SRX12594017 ExtDataFig5b_rep1_induced48h_FAA1_a1a2_12.fastq SRP341237 bp0 ExtDataFig5b_rep1_induced48h_FAA1_a1a2_12.fastq SRS10549311 ExtDataFig5b_rep1_induced48h_FAA1_a1a2_12.fastq ExtDataFig5b_rep1_induced48h_FAA1_a1a2_12.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594018 ExtDataFig5c_rep2_induced48h_CAN1_a1a2_27v2.fastq SRP341237 bp0 ExtDataFig5c_rep2_induced48h_CAN1_a1a2_27v2.fastq SRS10549313 ExtDataFig5c_rep2_induced48h_CAN1_a1a2_27v2.fastq ExtDataFig5c_rep2_induced48h_CAN1_a1a2_27v2.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594019 ExtDataFig5b_rep1_induced24h_FAA1_a1a2_27v2.fastq SRP341237 bp0 ExtDataFig5b_rep1_induced24h_FAA1_a1a2_27v2.fastq SRS10549312 ExtDataFig5b_rep1_induced24h_FAA1_a1a2_27v2.fastq ExtDataFig5b_rep1_induced24h_FAA1_a1a2_27v2.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594020 ExtDataFig5b_rep5_induced48h_FAA1_a1a2_27v2.fastq SRP341237 bp0 ExtDataFig5b_rep5_induced48h_FAA1_a1a2_27v2.fastq SRS10549314 ExtDataFig5b_rep5_induced48h_FAA1_a1a2_27v2.fastq ExtDataFig5b_rep5_induced48h_FAA1_a1a2_27v2.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594021 ExtDataFig5c_rep6_induced24h_CAN1_a1a2_27v2.fastq SRP341237 bp0 ExtDataFig5c_rep6_induced24h_CAN1_a1a2_27v2.fastq SRS10549315 ExtDataFig5c_rep6_induced24h_CAN1_a1a2_27v2.fastq ExtDataFig5c_rep6_induced24h_CAN1_a1a2_27v2.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594022 Fig5d_rep3_induced72h_EMX1_Cas9.fastq SRP341237 bp0 Fig5d_rep3_induced72h_EMX1_Cas9.fastq SRS10549316 Fig5d_rep3_induced72h_EMX1_Cas9.fastq Fig5d_rep3_induced72h_EMX1_Cas9.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594023 Fig5a_rep1_induced48h_Cas9-linker2-RT.fastq SRP341237 bp0 Fig5a_rep1_induced48h_Cas9-linker2-RT.fastq SRS10549317 Fig5a_rep1_induced48h_Cas9-linker2-RT.fastq Fig5a_rep1_induced48h_Cas9-linker2-RT.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594024 Fig5h_rep2_induced72h_RNF2_Cas9+RT.fastq SRP341237 bp0 Fig5h_rep2_induced72h_RNF2_Cas9+RT.fastq SRS10549318 Fig5h_rep2_induced72h_RNF2_Cas9+RT.fastq Fig5h_rep2_induced72h_RNF2_Cas9+RT.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594025 Fig4d_rep4_a1a2_22.fastq SRP341237 bp0 Fig4d_rep4_a1a2_22.fastq SRS10549319 Fig4d_rep4_a1a2_22.fastq Fig4d_rep4_a1a2_22.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594026 Fig2c_rep2_RTDNA.fastq SRP341237 bp0 RT-DNA prep: DBR1 to remove the branched RNA from RT-DNA, then extending the 3 end dCTP, in a reaction with terminal deoxynucleotidyl transferase (TdT); complementary strand synthesis from the extended product using Klenow Fragment with a primer containing an Illumina adapter sequence, six guanines, and a non-guanine (H) anchor. Finally, ligation of Illumina adapters at the 3 end of the complementary strand using T4 ligase SRS10549320 Fig2c_rep2_RTDNA.fastq Fig2c_rep2_RTDNA.fastq OTHER OTHER PCR Illumina MiSeq SRX12594027 ExtDataFig5c_rep3_induced48h_CAN1_a1a2_27v2.fastq SRP341237 bp0 ExtDataFig5c_rep3_induced48h_CAN1_a1a2_27v2.fastq SRS10549321 ExtDataFig5c_rep3_induced48h_CAN1_a1a2_27v2.fastq ExtDataFig5c_rep3_induced48h_CAN1_a1a2_27v2.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594028 Fig5a_rep3_induced48h_RT-linker2-Cas9.fastq SRP341237 bp0 Fig5a_rep3_induced48h_RT-linker2-Cas9.fastq SRS10549322 Fig5a_rep3_induced48h_RT-linker2-Cas9.fastq Fig5a_rep3_induced48h_RT-linker2-Cas9.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594029 ExtDataFig5d_rep2_induced24h_LYP1_a1a2_27v2.fastq SRP341237 bp0 ExtDataFig5d_rep2_induced24h_LYP1_a1a2_27v2.fastq SRS10549324 ExtDataFig5d_rep2_induced24h_LYP1_a1a2_27v2.fastq ExtDataFig5d_rep2_induced24h_LYP1_a1a2_27v2.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594030 Fig4h_rep2_induced24h_Cas9_a1a2_12.fastq SRP341237 bp0 Fig4h_rep2_induced24h_Cas9_a1a2_12.fastq SRS10549323 Fig4h_rep2_induced24h_Cas9_a1a2_12.fastq Fig4h_rep2_induced24h_Cas9_a1a2_12.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594031 Fig4h_rep3_induced48h_empty_a1a2_12.fastq SRP341237 bp0 Fig4h_rep3_induced48h_empty_a1a2_12.fastq SRS10549325 Fig4h_rep3_induced48h_empty_a1a2_12.fastq Fig4h_rep3_induced48h_empty_a1a2_12.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594032 ExtDataFig5a_rep2_induced48h_TRP2_a1a2_27v2.fastq SRP341237 bp0 ExtDataFig5a_rep2_induced48h_TRP2_a1a2_27v2.fastq SRS10549326 ExtDataFig5a_rep2_induced48h_TRP2_a1a2_27v2.fastq ExtDataFig5a_rep2_induced48h_TRP2_a1a2_27v2.