAIHCV JFH1 in_vitro8,815transcriptome-wide
SHAPE (BioChemistry, 2013)1M7STMVSTMV in_vitro946transcriptome-wide
STMV ex_vitro1,011transcriptome-wide
SHAPE-seq (NAR, 2018)1M7CMVBn57-CMV lyRNA in_plant_cell_lysates2,216transcriptome-wide
Bn57-CMV viRNA in_vitro2,216transcriptome-wide
icSHAPE (Cell Host & Microbe, 2018)NAI-N3ZikaZIKV in_vivo21,530transcriptome-wide
ZIKV in_vitro21,530transcriptome-wide
icSHAPE (Cell, 2021)NAI-N3SARS-CoV-2Wuhan-Hu-1 in_vivo26,701transcriptome-wide
Wuhan-Hu-1 in_vitro27,649transcriptome-wide
icSHAPE (Nature, 2015)NAI-N3MousemES METTL3_KO in_vivo1,764,594transcriptome-wide
mES v65 in_vivo14,106,282transcriptome-wide
mES v65 in_vitro17,444,983transcriptome-wide
icSHAPE (Cell, 2016)NAI-N3HumanHEK293T in_vivo2,030,707transcriptome-wide
HEK293T in_vitro1,854,626transcriptome-wide
icSHAPE (NSMB, 2019)NAI-N3MousemES chromatin in_vivo3,871,974transcriptome-wide
mES chromatin in_vitro2,969,374transcriptome-wide
mES cytoplasm in_vivo8,292,181transcriptome-wide
mES cytoplasm in_vitro6,340,837transcriptome-wide
mES nucleoplasm in_vivo9,899,971transcriptome-wide
mES nucleoplasm in_vitro10,473,036transcriptome-wide
NAI-N3HumanHEK293 chromatin in_vivo2,296,220transcriptome-wide
HEK293 chromatin in_vitro3,701,135transcriptome-wide
HEK293 cytoplasm in_vivo2,146,114transcriptome-wide
HEK293 cytoplasm in_vitro6,895,344transcriptome-wide
HEK293 nucleoplasm in_vivo3,714,351transcriptome-wide
HEK293 nucleoplasm in_vitro8,169,250transcriptome-wide
icSHAPE (GenomeBiology, 2020)NAI-N3Zebrafishwidetype AB strain fertilized_egg in_vivo7,294,463transcriptome-wide
widetype AB strain 1-cell in_vivo8,107,635transcriptome-wide
widetype AB strain 4-cell in_vivo8,024,909transcriptome-wide
widetype AB strain 64-cell in_vivo9,507,124transcriptome-wide
widetype AB strain shield in_vivo7,501,747transcriptome-wide
widetype AB strain sphere in_vivo12,022,502transcriptome-wide
widetype AB strain shield elavl1a-mo in_vivo5,675,258transcriptome-wide
widetype AB strain sphere elavl1a-mo in_vivo7,033,200transcriptome-wide
Keth-seq (NCB, 2020)N3-kethoxalMousemES kethoxal vs kethoxal_removed in_vivo83,466transcriptome-wide
mES kethoxal_treated_1min vs no_treat in_vivo10,944transcriptome-wide
mES kethoxal_treated_5min vs no_treat in_vivo6,947transcriptome-wide
mES kethoxal vs no_treat in_vitro189,658transcriptome-wide
mES kethoxal vs no_treat in_vivo116,232transcriptome-wide
mES kethoxal vs no_treat 60,593transcriptome-wide
N3-kethoxalHumanHeLa kethoxal vs no treat in_vivo351,732transcriptome-wide
HeLa kethoxal vs no treat in_vitro203,319transcriptome-wide
HeLa kethoxal vs no treat PDS in_vivo 336,513transcriptome-wide
HeLa kethoxal vs no treat PDS in_vitro 229,126transcriptome-wide
Lead-seq (NAR, 2020)Lead(II)Y.pseudotuberculosisLead-seq_25degree1,057,814transcriptome-wide
Lead-seq_37degree1,308,701transcriptome-wide
SHAPE-MaP (Biochemistry, 2019)1M6Denguestrain S16803 exvirion_1M610,649transcriptome-wide
