Data sources

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

Datasets

Methods/Resource Data source Reagent Species Cell line / Condition Number of bases with score Number of RNAs with scores
Total mRNA pseudogene lncRNA others
PARS (Nature, 2010) Reproduction V1 & S1 Yeast S288C in_vivo 3,254,906 5,661 5,524 4 0 133
PARS (Nature, 2014) Reproduction V1 & S1 Human GM12878 native deproteinized in_vitro 240,200 4,804 2,588 1 750 1,465
GM12878 native deproteinized followed by renatured in_vitro 40,879 828 411 0 102 315
GM12878 renatured in_vitro 3,265,933 33,801 17,867 10 5,063 10,861
GM12891 renatured in_vitro 2,526,825 29,541 15,798 11 4,391 9,341
GM12892 renatured in_vitro 2,921,326 31,488 16,794 10 4,707 9,977
PARTE (Mol Cell, 2012) Reproduction V1 Yeast S288C 23℃ in_vitro 1,029,095 2,474 2,393 0 0 81
S288C 30℃ in_vitro 953,300 2,285 2,205 0 0 80
S288C 37℃ in_vitro 983,672 2,358 2,280 0 0 78
S288C 55℃ in_vitro 1,084,136 2,616 2,549 0 0 67
S288C 75℃ in_vitro 765,720 2,271 2,196 0 0 75
DMS-seq (Nature, 2014) Reproduction DMS Human K562 in_vivo 7,095,073 61,615 31,518 890 9,798 19,409
K652 in_vitro 2,722,195 43,276 17,819 437 5,231 19,789
K562 denatured 4,391,436 46,884 24,266 634 7,326 14,658
FBL in_vivo 1,336,825 16,953 9,531 208 2,436 4,778
FBL in_vitro 2,872,416 30,845 16,869 327 4,515 9,134
FBL denatured 1,435,069 16,820 9,429 227 2,446 4,718
Yeast BY4741 in_vivo 2,120,926 4,275 4,212 1 0 62
BY4741 in_vitro 1,501,023 3,186 3,123 0 0 63
BY4741 denatuerd 1,472,051 3,254 3,191 0 0 63
DMS-seq & SHAPE (Science, 2016) Reproduction None Human HEK293T K+ no-reagent 509,106 7,042 3,833 87 1,023 2,099
HEK293T Na+ no-reagent 384,681 5,475 3,013 67 785 1,610
HeLa K+ no-reagent 455,380 6,275 3,592 71 864 1,748
HeLa Na+ no-reagent 713,806 9,268 5,173 103 1,333 2,659
DMS Mouse mES DMS in_vitro 95℃ 234,705 1,966 1,066 78 253 569
mES DMS in_vitro 0mM K+ 1,454,858 8,606 4,824 274 1,035 2,473
mES DMS in_vitro 150mM K+ 384,510 2,688 1,484 114 356 734
mES DMS in_vivo PDS 1,426,567 8,609 4,727 302 1,071 2,509
mES DMS in_vivo 1,596,053 9,449 5,212 323 1,170 2,744
NAI mES NAI in_vitro 0mM K+ 2,681,830 14,180 7,503 344 1,998 4,335
mES NAI in_vitro 150mM K+ 3,076,217 15,771 8,343 340 2,248 4,840
mES NAI in_vivo 5,171,130 22,796 11,991 536 3,266 7,003
None mES K+ no-reagent 309,922 2,299 1,246 92 297 664
mES Na+ no-reagent 86,082 752 390 40 114 208
mES Li+ no-reagent 135,738 1,177 634 53 154 336
DMS Yeast yRH101 DMS in_vitro 0mMK+ 2,611,745 4,633 4,607 1 0 25
yRH101 DMS in_vitro 150mMK+ 2,202,509 4,057 4,033 1 0 23
yRH101 DMS in_vivo 2,326,412 4,453 4,427 1 0 25
None yRH101 K+ no-reagent 1,333,943 2,641 2,624 1 0 16
yRH101 Na+ no-reagent 1,645,607 3,123 3,104 1 0 18