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594033 Fig2c_rep2_plasmid_pre.fastq SRP341237 bp0 RT-DNA prep: DBR1 to remove the branched RNA from RT-DNA, then extending the 3 end dCTP, in a reaction with terminal deoxynucleotidyl transferase (TdT); complementary strand synthesis from the extended product using Klenow Fragment with a primer containing an Illumina adapter sequence, six guanines, and a non-guanine (H) anchor. Finally, ligation of Illumina adapters at the 3 end of the complementary strand using T4 ligase SRS10549327 Fig2c_rep2_plasmid_pre.fastq Fig2c_rep2_plasmid_pre.fastq OTHER OTHER PCR Illumina MiSeq SRX12594034 Fig5g_rep1_induced72h_HEK4_Cas9+RT.fastq SRP341237 bp0 Fig5g_rep1_induced72h_HEK4_Cas9+RT.fastq SRS10549328 Fig5g_rep1_induced72h_HEK4_Cas9+RT.fastq Fig5g_rep1_induced72h_HEK4_Cas9+RT.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594035 Fig5c_rep1_induced72h_AAVS1_Cas9+RT.fastq SRP341237 bp0 Fig5c_rep1_induced72h_AAVS1_Cas9+RT.fastq SRS10549329 Fig5c_rep1_induced72h_AAVS1_Cas9+RT.fastq Fig5c_rep1_induced72h_AAVS1_Cas9+RT.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594036 Fig4h_rep1_induced24h_empty_a1a2_12.fastq SRP341237 bp0 Fig4h_rep1_induced24h_empty_a1a2_12.fastq SRS10549330 Fig4h_rep1_induced24h_empty_a1a2_12.fastq Fig4h_rep1_induced24h_empty_a1a2_12.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594037 ExtDataFig3b_rep2_a1a2_12.fastq SRP341237 bp0 ExtDataFig3b_rep2_a1a2_12.fastq SRS10549331 ExtDataFig3b_rep2_a1a2_12.fastq ExtDataFig3b_rep2_a1a2_12.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594038 Fig4h_rep2_induced48h_RT_a1a2_12.fastq SRP341237 bp0 Fig4h_rep2_induced48h_RT_a1a2_12.fastq SRS10549332 Fig4h_rep2_induced48h_RT_a1a2_12.fastq Fig4h_rep2_induced48h_RT_a1a2_12.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594039 ExtDataFig5c_rep2_induced48h_CAN1_a1a2_12.fastq SRP341237 bp0 ExtDataFig5c_rep2_induced48h_CAN1_a1a2_12.fastq SRS10549333 ExtDataFig5c_rep2_induced48h_CAN1_a1a2_12.fastq ExtDataFig5c_rep2_induced48h_CAN1_a1a2_12.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594040 Fig2b_rep1_plasmid_pre.fastq SRP341237 bp0 RT-DNA prep: DBR1 to remove the branched RNA from RT-DNA, then extending the 3 end dCTP, in a reaction with terminal deoxynucleotidyl transferase (TdT); complementary strand synthesis from the extended product using Klenow Fragment with a primer containing an Illumina adapter sequence, six guanines, and a non-guanine (H) anchor. Finally, ligation of Illumina adapters at the 3 end of the complementary strand using T4 ligase SRS10549335 Fig2b_rep1_plasmid_pre.fastq Fig2b_rep1_plasmid_pre.fastq OTHER OTHER PCR Illumina MiSeq SRX12594041 ExtDataFig5d_rep2_induced48h_LYP1_a1a2_12.fastq SRP341237 bp0 ExtDataFig5d_rep2_induced48h_LYP1_a1a2_12.fastq SRS10549334 ExtDataFig5d_rep2_induced48h_LYP1_a1a2_12.fastq ExtDataFig5d_rep2_induced48h_LYP1_a1a2_12.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594042 ExtDataFig3b_rep1_a1a2_12.fastq SRP341237 bp0 ExtDataFig3b_rep1_a1a2_12.fastq SRS10549336 ExtDataFig3b_rep1_a1a2_12.fastq ExtDataFig3b_rep1_a1a2_12.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594043 ExtDataFig5b_rep5_induced24h_FAA1_a1a2_27v2.fastq SRP341237 bp0 ExtDataFig5b_rep5_induced24h_FAA1_a1a2_27v2.fastq SRS10549337 ExtDataFig5b_rep5_induced24h_FAA1_a1a2_27v2.fastq ExtDataFig5b_rep5_induced24h_FAA1_a1a2_27v2.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594044 Fig4h_rep2_induced48h_Cas9+RT_a1a2_12.fastq SRP341237 bp0 Fig4h_rep2_induced48h_Cas9+RT_a1a2_12.fastq SRS10549338 Fig4h_rep2_induced48h_Cas9+RT_a1a2_12.fastq Fig4h_rep2_induced48h_Cas9+RT_a1a2_12.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594045 ExtDataFig5c_rep6_induced48h_CAN1_a1a2_27v2.fastq SRP341237 bp0 ExtDataFig5c_rep6_induced48h_CAN1_a1a2_27v2.fastq SRS10549339 ExtDataFig5c_rep6_induced48h_CAN1_a1a2_27v2.fastq ExtDataFig5c_rep6_induced48h_CAN1_a1a2_27v2.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594046 Fig2b_rep1_RTDNA.fastq SRP341237 bp0 RT-DNA prep: DBR1 to remove the branched RNA from RT-DNA, then extending the 3 end dCTP, in a reaction with terminal deoxynucleotidyl transferase (TdT); complementary strand synthesis from the extended product using Klenow Fragment with a primer containing an Illumina adapter sequence, six guanines, and a non-guanine (H) anchor. Finally, ligation of Illumina adapters at the 3 end of the complementary strand using T4 ligase SRS10549341 Fig2b_rep1_RTDNA.fastq Fig2b_rep1_RTDNA.fastq OTHER OTHER PCR Illumina MiSeq SRX12594047 Fig5a_rep2_induced48h_Cas9-P2A-RT.fastq SRP341237 bp0 Fig5a_rep2_induced48h_Cas9-P2A-RT.fastq SRS10549340 Fig5a_rep2_induced48h_Cas9-P2A-RT.fastq Fig5a_rep2_induced48h_Cas9-P2A-RT.