The following studies are included in crisprSQL:
| No. | study | assay | cell line | delivery mode | total guides | total targets | epigenetically annotated targets | cleaved gene IDs (CF > 1%, on-targets in bold) |
|---|---|---|---|---|---|---|---|---|
| 1 | Kim | Digenome-seq | HAP1 | 2 | 162 | 7 | HBB, IGDCC3, KRT42P, PVALB, CTD-2066L21.3, RP11-638F5.1 | |
| 2 | Cho | targeted PCR | K562 | EP | 10 | 116 | 11 | RP11-24F11.2, CCR2 |
| 3 | Ran | BLESS | HEK293 | LF | 4 | 53 | 53 | EMX1, C1QTNF3-AMACR |
| 4 | Ran | BLESS | N2A | LF | 2 | 34 | 0 | "Pcsk9" |
| 5 | Tsai | Guide-seq | HEK293 | EP | 4 | 153 | 153 | RP11-363D24.1, KIAA1024, CDH4, CEP89, CTBP2, RP11-115D19.1, MKNK1-AS1, RP11-399K21.6, RMDN3, SIPA1L3, FREM2, IGF2R, RP11-295P9.13, SLC2A10, SEPT9, PSMF1, ADCY7, ADCK4, LAMA5, MROH9, RPH3AL, TEX264, AC003088.1, RP11-244M2.1, PPP1R16B |
| 6 | Tsai | Guide-seq | U2OS | EP | 8 | 422 | 228 | RNF2, FANCF, EMX1, VEGFA, RNF2, EMX1, FANCF, IGDCC3, HCN1, RP11-674N23.1, KRT42P, MAX, MFAP1, COMMD10, TRIM42, PAPD7, TPCN2, AC097468.5, SLIT1, HDLBP, RP11-638F5.1, RP11-47I22.4, IL27RA, JAKMIP3, BBC3, INPPL1, ZNF780B, PTGR2, CACNA2D4, SPNS3, ACLY, MOB3B, CFAP61, RP11-429J17.8, ABLIM1, SBF1, ELAVL2, TSKU, CDC42SE1, HULC, PLEC, SEMA5A, PVALB, CTD-2066L21.3, SCUBE1, PAX6, RPTOR, ZNF511-PRAP1, NEURL1, AC096559.2, ERCC1, FMN1, MPRIP, NRG2, SORCS2, LAMA3, MICAL2, PHF21A, MTMR1, DPYSL3, AIG1, MSI2, CLYBL, NFIX, CDH13, RP4-537K23.4, NPAS2, RP11-122F24.1, B4GALNT4 |
| 7 | Fu | T7E1 | HEK293 | EP | 3 | 30 | 0 | |
| 8 | Fu | T7E1 | K562 | EP | 3 | 28 | 0 | |
| 9 | Fu | T7E1 | U2OS | EP | 3 | 30 | 0 | |
| 10 | Anderson | Guide-seq | embryo | EP | 31 | 426 | 0 | Stambpl1, Tacc1, Hcls1, Gm40999, Col6a3, Arhgap15, Srrm1, Ptprn2, Ice1, Btk, Pcolce2, Fggy, Ptpn13, Map6, Rptor, Dram2, Junos |
| 11 | Tsai_circle | CircleSeq | HEK293 | EP | 4 | 1257 | 1257 | RP11-363D24.1, RP11-109A6.5, RP1-93I3.1, NTF3, KIAA1024, ATP11A, MKNK1-AS1, MRPL4, PSMB2, CNGA3, C5orf63, RP11-449D8.5, MEGF6, RP11-115D19.1, MEIKIN, NEDD4, RP11-739G5.1, MCM4, DHRS11, RP11-818C3.1, ARMC6, RP11-744N12.3, ST14, KDM4B, RP11-305P22.9, CTD-3049M7.1, RABEPK, RP11-203B7.2, GLDC, ABRACL |
| 12 | Tsai_circle | CircleSeq | K562 | EP | 6 | 1155 | 160 | RP11-363D24.1, FANCF, RNF2, EMX1, HBB, HIVEP2, ADGRD1, KIAA1024, MKNK1-AS1, RP11-146N18.1, CDH23, PSMB2, RP11-511B23.2, RP11-449D8.5, CHI3L2, RP11-109A6.5, MRPL4, CNGA3, MEGF6, C5orf63, RP1-93I3.1, NTF3, ENPP2, RP11-666O2.5, RP11-739G5.1, AC097468.5, ATP11A, NEDD4, MEIKIN, ARMC6, RP5-827C21.1, ZNF423, AC007969.5, RP11-674N23.1, RP11-13B9.5, RIT2, CKAP4, MCM4, RP11-115D19.1, ZNF254, DHRS11, SPTBN2, SVEP1, CD82, RP11-744N12.3, MFAP1, NDEL1, SPTBN1, ADGRE2, CLVS1, DRC7, ECE1, TCEA3, DIRC3, HULC, ST14, RASA3, RP11-472I20.4, KNOWN, AHDC1, PDE1C, HCN1, MYO16, FRYL, RPS15, ABRACL, PRKG1, GRID1, CWF19L2, RACGAP1, AC092662.5, PTH2R, DKK2, PTBP3, NEXMIF, AC034110.1, CALCR, SMARCC1, MITF, NAV1, CHD2, TMEM120B, TBC1D5, GLDC, RP11-818C3.1, RP11-964E11.3, MTA2, FIS1, SEMA3E |