DMS E.coli TOP10 DMS in_vitro 0mMK+ 71,848 245 124 0 0 121
TOP10 DMS in_vitro 150mMK+ 57,462 206 88 0 0 118
TOP10 DMS in_vivo 42,686 134 43 0 0 91
None TOP10 K+ no-reagent 42,095 140 33 0 0 107
TOP10 Na+ no-reagent 39,846 130 24 0 0 106
DMS P.putida KT2440 DMS in_vitro 0mMK+ 354,429 997 913 11 0 73
KT2440 DMS in_vitro 150mMK+ 286,808 823 738 8 0 77
KT2440 DMS in_vivo 317,943 892 810 4 0 78
None KT2440 K+ no-reagent 27,906 86 21 0 0 65
KT2440 Na+ no-reagent 26,050 76 16 0 0 60
DMS Synechococcus WH8102 DMS in_vitro 0mMK+ 9,752 43 10 0 0 33
WH8102 DMS in_vitro 150mMK+ 10,176 44 10 0 0 34
None WH8102 K+ no-reagent 5,455 30 2 0 0 28
WH8102 Na+ no-reagent 5,239 31 2 0 0 29
DMS-seq (NSMB, 2018) Download DMS Zebrafish GRCZ11 DMS in_vivo 64c 5,027,519 10,078 8,055 3 671 1,349
GRCZ11 DMS in_vivo sphere 3,621,907 7,462 5,847 1 549 1,065
GRCZ11 DMS in_vivo shield 3,538,202 7,143 5,581 1 515 1,046
GRCZ11 DMS in_vitro 5,209,188 10,755 8,625 4 699 1,427
GRCZ11 DMS in_vivo 64c for translation inhibition 3,551,200 7,630 5,997 3 552 1,078
GRCZ11 DMS in_vivo 64c PatA treated for translation inhibition 4,398,966 9,210 7,325 3 644 1,238
GRCZ11 DMS in_vivo 64c CHX treated for translation inhibition 3,253,266 7,022 5,502 3 519 998
DMS-seq (eLife, 2017) Download DMS E.coli MG1655 37℃ in_vitro WT 90,566 2,274 2,215 22 0 37
MG1655 95℃ in_vitro WT 247,648 621 586 2 0 33
MG1655 37℃ in_vivo WT 1,058,069 2,615 2,542 35 0 38
MG1655 37℃ in_vivo dusB-M3 698,581 1,770 1,741 8 0 21
MG1655 37℃ in_vivo dusB-M3:2 561,410 1,407 1,384 4 0 19
MG1655 37℃ in_vivo ∆gcvB 679,085 1,710 1,684 6 0 20
MG1655 37℃ in_vivo ∆gcvB+ksg 754,811 2,036 1,980 31 0 25
Structure-seq (Nature, 2014) Reproduction DMS Arabidopsis thaliana seeding in_vivo 717,266 4,885 4,844 0 0 41
Structure-seq2 (NAR, 2017) Reproduction DMS Rice shoot_tissue in_vivo BiotinVAR custom_primer 27,858 226 191 0 0 35
shoot_tissue in_vivo BiotinVAR standard_primer 19,378 145 113 0 0 32
shoot_tissue custom_primer 78,386 611 561 0 0 50
shoot_tissue standard_primer 42,321 323 283 0 0 40
CIRS-seq (GenomeBiology, 2014) Download DMS & CMCT Mouse mES in_vivo 6,587,101 31,743 15,152 2,459 4,363 9,769
Mod-seq (RNA, 2014) Download DMS Yeast rpl26Δ in_vivo 1,222 0 0 0 0 0
BY4741 in_vivo 1,258 0 0 0 0 0
DIM-2P-seq (Cell, 2017) Download DMS Human HEK293T in_vivo 1,777,482 5,757 2,966 404 1,017 1,370
DMS-MaPseq (Nature Methods, 2017) Download DMS Human HEK293T in_vivo 2,398,505 20,455 11,247 6 3,113 6,089
DMS Yeast BY4741 DMS in_vivo TGIRT 5,407,062 5,765 5,423 2 0 340
BY4741 DMS in_vivo SSii/Mn+ 3,507,962 5,313 4,954 1 0 358
BY4741 2.5% DMS in_vivo 1,169,814 2,484 2,435 0 0 49
BY4741 5% DMS in_vivo 1,519,676 3,129 3,077 0 0 52
None BY4741 TGIRT no-reagent 1,491,993 3,063 2,780 0 0 283