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594048 ExtDataFig5a_rep2_induced24h_TRP2_a1a2_12.fastq SRP341237 bp0 ExtDataFig5a_rep2_induced24h_TRP2_a1a2_12.fastq SRS10549342 ExtDataFig5a_rep2_induced24h_TRP2_a1a2_12.fastq ExtDataFig5a_rep2_induced24h_TRP2_a1a2_12.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594049 ExtDataFig3a_rep2_a1a2_12.fastq SRP341237 bp0 ExtDataFig3a_rep2_a1a2_12.fastq SRS10549343 ExtDataFig3a_rep2_a1a2_12.fastq ExtDataFig3a_rep2_a1a2_12.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594050 ExtDataFig5b_rep5_induced48h_FAA1_a1a2_12.fastq SRP341237 bp0 ExtDataFig5b_rep5_induced48h_FAA1_a1a2_12.fastq SRS10549344 ExtDataFig5b_rep5_induced48h_FAA1_a1a2_12.fastq ExtDataFig5b_rep5_induced48h_FAA1_a1a2_12.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594051 ExtDataFig5d_rep1_induced24h_LYP1_a1a2_27v2.fastq SRP341237 bp0 ExtDataFig5d_rep1_induced24h_LYP1_a1a2_27v2.fastq SRS10549347 ExtDataFig5d_rep1_induced24h_LYP1_a1a2_27v2.fastq ExtDataFig5d_rep1_induced24h_LYP1_a1a2_27v2.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594052 Fig5e_rep1_induced72h_FANCF_Cas9.fastq SRP341237 bp0 Fig5e_rep1_induced72h_FANCF_Cas9.fastq SRS10549345 Fig5e_rep1_induced72h_FANCF_Cas9.fastq Fig5e_rep1_induced72h_FANCF_Cas9.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594053 ExtDataFig5b_rep3_induced24h_FAA1_a1a2_27v2.fastq SRP341237 bp0 ExtDataFig5b_rep3_induced24h_FAA1_a1a2_27v2.fastq SRS10549346 ExtDataFig5b_rep3_induced24h_FAA1_a1a2_27v2.fastq ExtDataFig5b_rep3_induced24h_FAA1_a1a2_27v2.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594054 ExtDataFig3c_rep2_a1a2_22.fastq SRP341237 bp0 ExtDataFig3c_rep2_a1a2_22.fastq SRS10549349 ExtDataFig3c_rep2_a1a2_22.fastq ExtDataFig3c_rep2_a1a2_22.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594055 Fig4h_rep1_induced48h_Cas9_a1a2_12.fastq SRP341237 bp0 Fig4h_rep1_induced48h_Cas9_a1a2_12.fastq SRS10549348 Fig4h_rep1_induced48h_Cas9_a1a2_12.fastq Fig4h_rep1_induced48h_Cas9_a1a2_12.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594056 Fig2f_rep3_plasmid_post.fastq SRP341237 bp0 RT-DNA prep: DBR1 to remove the branched RNA from RT-DNA, then extending the 3 end dCTP, in a reaction with terminal deoxynucleotidyl transferase (TdT); complementary strand synthesis from the extended product using Klenow Fragment with a primer containing an Illumina adapter sequence, six guanines, and a non-guanine (H) anchor. Finally, ligation of Illumina adapters at the 3 end of the complementary strand using T4 ligase SRS10549351 Fig2f_rep3_plasmid_post.fastq Fig2f_rep3_plasmid_post.fastq OTHER OTHER PCR Illumina MiSeq SRX12594057 Fig4h_rep3_induced24h_Cas9+RT_a1a2_27v2.fastq SRP341237 bp0 Fig4h_rep3_induced24h_Cas9+RT_a1a2_27v2.fastq SRS10549350 Fig4h_rep3_induced24h_Cas9+RT_a1a2_27v2.fastq Fig4h_rep3_induced24h_Cas9+RT_a1a2_27v2.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594058 ExtDataFig3b_rep3_a1a2_22.fastq SRP341237 bp0 ExtDataFig3b_rep3_a1a2_22.fastq SRS10549352 ExtDataFig3b_rep3_a1a2_22.fastq ExtDataFig3b_rep3_a1a2_22.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594059 Fig4h_rep3_induced24h_Cas9+RT_a1a2_27v1.fastq SRP341237 bp0 Fig4h_rep3_induced24h_Cas9+RT_a1a2_27v1.fastq SRS10549353 Fig4h_rep3_induced24h_Cas9+RT_a1a2_27v1.fastq Fig4h_rep3_induced24h_Cas9+RT_a1a2_27v1.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594060 ExtDataFig5a_rep1_induced48h_TRP2_a1a2_27v2.fastq SRP341237 bp0 ExtDataFig5a_rep1_induced48h_TRP2_a1a2_27v2.fastq SRS10549354 ExtDataFig5a_rep1_induced48h_TRP2_a1a2_27v2.fastq ExtDataFig5a_rep1_induced48h_TRP2_a1a2_27v2.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594061 ExtDataFig3a_rep4_a1a2_22.fastq SRP341237 bp0 ExtDataFig3a_rep4_a1a2_22.fastq SRS10549355 ExtDataFig3a_rep4_a1a2_22.fastq ExtDataFig3a_rep4_a1a2_22.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594062 ExtDataFig5b_rep3_induced48h_FAA1_a1a2_12.fastq SRP341237 bp0 ExtDataFig5b_rep3_induced48h_FAA1_a1a2_12.fastq SRS10549356 ExtDataFig5b_rep3_induced48h_FAA1_a1a2_12.fastq ExtDataFig5b_rep3_induced48h_FAA1_a1a2_12.