strain S16803 refolded_1M610,624transcriptome-wide
1M7strain S16803 exvirion_1M710,647transcriptome-wide
strain S16803 refolded_1M710,624transcriptome-wide
NMIAstrain S16803 exvirion_NMIA10,650transcriptome-wide
strain S16803 exvirion_NMIA10,624transcriptome-wide
SHAPE-MaP (J. Virol, 2020)1M7CHIKVCHIKV genome11,980transcriptome-wide
CHIKV 3'UTR dup798target-specific
CHIKV 3'UTR con633target-specific
CHIKV 3'UTR del520target-specific
SHAPE-MaP (J. Virol, 2022)NAIHCVJc1 invitro_full_genome9,432transcriptome-wide
pSGR-JFH1 invivo_subgenomic_replicon5,968target-specific
SHAPE-MaP & DMS-MaPseq (NAR, 2022)5NIARotavirusRF invitro_transcriptome_0uM_NSP217,910transcriptome-wide
RF invitro_transcriptome_5uM_NSP217,844transcriptome-wide
RF invitro_transcriptome_10uM_NSP217,798transcriptome-wide
RF invitro_transcriptome_20uM_NSP217,801transcriptome-wide
RF invitro_segment_5_6_10_11_0uM_NSP24,238transcriptome-wide
RF invitro_segment_5_6_10_11_5uM_NSP24,236transcriptome-wide
RF invitro_segment_5_6_10_11_10uM_NSP24,240transcriptome-wide
RF invitro_segment_5_6_10_11_20uM_NSP24,250transcriptome-wide
RF invivo_RFS11597target-specific
DMSRF RFS11_50mM_DMS598target-specific
RF RFS11_20uM_NSP2_50mM_DMS590target-specific
RF RFS11_10mM_DMS590target-specific
RF RFS11_20uM_NSP2_10mM_DMS590target-specific
SHAPE-MaP (Nat. Microbiol., 2019)1M7IAVWSN/PR8/Udorn vRNP_invirio40,227transcriptome-wide
WSN in vitro transcribed RNA13,474transcriptome-wide
WSN naked viral RNA13,473transcriptome-wide
SHAPE-MaP & DMS-MaPseq (NAR, 2020)NAISARS-CoV-2Leiden-0002 in vitro29,199transcriptome-wide
Leiden-0002 in vivo29,607transcriptome-wide
DMSLeiden-0002 in vitro14,351transcriptome-wide
DMS-MaPseq (NC, 2022)DMSSARS-CoV-2USA-WA1 in vivo Huh710,228transcriptome-wide
USA-WA1 in vivo Vero14,413transcriptome-wide
SHAPE-MaP (NC, 2022)NAISARS-CoV-2Wuhan-Hu-1 in vivo23,105transcriptome-wide
delta382 in vivo23,578transcriptome-wide
DMS-MaPseq (NM, 2021)DMSSARS-CoV-2Leiden-0002 in vitro14,413transcriptome-wide
SHAPE-MaP (Nature, 2021)1M7Humanhuman in vitro transcribed ABAT348target-specific
icSHAPE (Cell Res., 2021)NAI-N3HumanHEK293 in vivo13,770,965transcriptome-wide
HeLa in vivo9,686,389transcriptome-wide
K562 in vivo12,566,202transcriptome-wide
HepG2 in vivo7,723,921transcriptome-wide
H9 in vivo11,994,944transcriptome-wide
MousemES in vivo6,099,199transcriptome-wide
smartSHAPE (Fundamental Research, 2022)NAI-N3HumanHEK293T in vivo 1ng 9,509,617transcriptome-wide
HEK293T in vivo 5ng 11,986,785transcriptome-wide
HEK293T in vivo 25ng 11,120,239transcriptome-wide
HEK293T in vivo 125ng 10,755,489transcriptome-wide
MouseC57BL/6J mouse Ly6Clo macrophages in vivo7,339,328transcriptome-wide
C57BL/6J mouse Ly6Chi macrophages in vivo4,997,290transcriptome-wide
SHAPE-MaP (Nature, 2023)NAIA.thalianaseedling in planta elf6,864,135transcriptome-wide
seedling in planta mock6,749,684transcriptome-wide