BY4741 SSii/Mn+ no-reagent 2,316,911 4,489 4,135 0 0 354
DMS-MaPseq (Nature, 2018) Download DMS Yeast BY4741 Ded1p_Mutate in_vivo 3,035,616 4,798 4,785 0 0 13
BY4741 WT in_vivo 3,620,439 4,905 4,890 0 0 15
RAPiD-MaPseq (NAR, 2019) Download DMS IAV A/Puerto Rico/8/1934(H1N1) in_vivo 6,989 8 - - - -
A/Puerto Rico/8/1934(H1N1) in_vitro 6,991 8 - - - -
SHAPE-MaP (Biochemistry, 2015) Download 1M7 Mouse trophoblast stem cells incell 30,944 42 16 0 9 17
trophoblast stem cells exvivo 534 2 0 0 1 1
SHAPE-MaP (Cell, 2018) Download 1M7 E.coli MG1655 cell_free 368,290 442 414 0 0 28
MG1655 in_cell 384,796 446 418 0 0 28
MG1655 Kasugamycin in_cell 244,826 362 336 0 0 26
SHAPE-MaP (PNAS, 2015) Download 1M7 HCV HCV in_vitro 28,426 3 - - - -
SHAPE-MaP (Nature, 2009) Download 1M7 HIV HIV-1 in_vivo 9,120 1 - - - -
SHAPE-MaP (Nature Methods, 2014) Download 1M6 HIV HIV-1 1M6 in_vivo 9,159 1 - - - -
1M7 HIV-1 1M7 in_vivo 9,150 1 - - - -
NMIA HIV-1 NMIA in_vivo 9,157 1 - - - -
SHAPE-MaP (PLOS CompBio, 2015) Download 1M7 HIV HIV in_vivo 27,837 3 - - - -
SHAPE-MaP (bioRxiv, 2020) Download NAI SARS-CoV-2 VeroE6 in_vitro 28,827 1 - - - -
SHAPE-MaP (bioRxiv, 2020) Download NAI SARS-CoV-2 VeroE6 in_vivo 29,841 1 - - - -
SHAPE-MaP (PNAS, 2018) Download 1M6 Dengue strain S16803 exviron_1M6 10,628 1 - - - -
strain S16803 inviron_1M6 10,443 1 - - - -
1M7 strain S16803 exviron_1M7 10,628 1 - - - -
strain S16803 inviron_1M7 10,583 1 - - - -
NMIA strain S16803 exviron_NMIA 10,633 1 - - - -
strain S16803 inviron_NMIA 10,637 1 - - - -
NAI-MaP (Nature Communication, 2019) Download NAI Dengue Dengue in_vivo 42,545 4 - - - -
Zika ZIKV in_vivo 42,932 4 - - - -
SHAPE (Mol Cell, 2016) Download NAI HCV JFH1 in_vitro 8,815 1 - - - -
SHAPE (BioChemistry, 2013) Download 1M7 STMV STMV in_vitro 946 1 - - - -
STMV ex_vitro 1,011 1 - - - -
SHAPE-seq (NAR, 2018) Download 1M7 CMV Bn57-CMV lyRNA in_plant_cell_lysates 2,216 1 - - - -
Bn57-CMV viRNA in_vitro 2,216 1 - - - -
icSHAPE (Cell Host & Microbe, 2018) Download NAI-N3 Zika ZIKV in_vivo 21,530 2 - - - -
ZIKV in_vitro 21,530 2 - - - -
icSHAPE (bioRxiv, 2020) Download NAI-N3 SARS-CoV-2 Huh7 in_vivo 29,965 1 - - - -
Huh7 in_vitro 30,004 1 - - - -
icSHAPE (Nature, 2015) Download NAI-N3 Mouse mES METTL3_KO in_vivo 1,764,594 6,936 3,629 431 879 1,997
mES v65 in_vivo 14,106,282 34,186 18,018 1,260 4,765 10,143
mES v65 in_vitro 17,444,983 31,098 16,238 1,098 4,433 9,329
icSHAPE (Cell, 2016) Download NAI-N3 Human HEK293T in_vivo 2,030,707 10,048 5,561 459 1,418 2,610
HEK293T in_vitro 1,854,626 9,887 5,475 451 1,395 2,566
icSHAPE (NSMB, 2019) Download NAI-N3 Mouse mES chromatin in_vivo 3,871,974 7,403 2,875 387 965 3,176