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594063 Fig2b_rep2_RTDNA.fastq SRP341237 bp0 RT-DNA prep: DBR1 to remove the branched RNA from RT-DNA, then extending the 3 end dCTP, in a reaction with terminal deoxynucleotidyl transferase (TdT); complementary strand synthesis from the extended product using Klenow Fragment with a primer containing an Illumina adapter sequence, six guanines, and a non-guanine (H) anchor. Finally, ligation of Illumina adapters at the 3 end of the complementary strand using T4 ligase SRS10549357 Fig2b_rep2_RTDNA.fastq Fig2b_rep2_RTDNA.fastq OTHER OTHER PCR Illumina MiSeq SRX12594064 ExtDataFig5c_rep4_induced48h_CAN1_a1a2_12.fastq SRP341237 bp0 ExtDataFig5c_rep4_induced48h_CAN1_a1a2_12.fastq SRS10549358 ExtDataFig5c_rep4_induced48h_CAN1_a1a2_12.fastq ExtDataFig5c_rep4_induced48h_CAN1_a1a2_12.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594065 Fig2c_rep1_plasmid_pre.fastq SRP341237 bp0 RT-DNA prep: DBR1 to remove the branched RNA from RT-DNA, then extending the 3 end dCTP, in a reaction with terminal deoxynucleotidyl transferase (TdT); complementary strand synthesis from the extended product using Klenow Fragment with a primer containing an Illumina adapter sequence, six guanines, and a non-guanine (H) anchor. Finally, ligation of Illumina adapters at the 3 end of the complementary strand using T4 ligase SRS10549359 Fig2c_rep1_plasmid_pre.fastq Fig2c_rep1_plasmid_pre.fastq OTHER OTHER PCR Illumina MiSeq SRX12594066 Fig4h_rep2_induced24h_Cas9+RT_a1a2_27v1.fastq SRP341237 bp0 Fig4h_rep2_induced24h_Cas9+RT_a1a2_27v1.fastq SRS10549360 Fig4h_rep2_induced24h_Cas9+RT_a1a2_27v1.fastq Fig4h_rep2_induced24h_Cas9+RT_a1a2_27v1.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594067 ExtDataFig5d_rep4_induced48h_LYP1_a1a2_12.fastq SRP341237 bp0 ExtDataFig5d_rep4_induced48h_LYP1_a1a2_12.fastq SRS10549362 ExtDataFig5d_rep4_induced48h_LYP1_a1a2_12.fastq ExtDataFig5d_rep4_induced48h_LYP1_a1a2_12.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594068 Fig4h_rep1_induced24h_RT_a1a2_12.fastq SRP341237 bp0 Fig4h_rep1_induced24h_RT_a1a2_12.fastq SRS10549361 Fig4h_rep1_induced24h_RT_a1a2_12.fastq Fig4h_rep1_induced24h_RT_a1a2_12.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594069 Fig4h_rep1_induced48h_Cas9+RT_a1a2_12.fastq SRP341237 bp0 Fig4h_rep1_induced48h_Cas9+RT_a1a2_12.fastq SRS10549363 Fig4h_rep1_induced48h_Cas9+RT_a1a2_12.fastq Fig4h_rep1_induced48h_Cas9+RT_a1a2_12.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594070 ExtDataFig5c_rep3_induced24h_CAN1_a1a2_27v2.fastq SRP341237 bp0 ExtDataFig5c_rep3_induced24h_CAN1_a1a2_27v2.fastq SRS10549364 ExtDataFig5c_rep3_induced24h_CAN1_a1a2_27v2.fastq ExtDataFig5c_rep3_induced24h_CAN1_a1a2_27v2.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594071 Fig4d_rep6_a1a2_12.fastq SRP341237 bp0 Fig4d_rep6_a1a2_12.fastq SRS10549365 Fig4d_rep6_a1a2_12.fastq Fig4d_rep6_a1a2_12.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594072 Fig4h_rep1_induced48h_Cas9+RT_a1a2_27v1.fastq SRP341237 bp0 Fig4h_rep1_induced48h_Cas9+RT_a1a2_27v1.fastq SRS10549366 Fig4h_rep1_induced48h_Cas9+RT_a1a2_27v1.fastq Fig4h_rep1_induced48h_Cas9+RT_a1a2_27v1.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594073 ExtDataFig5c_rep1_induced24h_CAN1_a1a2_12.fastq SRP341237 bp0 ExtDataFig5c_rep1_induced24h_CAN1_a1a2_12.fastq SRS10549367 ExtDataFig5c_rep1_induced24h_CAN1_a1a2_12.fastq ExtDataFig5c_rep1_induced24h_CAN1_a1a2_12.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594074 Fig5f_rep1_induced72h_HEK3_Cas9+RT.fastq SRP341237 bp0 Fig5f_rep1_induced72h_HEK3_Cas9+RT.fastq SRS10549369 Fig5f_rep1_induced72h_HEK3_Cas9+RT.fastq Fig5f_rep1_induced72h_HEK3_Cas9+RT.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594075 Fig2f_rep3_plasmid_pre.fastq SRP341237 bp0 RT-DNA prep: DBR1 to remove the branched RNA from RT-DNA, then extending the 3 end dCTP, in a reaction with terminal deoxynucleotidyl transferase (TdT); complementary strand synthesis from the extended product using Klenow Fragment with a primer containing an Illumina adapter sequence, six guanines, and a non-guanine (H) anchor. Finally, ligation of Illumina adapters at the 3 end of the complementary strand using T4 ligase SRS10549368 Fig2f_rep3_plasmid_pre.fastq Fig2f_rep3_plasmid_pre.fastq OTHER OTHER PCR Illumina MiSeq SRX12594076 ExtDataFig5d_rep4_induced24h_LYP1_a1a2_27v2.fastq SRP341237 bp0 ExtDataFig5d_rep4_induced24h_LYP1_a1a2_27v2.fastq SRS10549370 ExtDataFig5d_rep4_induced24h_LYP1_a1a2_27v2.fastq ExtDataFig5d_rep4_induced24h_LYP1_a1a2_27v2.