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| Methods/Resource | Reagent | Species | Cell line / Condition | Number of interactions |
| PARIS (Cell Host & Microbe, 2018) | AMT | Zika | in vivo | 2,764 |
| in vitro | 1,470 | |||
| SPLASH (NC, 2019) | biotinylated psoralen | Zika | in virion | 400 |
| in cell | 400 | |||
| Dengue | in virion | 400 | ||
| in cell | 400 | |||
| SPLASH (NC, 2022) | biotinylated psoralen | SARS-CoV-2 | in vivo | 424 |
| SPLASH (NC, 2021) | Psoralen-PEG3-Biotin | SARS-CoV-2 | cell | 47,295 |
| lysate | 78,715 | |||
| virion | 139,941 | |||
| PARIS2 (NC, 2021) | amotosalen | Human | HEK293 in vivo snoRNA | 187,689 |
| HEK293 in vivo mRNA | 331,803 | |||
| Mouse | C57BL/6J brain in vivo snoRNA | 63,000 | ||
| C57BL/6J brain in vivo mRNA | 446,421 | |||
| SHARC (NC, 2022) | DPI | Human | HeLa in vivo 5mM RNaseR0h | 53,411 |
| HeLa in vivo 5mM RNaseR2h | 2,066 | |||
| HeLa in vivo 5mM RNaseR12h | 9,050 | |||
| HeLa in vivo 12.5mM RNaseR0h | 19,544 | |||
| HeLa in vivo 12.5mM RNaseR2h | 10,536 | |||
| HeLa in vivo 12.5mM RNaseR12h | 5,217 | |||
| HeLa in vivo 12.5mM RNaseR24h | 61 | |||
| HeLa in vivo 25mM RNaseR0h | 138,166 | |||
| HeLa in vivo 25mM RNaseR2h | 53,615 | |||
| HeLa in vivo 25mM RNaseR24h | 1,917 | |||
| CRIC-seq (Mol. Cell, 2023) | formaldehyde | Human | HeLa hnRNPA1_IP_pCp_plus | 2,087,126 |
| HeLa PTBP1_IP_pCp_plus | 4,082,863 | |||
| HeLa SRSF1_IP_pCp_plus | 1,077,827 | |||
| PARIS (GPB, 2022) | AMT | Human | in vivo PC9 | 8,609 |
| in vivo PC9 gefitinib-R | 10,401 | |||
| in vivo PC9 AZD9291-R | 7,198 | |||
| KARR-seq (NBT, 2024) | formaldehyde | Mouse | mESC_G1 | 1,168,142 |
| mESC_G3 | 1,227,779 | |||
| mESC_G5 | 644,462 | |||
| mESC_G7 | 458,351 | |||
| mESC_invivo_G1 | 857,802 | |||
| mESC_refold_G1 | 789,202 | |||
| Human | HEK293T_invivo_G1 | 1,369,972 | ||
| HEK293T_refold_G1 | 942,422 | |||
| HepG2_invivo_G1 | 647,932 | |||
| HepG2_refold_G1 | 917,682 | |||
| HepG2_siControl_G1 | 739,234 | |||
| HepG2_siDDX3X_G1 | 695,100 | |||
| HepG2_CHX_G1 | 1,020,981 | |||
| HepG2_HT_G1 | 1,084,495 | |||
| HepG2_TotalRNA_G1 | 92,547 | |||
| K562_invivo_G1 | 1,652,573 | |||
| K562_refold_G1 | 1,271,777 | |||
| K562_Nuclear_G1 | 1,326,026 | |||
| K562_siControl_G1 | 2,082,184 | |||
| K562_siYBX3_G1 | 2,248,864 | |||
| K562_siSRSF1_Total_G1 | 1,611,397 | |||
| K562_siSRSF1_Nuclear_G1 | 1,249,875 | |||
| K562_Arsenite_Total_G1 | 1,432,362 | |||
| K562_Arsenite_Nuclear_G1 | 1,306,850 | |||
| K562_lowXL_G1 | 2,115,061 | |||
| K562_noXL_G1 | 3,209,748 | |||
| A549_Mock_G1 | 2,546,888 | |||
| A549_RSV_G1 | 1,509,324 | |||
| A549_VSV_G1 | 873,474 | |||
| PARIS (Cell Rep., 2024) | AMT | IAV | WSN invivo | 832 |
| WSN invirio | 1,712 | |||
| COMRADES (Mol. Cell, 2020) | Psoralen-TEG azide | SARS-CoV-2 | control | 5,046 |
| sample | 7,432 | |||