icSHAPE & icLASER (NAR, 2021)NAI-N3HumanK562 icSHAPE in vitro7,904,484transcriptome-wide
K562 icSHAPE in vivo9,538,140transcriptome-wide
Naz-N3K562 icLASER in vitro11,336,979transcriptome-wide
K562 icLASER in vivo10,769,117transcriptome-wide
icSHAPE (Cell, 2018)NAI-N3HumanCoilin KO Hela in vitro hTR445target-specific
human in vitro transcribed hTR445target-specific
TCAB1 KO Hela in vitro hTR445target-specific
TCAB1 KO Hela in vitro rescue hTR445target-specific
TCAB1 KO Hela rescue hTR445target-specific
WT Hela in vitro hTR445target-specific
icSHAPE-MaP (NC, 2021)NAI-N3HumanHEK293T in vivo sRNA25,320transcriptome-wide
HEK293T in vitro sRNA32,050transcriptome-wide
HEK293T Dicer-enriched RNA71,468transcriptome-wide
SHAPE-MaP (PNAS, 2016)1M6MouseTSC ex vivo 1M6 Xist15,356target-specific
NMIATSC ex vivo NMIA Xist15,368target-specific
1M7TSC ex vivo 1M7 Xist15,412target-specific
TSC in cell 1M7 Xist15,412target-specific
SHAPE-MaP (RNA, 2023)5NIAHumanA549 in vivo MALAT16,674target-specific
HEK293 in vivo MALAT16,583target-specific
Human ex vivo MALAT16,630target-specific
Green monkeyVero in vivo MALAT16,712target-specific
Vero ex vivo MALAT16,705target-specific
DMS-MaPseq (RNA, 2021)DMSB.subtilisBS168 in vivo ctc isoform228target-specific
BS168 in vivo yvrE isoform206target-specific
SHAPE-seq & Cotranscriptional SHAPE-seq (NAR, 2022)BzCNB.subtilisB. subtilis in vitro transcribed equilibrium 135nt yxjA135target-specific
B. subtilis in vitro transcribed equilibrium 160nt yxjA160target-specific
B. subtilis in vitro transcribed equilibrium 220nt yxjA220target-specific
B. subtilis in vitro transcribed cotranscriptional 135nt yxjA135target-specific
B. subtilis in vitro transcribed cotranscriptional 160nt yxjA160target-specific
B. subtilis in vitro transcribed cotranscriptional 220nt yxjA220target-specific
SHAPE-MaP (NAR, 2021)1M4E.coliDH10B in vivo 1M4 16S & 23S4,296target-specific
DH10B ex vivo 1M4 16S & 23S4,356target-specific
2A3DH10B in vivo 2A3 16S & 23S4,269target-specific
DH10B ex vivo 2A3 16S & 23S4,277target-specific
6A3DH10B in vivo 6A3 16S & 23S4,385target-specific
DH10B ex vivo 6A3 16S & 23S4,352target-specific
B5DH10B in vivo B5 16S & 23S4,267target-specific
DH10B ex vivo B5 16S & 23S4,335target-specific
I5DH10B in vivo I5 16S & 23S4,297target-specific
DH10B ex vivo I5 16S & 23S4,354target-specific
NAIDH10B in vivo NAI 16S & 23S4,291target-specific
DH10B ex vivo NAI 16S & 23S4,359target-specific
NICDH10B in vivo NIC 16S & 23S4,270target-specific
DH10B ex vivo NIC 16S & 23S4,357target-specific
1M4B.subtilisBS168 in vivo 1M4 16S & 23S4,370target-specific
2A3BS168 in vivo 2A3 16S & 23S4,360target-specific
6A3BS168 in vivo 6A3 16S & 23S4,366target-specific
B5BS168 in vivo B5 16S & 23S4,370target-specific
I5BS168 in vivo I5 16S & 23S4,370target-specific
NAIBS168 in vivo NAI 16S & 23S4,363target-specific
NICBS168 in vivo NIC 16S & 23S4,361target-specific