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594077 ExtDataFig5a_rep3_induced24h_TRP2_a1a2_12.fastq SRP341237 bp0 ExtDataFig5a_rep3_induced24h_TRP2_a1a2_12.fastq SRS10549371 ExtDataFig5a_rep3_induced24h_TRP2_a1a2_12.fastq ExtDataFig5a_rep3_induced24h_TRP2_a1a2_12.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594078 Fig2f_rep1_RTDNA_PCRd.fastq SRP341237 bp0 RT-DNA prep: DBR1 to remove the branched RNA from RT-DNA, then extending the 3 end dCTP, in a reaction with terminal deoxynucleotidyl transferase (TdT); complementary strand synthesis from the extended product using Klenow Fragment with a primer containing an Illumina adapter sequence, six guanines, and a non-guanine (H) anchor. Finally, ligation of Illumina adapters at the 3 end of the complementary strand using T4 ligase SRS10549372 Fig2f_rep1_RTDNA_PCRd.fastq Fig2f_rep1_RTDNA_PCRd.fastq OTHER OTHER PCR Illumina MiSeq SRX12594079 ExtDataFig5d_rep1_induced24h_LYP1_a1a2_12.fastq SRP341237 bp0 ExtDataFig5d_rep1_induced24h_LYP1_a1a2_12.fastq SRS10549373 ExtDataFig5d_rep1_induced24h_LYP1_a1a2_12.fastq ExtDataFig5d_rep1_induced24h_LYP1_a1a2_12.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594080 Fig2b_rep2_plasmid_pre.fastq SRP341237 bp0 RT-DNA prep: DBR1 to remove the branched RNA from RT-DNA, then extending the 3 end dCTP, in a reaction with terminal deoxynucleotidyl transferase (TdT); complementary strand synthesis from the extended product using Klenow Fragment with a primer containing an Illumina adapter sequence, six guanines, and a non-guanine (H) anchor. Finally, ligation of Illumina adapters at the 3 end of the complementary strand using T4 ligase SRS10549374 Fig2b_rep2_plasmid_pre.fastq Fig2b_rep2_plasmid_pre.fastq OTHER OTHER PCR Illumina MiSeq SRX12594081 Fig2c_rep3_plasmid_pre.fastq SRP341237 bp0 RT-DNA prep: DBR1 to remove the branched RNA from RT-DNA, then extending the 3 end dCTP, in a reaction with terminal deoxynucleotidyl transferase (TdT); complementary strand synthesis from the extended product using Klenow Fragment with a primer containing an Illumina adapter sequence, six guanines, and a non-guanine (H) anchor. Finally, ligation of Illumina adapters at the 3 end of the complementary strand using T4 ligase SRS10549375 Fig2c_rep3_plasmid_pre.fastq Fig2c_rep3_plasmid_pre.fastq OTHER OTHER PCR Illumina MiSeq SRX12594082 ExtDataFig5c_rep5_induced48h_CAN1_a1a2_27v2.fastq SRP341237 bp0 ExtDataFig5c_rep5_induced48h_CAN1_a1a2_27v2.fastq SRS10549376 ExtDataFig5c_rep5_induced48h_CAN1_a1a2_27v2.fastq ExtDataFig5c_rep5_induced48h_CAN1_a1a2_27v2.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594083 Fig4d_rep2_a1a2_12.fastq SRP341237 bp0 Fig4d_rep2_a1a2_12.fastq SRS10549377 Fig4d_rep2_a1a2_12.fastq Fig4d_rep2_a1a2_12.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594084 ExtDataFig5b_rep6_induced24h_FAA1_a1a2_12.fastq SRP341237 bp0 ExtDataFig5b_rep6_induced24h_FAA1_a1a2_12.fastq SRS10549378 ExtDataFig5b_rep6_induced24h_FAA1_a1a2_12.fastq ExtDataFig5b_rep6_induced24h_FAA1_a1a2_12.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594085 Fig5a_rep1_induced48h_RT-P2A-Cas9.fastq SRP341237 bp0 Fig5a_rep1_induced48h_RT-P2A-Cas9.fastq SRS10549379 Fig5a_rep1_induced48h_RT-P2A-Cas9.fastq Fig5a_rep1_induced48h_RT-P2A-Cas9.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594086 Fig5c_rep1_induced72h_AAVS1_Cas9.fastq SRP341237 bp0 Fig5c_rep1_induced72h_AAVS1_Cas9.fastq SRS10549380 Fig5c_rep1_induced72h_AAVS1_Cas9.fastq Fig5c_rep1_induced72h_AAVS1_Cas9.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594087 Fig5e_rep3_induced72h_FANCF_Cas9+RT.fastq SRP341237 bp0 Fig5e_rep3_induced72h_FANCF_Cas9+RT.fastq SRS10549381 Fig5e_rep3_induced72h_FANCF_Cas9+RT.fastq Fig5e_rep3_induced72h_FANCF_Cas9+RT.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594088 ExtDataFig5b_rep4_induced48h_FAA1_a1a2_12.fastq SRP341237 bp0 ExtDataFig5b_rep4_induced48h_FAA1_a1a2_12.fastq SRS10549382 ExtDataFig5b_rep4_induced48h_FAA1_a1a2_12.fastq ExtDataFig5b_rep4_induced48h_FAA1_a1a2_12.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594089 Fig4d_rep5_a1a2_12.fastq SRP341237 bp0 Fig4d_rep5_a1a2_12.fastq SRS10549384 Fig4d_rep5_a1a2_12.fastq Fig4d_rep5_a1a2_12.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594090 ExtDataFig5d_rep3_induced48h_LYP1_a1a2_12.fastq SRP341237 bp0 ExtDataFig5d_rep3_induced48h_LYP1_a1a2_12.fastq SRS10549383 ExtDataFig5d_rep3_induced48h_LYP1_a1a2_12.fastq ExtDataFig5d_rep3_induced48h_LYP1_a1a2_12.