| 13 | Tsai_circle | CircleSeq | U2OS | EP | 8 | 4962 | 2076 | RNF2, FANCF, EMX1, ADGRD1, RP11-146N18.1, ENPP2, HIVEP2, CDH23, RP11-13B9.5, AC097468.5, RP11-666O2.5, IGDCC3, RASA3, ZNF423, AGPAT1, SPTBN1, SPTBN2, RP11-674N23.1, MYO16, DIRC3, CACNA2D4, KRT42P, LRRC7, KLHL1, ADAM2, MID1, CNTNAP4, UBE2D4, CACNA1C, TCEA3, RP5-827C21.1, TMEM120B, RP11-472I20.4, CKAP4, HCN1, ECE1, CTD-2307P3.1, AC007969.5, RP4-718J7.4, CPVL, WWOX, SVEP1, MFAP1, PDE1C, COLEC12, KNOWN, GNA13, AHDC1, CTD-2066L21.3, RP11-2G1.1, TBC1D5, RPS15, FRYL, RP11-524K22.1, PTH2R, ACYP2, NCALD, MICAL3 |
| 14 | Cameron | SITE-Seq | HEK293 | 8 | 1630 | 210 | XRCC5, CD34, FANCF, PAPSS2, PTPRC, CD151, IGDCC3, KRT42P, RP11-674N23.1, TPM3, RAPGEF1, SPX | |
| 15 | Kim16 | Digenome-seq | HeLa | LF | 10 | 258 | 234 | VEGFA, RNF2, RP11-363D24.1, EMX1, FANCF, ABLIM1, DNER, HCN1, MFAP1, MAX, LAMA3, KIAA1024, ADAMTSL1, COMMD10, RP11-674N23.1, IGDCC3, SLIT1, SIPA1L3, KRT42P, RP11-115D19.1, MKNK1-AS1, CLYBL, PTGR2, FREM2, CEP135, CACNA2D4, CTBP2, TPCN2, ZNF511-PRAP1, NRG2, HDLBP, RP11-638F5.1, AC097468.5, PAPD7, IGF2R, RMDN3, RP11-399K21.6, MAP3K1, RPTOR, CEP89, CDH4, RAB11FIP5, PAX6, CTPS2, PTPRN2, NFIX, FAM208B, SLC2A10, PSMF1, TRIM42, RP11-109A6.5, PVALB, RPH3AL |
| 16 | Wang | IDLV | HEK293 | LF | 1 | 13 | 13 | PTPRA, OSBPL1A |
| 17 | Frock | HTGTS | HEK293 | 3 | 87 | 87 | EMX1, MFAP1, IGDCC3, KRT42P, HCN1 | |
| 18 | KimChromatin | Digenome-seq | HeLa | LF | 7 | 141 | 132 | RP11-24F11.2, RNF2, RP11-363D24.1, EMX1, FANCF, HBB, HCN1, MFAP1, KIAA1024, RP11-674N23.1, IGDCC3, SEMA5A, KRT42P, RP11-115D19.1, MKNK1-AS1, CACNA2D4, NRG2, RP11-638F5.1, RPTOR, PVALB, RP11-109A6.5 |
| 19 | Kleinstiver | Guide-seq | U2OS | EP | 7 | 61 | 28 | KRTAP1-1, ART1, GRM6, NCR2, EMX1, IL1F10, IL1RAPL2, HCN1, DYSF, CSRNP3, RBFOX1, MBOAT2, CBARP, MFAP1, POLR1A, RHBDF2, KRTAP1-4, RP11-284E5.1, MYO3B, RP5-965F6.2, TSPAN4, SEPT10, ANKUB1, DMD, KLK2, RXRA |
| 20 | Listgarten | Guide-seq | U2OS | EP | 10 | 272 | 160 | FANCF, RUNX1, RP11-182J1.18, EMX1, VEGFA, VRK1, HCN1, RP11-15A1.2, HDLBP, RP11-674N23.1, FMN1, PVT1, SPOCK1, COMMD10, MFAP1, MAX, TPCN2, COL6A4P1, CDH13, SLIT1, PTGR2, KLHL23, ELAVL2, RP11-613D13.4, RP11-108M21.1, RP11-47I22.4, AC097468.5, AC096559.2, PAPD7, SBF1, NCOA1, SBNO1, AIG1, RP11-429J17.8, THADA, MTMR1, BTN2A1, ACLY, CFAP61, SPNS3, RP11-103J8.1, ABLIM1, NFIX, FZR1, TSKU, LAMA3, CLYBL, CTIF, MOB3B, NAT1, WARS, PAX6, C11orf80, SDC4, INPPL1, MAGI1, SEMA5A, SAMD11, MICAL2, ZNF511-PRAP1, MPRIP |
| 21 | Chen17 | Guide-seq | U2OS | EP | 5 | 203 | 107 | FANCF, DNMT1, VEGFA, MYH9, MAX, RP11-735B13.1, SNX1, COMMD10, SEC13, SLIT1, RALGPS1, DAB2, RP11-377D9.3, RP11-613D13.4, PAPD7, FMN1, INPPL1, COL6A4P1, TMEM184A, DGKG, CTD-2643I7.5, PLEC, IQCE, HDLBP, TSKU, PTGR2, RP11-429J17.8, CDH13, MTMR1, LAMA3, AC096559.2, ACLY, CRB2, RP11-103J8.1, PHLDB1, MOB3B, ERN1, TRIM42, NAA40, DLG2, SBF1, SPNS3, SIGLEC10, CLYBL, SRPK2, MPRIP, MICAL2, NCOA1 |
| 22 | Slaymaker | BLESS | HEK293 | LF | 3 | 31 | 31 | EMX1, HCN1, COMMD10, MFAP1, MAX, TPCN2, CFAP61, SEMA5A, RP11-47I22.4, SLIT1, RFX2, PTGR2 |
| 23 | Finkelstein | NucleaSeq | 2 | 14108 | 0 | |||
| sum | 144 | 25632 | 4947 |
crisprSQL is developed at Oxford University, 2020 – 2022