mES chromatin in_vitro 2,969,374 7,331 2,859 351 961 3,160
mES cytoplasm in_vivo 8,292,181 23,356 12,427 1,554 2,921 6,454
mES cytoplasm in_vitro 6,340,837 20,902 10,893 1,300 2,695 6,014
mES nucleoplasm in_vivo 9,899,971 23,373 12,363 1,217 2,907 6,886
mES nucleoplasm in_vitro 10,473,036 23,911 12,473 1,206 3,011 7,221
Human HEK293 chromatin in_vivo 2,296,220 6,837 2,587 453 1140 2657
HEK293 chromatin in_vitro 3,701,135 10,507 3,525 589 2,102 4,291
HEK293 cytoplasm in_vivo 2,146,114 12,516 6,020 843 1,817 3,836
HEK293 cytoplasm in_vitro 6,895,344 23,670 12,580 1,398 3,258 6,434
HEK293 nucleoplasm in_vivo 3,714,351 16,017 8,044 796 2,289 4,888
HEK293 nucleoplasm in_vitro 8,169,250 23,229 12,238 1,211 3,294 6,486
icSHAPE (GenomeBiology, 2020) Download NAI-N3 Zebrafish widetype AB strain fertilized_egg in_vivo 7,294,463 11,078 9,116 2 641 1,319
widetype AB strain 1-cell in_vivo 8,107,635 11,636 9,508 2 695 1,431
widetype AB strain 4-cell in_vivo 8,024,909 12,623 10,395 2 718 1,508
widetype AB strain 64-cell in_vivo 9,507,124 14,602 12,074 2 816 1,710
widetype AB strain shield in_vivo 7,501,747 11,146 9,087 3 664 1,392
widetype AB strain sphere in_vivo 12,022,502 15,932 13,141 2 911 1,878
widetype AB strain shield elavl1a-mo in_vivo 5,675,258 8,958 7,216 1 564 1,177
widetype AB strain sphere elavl1a-mo in_vivo 7,033,200 11,834 9,715 1 705 1,413
Keth-seq (NCB, 2020) Download N3-kethoxal Mouse mES kethoxal vs kethoxal_removed in_vivo 83,466 656 293 135 49 179
mES kethoxal_treated_1min vs no_treat in_vivo 10,944 128 2 0 4 122
mES kethoxal_treated_5min vs no_treat in_vivo 6,947 80 0 0 3 77
mES kethoxal vs no_treat in_vitro 189,658 1,250 475 255 128 392
mES kethoxal vs no_treat in_vivo 116,232 981 427 196 87 271
mES kethoxal vs no_treat 60,593 650 274 151 50 175
Human HeLa kethoxal vs no treat in_vivo 351,732 4,032 2,094 393 488 1,057
HeLa kethoxal vs no treat in_vitro 203,319 1,888 881 48 258 701
HeLa kethoxal vs no treat PDS in_vivo 336,513 3,736 1,950 344 457 985
HeLa kethoxal vs no treat PDS in_vitro 229,126 2,476 1,237 60 343 836
FragSeq (NatureMethods, 2010) Download PNK (polynucleotide kinase) Mouse KH2 Embryonic stem cells PNK-treated in_vitro 220,008 38 7 4 1 26
KH3 Neural precursor cells PNK-treated in_vitro 476,460 187 11 2 5 169
Nuclease P1 KH2 Embryonic stem cells NUCLEASE-treated in_vitro 537,628 46 10 11 5 20
KH3 Neural precursor cells NUCLEASE-treated in_vitro 271,276 12 0 0 0 12
None KH2 Embryonic stem cells on-reagent in_vitro 86,778 11 0 0 0 11
KH3 Neural precursor cells on-reagent in_vitro 517,472 21 3 0 0 18
Lead-seq (NAR, 2020) Download Lead(II) Y_pseudotuberculosis Lead-seq_25degree 1,057,814 1,794 1,602 0 0 192
Lead-seq_37degree 1,308,701 1,794 1,602 0 0 192