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594091 Fig2b_rep3_plasmid_post.fastq SRP341237 bp0 RT-DNA prep: DBR1 to remove the branched RNA from RT-DNA, then extending the 3 end dCTP, in a reaction with terminal deoxynucleotidyl transferase (TdT); complementary strand synthesis from the extended product using Klenow Fragment with a primer containing an Illumina adapter sequence, six guanines, and a non-guanine (H) anchor. Finally, ligation of Illumina adapters at the 3 end of the complementary strand using T4 ligase SRS10549385 Fig2b_rep3_plasmid_post.fastq Fig2b_rep3_plasmid_post.fastq OTHER OTHER PCR Illumina MiSeq SRX12594092 ExtDataFig5d_rep2_induced48h_LYP1_a1a2_27v2.fastq SRP341237 bp0 ExtDataFig5d_rep2_induced48h_LYP1_a1a2_27v2.fastq SRS10549386 ExtDataFig5d_rep2_induced48h_LYP1_a1a2_27v2.fastq ExtDataFig5d_rep2_induced48h_LYP1_a1a2_27v2.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594093 Fig4d_rep1_a1a2_12.fastq SRP341237 bp0 Fig4d_rep1_a1a2_12.fastq SRS10549387 Fig4d_rep1_a1a2_12.fastq Fig4d_rep1_a1a2_12.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594094 ExtDataFig5a_rep1_induced48h_TRP2_a1a2_12.fastq SRP341237 bp0 ExtDataFig5a_rep1_induced48h_TRP2_a1a2_12.fastq SRS10549389 ExtDataFig5a_rep1_induced48h_TRP2_a1a2_12.fastq ExtDataFig5a_rep1_induced48h_TRP2_a1a2_12.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594095 ExtDataFig5d_rep1_induced48h_LYP1_a1a2_27v2.fastq SRP341237 bp0 ExtDataFig5d_rep1_induced48h_LYP1_a1a2_27v2.fastq SRS10549388 ExtDataFig5d_rep1_induced48h_LYP1_a1a2_27v2.fastq ExtDataFig5d_rep1_induced48h_LYP1_a1a2_27v2.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594096 Fig5a_rep2_induced48h_RT-P2A-Cas9.fastq SRP341237 bp0 Fig5a_rep2_induced48h_RT-P2A-Cas9.fastq SRS10549390 Fig5a_rep2_induced48h_RT-P2A-Cas9.fastq Fig5a_rep2_induced48h_RT-P2A-Cas9.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594097 ExtDataFig5b_rep3_induced48h_FAA1_a1a2_27v2.fastq SRP341237 bp0 ExtDataFig5b_rep3_induced48h_FAA1_a1a2_27v2.fastq SRS10549391 ExtDataFig5b_rep3_induced48h_FAA1_a1a2_27v2.fastq ExtDataFig5b_rep3_induced48h_FAA1_a1a2_27v2.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594098 Fig5h_rep1_induced72h_RNF2_Cas9.fastq SRP341237 bp0 Fig5h_rep1_induced72h_RNF2_Cas9.fastq SRS10549392 Fig5h_rep1_induced72h_RNF2_Cas9.fastq Fig5h_rep1_induced72h_RNF2_Cas9.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594099 ExtDataFig5c_rep3_induced48h_CAN1_a1a2_12.fastq SRP341237 bp0 ExtDataFig5c_rep3_induced48h_CAN1_a1a2_12.fastq SRS10549393 ExtDataFig5c_rep3_induced48h_CAN1_a1a2_12.fastq ExtDataFig5c_rep3_induced48h_CAN1_a1a2_12.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594100 Fig4h_rep2_induced48h_empty_a1a2_12.fastq SRP341237 bp0 Fig4h_rep2_induced48h_empty_a1a2_12.fastq SRS10549394 Fig4h_rep2_induced48h_empty_a1a2_12.fastq Fig4h_rep2_induced48h_empty_a1a2_12.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594101 ExtDataFig5a_rep1_induced24h_TRP2_a1a2_27v2.fastq SRP341237 bp0 ExtDataFig5a_rep1_induced24h_TRP2_a1a2_27v2.fastq SRS10549395 ExtDataFig5a_rep1_induced24h_TRP2_a1a2_27v2.fastq ExtDataFig5a_rep1_induced24h_TRP2_a1a2_27v2.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594102 Fig5g_rep1_induced72h_HEK4_Cas9.fastq SRP341237 bp0 Fig5g_rep1_induced72h_HEK4_Cas9.fastq SRS10549396 Fig5g_rep1_induced72h_HEK4_Cas9.fastq Fig5g_rep1_induced72h_HEK4_Cas9.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594103 ExtDataFig3c_rep3_a1a2_12.fastq SRP341237 bp0 ExtDataFig3c_rep3_a1a2_12.fastq SRS10549397 ExtDataFig3c_rep3_a1a2_12.fastq ExtDataFig3c_rep3_a1a2_12.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594104 Fig4h_rep2_induced24h_Cas9+RT_a1a2_27v2.fastq SRP341237 bp0 Fig4h_rep2_induced24h_Cas9+RT_a1a2_27v2.fastq SRS10549398 Fig4h_rep2_induced24h_Cas9+RT_a1a2_27v2.fastq Fig4h_rep2_induced24h_Cas9+RT_a1a2_27v2.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594105 Fig4h_rep3_induced24h_Cas9+RT_a1a2_12.fastq SRP341237 bp0 Fig4h_rep3_induced24h_Cas9+RT_a1a2_12.fastq SRS10549399 Fig4h_rep3_induced24h_Cas9+RT_a1a2_12.fastq Fig4h_rep3_induced24h_Cas9+RT_a1a2_12.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594106 ExtDataFig3c_rep1_a1a2_22.fastq SRP341237 bp0 ExtDataFig3c_rep1_a1a2_22.fastq SRS10549401 ExtDataFig3c_rep1_a1a2_22.fastq ExtDataFig3c_rep1_a1a2_22.