| Methods/Resource | Species | Cell line / Condition | Number of interactions |
| PARIS (Cell, 2016) | Human | HEK293T | 25,815 |
| HeLa (high RNase) | 25,549 | ||
| HeLa (low RNase) | 20,328 | ||
| Mouse | mESC | 29,514 | |
| MARIO (NC, 2016) | Mouse | MEF | 7,167 |
| mESC (one protein) | 99,284 | ||
| mESC (multi proteins) | 37,441 | ||
| SPLASH (Nature, 2013) | Human | hESC | 3,345 |
| SPLASH (Mol. Cell, 2016) | Human | HeLa | 5,799 |
| LCL | 4,213 | ||
| RA | 1,770 | ||
| LIGR-seq (Mol. Cell, 2016) | Human | HEK293T | 641 |
| RIA-seq (Cell, 2014) | Human | Keratinocytes (TINCR) | 3,575 |
| RAP-RNA (Cell, 2016) | Mouse | mESC (MALAT1) | 495 |
| RAP-RNA (Cell, 2014) | Mouse | mESC (U1 snRNA) | 12,278 |
| CLASH (Cell, 2013) | Human | HEK293 (miRNAs) | 18,505 |
| CLASH (PNAS, 2011) | Yeast | BY4741 (miRNAs) | 253 |
| PARIS2 (NC, 2021) | Human | HEK293 in vivo snoRNA | 42,057 |
| HEK293 in vivo mRNA | 74,997 | ||
| Mouse | C57BL/6J brain in vivo snoRNA | 11,596 | |
| C57BL/6J brain in vivo mRNA | 77,981 | ||
| SHARC (NC, 2022) | Human | HeLa in vivo 5mM RNaseR0h | 18,497 |
| HeLa in vivo 5mM RNaseR2h | 1,839 | ||
| HeLa in vivo 5mM RNaseR12h | 6,041 | ||
| HeLa in vivo 12.5mM RNaseR0h | 6,646 | ||
| HeLa in vivo 12.5mM RNaseR2h | 6,874 | ||
| HeLa in vivo 12.5mM RNaseR12h | 3,930 | ||
| HeLa in vivo 12.5mM RNaseR24h | 304 | ||
| HeLa in vivo 25mM RNaseR0h | 52,140 | ||
| HeLa in vivo 25mM RNaseR2h | 16,147 | ||
| HeLa in vivo 25mM RNaseR24h | 2,433 | ||
| CRIC-seq (Mol. Cell, 2023) | Human | HeLa hnRNPA1_IP_pCp_plus | 90,410 |
| HeLa PTBP1_IP_pCp_plus | 528,431 | ||
| HeLa SRSF1_IP_pCp_plus | 211,915 | ||
| PARIS (GPB, 2022) | Human | in vivo PC9 | 35,031 |
| in vivo PC9 gefitinib-R | 30,630 | ||
| in vivo PC9 AZD9291-R | 39,227 | ||
| KARR-seq (NBT, 2024) | Mouse | mESC_G1 | 182,663 |
| mESC_G3 | 194,758 | ||
| mESC_G5 | 94,065 | ||
| mESC_G7 | 71,738 | ||
| mESC_invivo_G1 | 122,530 | ||
| mESC_refold_G1 | 62,869 | ||
| Human | HEK293T_invivo_G1 | 162,569 | |
| HEK293T_refold_G1 | 121,360 | ||
| HepG2_invivo_G1 | 103,055 | ||
| HepG2_refold_G1 | 89,564 | ||
| HepG2_siControl_G1 | 135,405 | ||
| HepG2_siDDX3X_G1 | 136,192 | ||
| HepG2_CHX_G1 | 141,922 | ||
| HepG2_HT_G1 | 145,285 | ||
| HepG2_TotalRNA_G1 | 11,097 | ||
| K562_invivo_G1 | 180,697 | ||
| K562_refold_G1 | 112,046 | ||
| K562_Nuclear_G1 | 86,847 | ||
| K562_siControl_G1 | 144,897 | ||
| K562_siYBX3_G1 | 159,259 | ||
| K562_siSRSF1_Total_G1 | 139,191 | ||
| K562_siSRSF1_Nuclear_G1 | 82,409 | ||
| K562_Arsenite_Total_G1 | 144,923 | ||
| K562_Arsenite_Nuclear_G1 | 137,252 | ||
| K562_lowXL_G1 | 256,074 | ||
| K562_noXL_G1 | 349,369 | ||
| A549_Mock_G1 | 137,401 | ||
| A549_RSV_G1 | 69,697 | ||
| A549_VSV_G1 | 42,915 | ||
| PARIS (Cell Rep., 2024) | IAV | WSN invivo | 41 |
| WSN invirio | 5,045 | ||
| SPLASH (Nat Microbiol., 2019) | IAV | in virio | 4,041 |