1M4HumanHEK293 in vivo 1M4 18S & 28S6,586target-specific
2A3HEK293 in vivo 2A3 18S & 28S6,504target-specific
6A3HEK293 in vivo 6A3 18S & 28S6,752target-specific
B5HEK293 in vivo B5 18S & 28S6,404target-specific
I5HEK293 in vivo I5 18S & 28S6,554target-specific
NAIHEK293 in vivo NAI 18S & 28S6,590target-specific
NICHEK293 in vivo NIC 18S & 28S6,597target-specific
Structure-Seq (PLoS Genet., 2015)DMSMouseMEF higher DMS Xist8,262target-specific
MEF lower DMS Xist8,425target-specific
Structure-Seq (Genetics, 2019)DMSYeastBY4741 in vivo 7,573,162transcriptome-wide
dbp2delta in vivo7,876,634transcriptome-wide
tNet-MaPseq & tNet-RNase-seq (Mol. Cell, 2021)DMSHumanHEK293 tNet-MaP_WT nascent RNA119,951,120transcriptome-wide
HEK293 tNet-MaP_R749H nascent RNA54,430,713transcriptome-wide
RNaseHEK293 tNet-Rnase-seq WT without protein footprints60,728,379transcriptome-wide
HEK293 tNet-Rnase-seq WT including repetitive elements77,649,478transcriptome-wide
HEK293 tNet-Rnase-seq R749H without protein footprints45,637,400transcriptome-wide
HEK293 tNet-Rnase-seq R749H including repetitive elements52,697,302transcriptome-wide
DMS-MaPseq (Front. Plant Sci., 2022)NoneO.sativaseedling noDMS 18S rRNA353target-specific
seedling noDMS 5'UTR PHO2370target-specific
seedling root noDMS 18S rRNA353target-specific
seedling noDMS genome 65,406transcriptome-wide
DMSseedling shaking 1% DMS 18S rRNA353target-specific
seedling shaking 2% DMS 18S rRNA353target-specific
seedling shaking 2.5% DMS 18S rRNA353target-specific
seedling vacuum 1% DMS 18S rRNA353target-specific
seedling vacuum 2% DMS 18S rRNA353target-specific
seedling vacuum 2.5% DMS 18S rRNA353target-specific
seedling 5'UTR PHO2370target-specific
seedling root 1% DMS 18S rRNA353target-specific
seedling genome74,332transcriptome-wide
Nuc-SHAPE-Structure-Seq (Genome Biol., 2021)NAIA.thalianaseedling in vivo5,411,900transcriptome-wide
seedling deproteinized7,322,805transcriptome-wide
DMS-MaPseq (PNAS, 2021)DMSYeastBY4741 purified mature 40S1,800target-specific
BY4741 WT purified pre-40S1,800target-specific
BY4741 Rio2_dloop mutant purified pre-40S1,800target-specific
BY4741 S15_YRR mutant purified pre-40S1,800target-specific
ChemModSeq (NAR, 2014)1M7YeastBY4741 purified 20S Enp11,800target-specific
BY4741 purified 20S Ltv11,800target-specific
BY4741 purified 20S Rio21,800target-specific
BY4741 purified 20S Tsr11,800target-specific
BY4741 purified 20S Nob11,800target-specific
BY4741 purified 20S Rio11,800target-specific
BY4741 purified 20S 80S like1,800target-specific
BY4741 purified 18S 80S1,800target-specific
DMSBY4741 purified 18S1,800target-specific
NAIBY4741 purified 20S Tsr11,800target-specific
BY4741 purified 20S Rio11,800target-specific
BY4741 purified 18S 80S1,800target-specific
NoneBY4741 purified 20S midearly control1,800target-specific
BY4741 purified 18S late control1,800target-specific
BY4741 purified 18S DMS control1,800target-specific