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594107 ExtDataFig5d_rep6_induced24h_LYP1_a1a2_12.fastq SRP341237 bp0 ExtDataFig5d_rep6_induced24h_LYP1_a1a2_12.fastq SRS10549402 ExtDataFig5d_rep6_induced24h_LYP1_a1a2_12.fastq ExtDataFig5d_rep6_induced24h_LYP1_a1a2_12.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594108 Fig2f_rep2_plasmid_pre.fastq SRP341237 bp0 RT-DNA prep: DBR1 to remove the branched RNA from RT-DNA, then extending the 3 end dCTP, in a reaction with terminal deoxynucleotidyl transferase (TdT); complementary strand synthesis from the extended product using Klenow Fragment with a primer containing an Illumina adapter sequence, six guanines, and a non-guanine (H) anchor. Finally, ligation of Illumina adapters at the 3 end of the complementary strand using T4 ligase SRS10549400 Fig2f_rep2_plasmid_pre.fastq Fig2f_rep2_plasmid_pre.fastq OTHER OTHER PCR Illumina MiSeq SRX12594109 Fig2b_rep3_plasmid_pre.fastq SRP341237 bp0 RT-DNA prep: DBR1 to remove the branched RNA from RT-DNA, then extending the 3 end dCTP, in a reaction with terminal deoxynucleotidyl transferase (TdT); complementary strand synthesis from the extended product using Klenow Fragment with a primer containing an Illumina adapter sequence, six guanines, and a non-guanine (H) anchor. Finally, ligation of Illumina adapters at the 3 end of the complementary strand using T4 ligase SRS10549403 Fig2b_rep3_plasmid_pre.fastq Fig2b_rep3_plasmid_pre.fastq OTHER OTHER PCR Illumina MiSeq SRX12594110 Fig5a_rep2_induced48h_Cas9-linker2-RT.fastq SRP341237 bp0 Fig5a_rep2_induced48h_Cas9-linker2-RT.fastq SRS10549404 Fig5a_rep2_induced48h_Cas9-linker2-RT.fastq Fig5a_rep2_induced48h_Cas9-linker2-RT.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594111 Fig5d_rep2_induced72h_EMX1_Cas9.fastq SRP341237 bp0 Fig5d_rep2_induced72h_EMX1_Cas9.fastq SRS10549405 Fig5d_rep2_induced72h_EMX1_Cas9.fastq Fig5d_rep2_induced72h_EMX1_Cas9.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594112 ExtDataFig5b_rep1_induced24h_FAA1_a1a2_12.fastq SRP341237 bp0 ExtDataFig5b_rep1_induced24h_FAA1_a1a2_12.fastq SRS10549406 ExtDataFig5b_rep1_induced24h_FAA1_a1a2_12.fastq ExtDataFig5b_rep1_induced24h_FAA1_a1a2_12.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594113 Fig5a_rep3_induced48h_Cas9-linker1-RT.fastq SRP341237 bp0 Fig5a_rep3_induced48h_Cas9-linker1-RT.fastq SRS10549407 Fig5a_rep3_induced48h_Cas9-linker1-RT.fastq Fig5a_rep3_induced48h_Cas9-linker1-RT.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594114 Fig2c_rep1_RTDNA.fastq SRP341237 bp0 RT-DNA prep: DBR1 to remove the branched RNA from RT-DNA, then extending the 3 end dCTP, in a reaction with terminal deoxynucleotidyl transferase (TdT); complementary strand synthesis from the extended product using Klenow Fragment with a primer containing an Illumina adapter sequence, six guanines, and a non-guanine (H) anchor. Finally, ligation of Illumina adapters at the 3 end of the complementary strand using T4 ligase SRS10549408 Fig2c_rep1_RTDNA.fastq Fig2c_rep1_RTDNA.fastq OTHER OTHER PCR Illumina MiSeq SRX12594115 Fig5h_rep3_induced72h_RNF2_Cas9+RT.fastq SRP341237 bp0 Fig5h_rep3_induced72h_RNF2_Cas9+RT.fastq SRS10549409 Fig5h_rep3_induced72h_RNF2_Cas9+RT.fastq Fig5h_rep3_induced72h_RNF2_Cas9+RT.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594116 ExtDataFig5a_rep2_induced24h_TRP2_a1a2_27v2.fastq SRP341237 bp0 ExtDataFig5a_rep2_induced24h_TRP2_a1a2_27v2.fastq SRS10549410 ExtDataFig5a_rep2_induced24h_TRP2_a1a2_27v2.fastq ExtDataFig5a_rep2_induced24h_TRP2_a1a2_27v2.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594117 Fig4h_rep3_induced48h_RT_a1a2_12.fastq SRP341237 bp0 Fig4h_rep3_induced48h_RT_a1a2_12.fastq SRS10549411 Fig4h_rep3_induced48h_RT_a1a2_12.fastq Fig4h_rep3_induced48h_RT_a1a2_12.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594118 ExtDataFig5d_rep4_induced48h_LYP1_a1a2_27v2.fastq SRP341237 bp0 ExtDataFig5d_rep4_induced48h_LYP1_a1a2_27v2.fastq SRS10549412 ExtDataFig5d_rep4_induced48h_LYP1_a1a2_27v2.fastq ExtDataFig5d_rep4_induced48h_LYP1_a1a2_27v2.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594119 Fig5a_rep2_induced48h_RT-linker1-Cas9.fastq SRP341237 bp0 Fig5a_rep2_induced48h_RT-linker1-Cas9.fastq SRS10549413 Fig5a_rep2_induced48h_RT-linker1-Cas9.fastq Fig5a_rep2_induced48h_RT-linker1-Cas9.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594120 Fig5d_rep1_induced72h_EMX1_Cas9+RT.fastq SRP341237 bp0 Fig5d_rep1_induced72h_EMX1_Cas9+RT.fastq SRS10549414 Fig5d_rep1_induced72h_EMX1_Cas9+RT.fastq Fig5d_rep1_induced72h_EMX1_Cas9+RT.