BY4741 purified 20S Tsr1 DMSO1,800target-specific
BY4741 purified 18S 80S DMSO1,800target-specific
Mod-seq (NAR, 2018)1M7Mousemouse NEAT1_S3,176target-specific
Humanhuman NEAT1_S3,595target-specific
SHAPE-seq (Biochemistry, 2017)1M7S.entericaecoli TG1 30°C A29C mutant agsA 5'UTR61target-specific
ecoli TG1 30°C G21C mutant agsA 5'UTR61target-specific
ecoli TG1 30°C WT agsA 5'UTR61target-specific
ecoli TG1 42°C A29C mutant agsA 5'UTR61target-specific
ecoli TG1 42°C G21C mutant agsA 5'UTR61target-specific
ecoli TG1 42°C WT agsA 5'UTR61target-specific
in vitro folding 30°C A29C mutant agsA 5'UTR61target-specific
in vitro folding 30°C G21 mutant agsA 5'UTR61target-specific
in vitro folding 30°C WT agsA 5'UTR61target-specific
in vitro folding 42°C A29C mutant agsA 5'UTR61target-specific
in vitro folding 42°C G21 mutant agsA 5'UTR61target-specific
in vitro folding 42°C WT agsA 5'UTR61target-specific
in vitro folding 30°C modified protocol agsA 5'UTR61target-specific
in vitro folding 80°C modified protocol agsA 5'UTR61target-specific
in vitro PURExpress active trans 30°C61target-specific
in vitro PURExpress active trans 42°C61target-specific
in vitro PURExpress no ribosome trans 30°C61target-specific
in vitro PURExpress no ribosome trans 42°C61target-specific
in vitro PURExpress trans init stalled 30°C61target-specific
in vitro PURExpress trans init stalled 42°C61target-specific
Cotranscriptional SHAPE-seq (Mol. Cell, 2021)BzCNE.coliecoli U21C_C22U_G93A cotranscriptional SHAPE-seq SRP114target-specific
ecoli U21C cotranscriptional SHAPE-seq SRP114target-specific
ecoli U21C equilibrium-refolded SHAPE-seq SRP114target-specific
Cotranscriptional SHAPE-seq (Nat. Struct., 2016)BzCNB.cereusB.cereus WT 0mM NaF crcB82target-specific
B.cereus WT 10mM NaF crcB82target-specific
B.cereus WT refold 10mM NaF crcB82target-specific
B.cereus M18 0mM NaF crcB82target-specific
B.cereus M18 10mM NaF crcB82target-specific
B.cereus M19 0mM NaF crcB82target-specific
B.cereus M19 10mM NaF crcB82target-specific
B.cereus M20 0mM NaF crcB82target-specific
B.cereus M20 10mM NaF crcB82target-specific
B.cereus M21 0mM NaF crcB82target-specific
B.cereus M21 10mM NaF crcB82target-specific
B.cereus M22 0mM NaF crcB82target-specific
B.cereus M22 10mM NaF crcB82target-specific
B.cereus M23 0mM NaF crcB82target-specific
B.cereus M23 10mM NaF crcB82target-specific
E.coliE.coli BzCN SRP114target-specific
E.coli BzCN refold SRP114target-specific
DMSE.coli DMS SRP114target-specific
icSHAPE (Cell Rep., 2024)NAI-N3IAVWSN in vivo13,301transcriptome-wide
WSN in virio13,301transcriptome-wide
RL-seq (RNA Biol., 2022)hydroxyl radicalE.coliE.coli 16S UMI in vitro1,521target-specific
E.coli 23S UMI in vitro2,892target-specific
E.coli 5S UMI in vitro105target-specific

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Useful links

  • Zhanglab in Tsinghua University PrismNet web server RASP database RISE database