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594121 ExtDataFig3a_rep3_a1a2_22.fastq SRP341237 bp0 ExtDataFig3a_rep3_a1a2_22.fastq SRS10549415 ExtDataFig3a_rep3_a1a2_22.fastq ExtDataFig3a_rep3_a1a2_22.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594122 ExtDataFig5b_rep6_induced48h_FAA1_a1a2_27v2.fastq SRP341237 bp0 ExtDataFig5b_rep6_induced48h_FAA1_a1a2_27v2.fastq SRS10549416 ExtDataFig5b_rep6_induced48h_FAA1_a1a2_27v2.fastq ExtDataFig5b_rep6_induced48h_FAA1_a1a2_27v2.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594123 Fig5f_rep2_induced72h_HEK3_Cas9.fastq SRP341237 bp0 Fig5f_rep2_induced72h_HEK3_Cas9.fastq SRS10549417 Fig5f_rep2_induced72h_HEK3_Cas9.fastq Fig5f_rep2_induced72h_HEK3_Cas9.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594124 Fig4h_rep3_induced24h_Cas9_a1a2_12.fastq SRP341237 bp0 Fig4h_rep3_induced24h_Cas9_a1a2_12.fastq SRS10549418 Fig4h_rep3_induced24h_Cas9_a1a2_12.fastq Fig4h_rep3_induced24h_Cas9_a1a2_12.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594125 ExtDataFig5c_rep5_induced24h_CAN1_a1a2_27v2.fastq SRP341237 bp0 ExtDataFig5c_rep5_induced24h_CAN1_a1a2_27v2.fastq SRS10549419 ExtDataFig5c_rep5_induced24h_CAN1_a1a2_27v2.fastq ExtDataFig5c_rep5_induced24h_CAN1_a1a2_27v2.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594126 Fig5a_rep3_induced48h_RT-P2A-Cas9.fastq SRP341237 bp0 Fig5a_rep3_induced48h_RT-P2A-Cas9.fastq SRS10549420 Fig5a_rep3_induced48h_RT-P2A-Cas9.fastq Fig5a_rep3_induced48h_RT-P2A-Cas9.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594127 ExtDataFig3a_rep1_a1a2_12.fastq SRP341237 bp0 ExtDataFig3a_rep1_a1a2_12.fastq SRS10549421 ExtDataFig3a_rep1_a1a2_12.fastq ExtDataFig3a_rep1_a1a2_12.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594128 Fig4h_rep3_induced48h_Cas9+RT_a1a2_12.fastq SRP341237 bp0 Fig4h_rep3_induced48h_Cas9+RT_a1a2_12.fastq SRS10549422 Fig4h_rep3_induced48h_Cas9+RT_a1a2_12.fastq Fig4h_rep3_induced48h_Cas9+RT_a1a2_12.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594129 Fig2f_rep2_RTDNA_PCRd.fastq SRP341237 bp0 RT-DNA prep: DBR1 to remove the branched RNA from RT-DNA, then extending the 3 end dCTP, in a reaction with terminal deoxynucleotidyl transferase (TdT); complementary strand synthesis from the extended product using Klenow Fragment with a primer containing an Illumina adapter sequence, six guanines, and a non-guanine (H) anchor. Finally, ligation of Illumina adapters at the 3 end of the complementary strand using T4 ligase SRS10549423 Fig2f_rep2_RTDNA_PCRd.fastq Fig2f_rep2_RTDNA_PCRd.fastq OTHER OTHER PCR Illumina MiSeq SRX12594130 ExtDataFig5c_rep4_induced48h_CAN1_a1a2_27v2.fastq SRP341237 bp0 ExtDataFig5c_rep4_induced48h_CAN1_a1a2_27v2.fastq SRS10549424 ExtDataFig5c_rep4_induced48h_CAN1_a1a2_27v2.fastq ExtDataFig5c_rep4_induced48h_CAN1_a1a2_27v2.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594131 ExtDataFig5d_rep5_induced24h_LYP1_a1a2_27v2.fastq SRP341237 bp0 ExtDataFig5d_rep5_induced24h_LYP1_a1a2_27v2.fastq SRS10549425 ExtDataFig5d_rep5_induced24h_LYP1_a1a2_27v2.fastq ExtDataFig5d_rep5_induced24h_LYP1_a1a2_27v2.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594132 Fig4h_rep1_induced24h_Cas9+RT_a1a2_27v1.fastq SRP341237 bp0 Fig4h_rep1_induced24h_Cas9+RT_a1a2_27v1.fastq SRS10549426 Fig4h_rep1_induced24h_Cas9+RT_a1a2_27v1.fastq Fig4h_rep1_induced24h_Cas9+RT_a1a2_27v1.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594133 ExtDataFig5a_rep2_induced48h_TRP2_a1a2_12.fastq SRP341237 bp0 ExtDataFig5a_rep2_induced48h_TRP2_a1a2_12.fastq SRS10549427 ExtDataFig5a_rep2_induced48h_TRP2_a1a2_12.fastq ExtDataFig5a_rep2_induced48h_TRP2_a1a2_12.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594134 Fig4d_rep4_a1a2_12.fastq SRP341237 bp0 Fig4d_rep4_a1a2_12.fastq SRS10549428 Fig4d_rep4_a1a2_12.fastq Fig4d_rep4_a1a2_12.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594135 ExtDataFig3a_rep2_a1a2_22.fastq SRP341237 bp0 ExtDataFig3a_rep2_a1a2_22.fastq SRS10549429 ExtDataFig3a_rep2_a1a2_22.fastq ExtDataFig3a_rep2_a1a2_22.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594136 Fig2f_rep1_plasmid_post.fastq SRP341237 bp0 RT-DNA prep: DBR1 to remove the branched RNA from RT-DNA, then extending the 3 end dCTP, in a reaction with terminal deoxynucleotidyl transferase (TdT); complementary strand synthesis from the extended product using Klenow Fragment with a primer containing an Illumina adapter sequence, six guanines, and a non-guanine (H) anchor. Finally, ligation of Illumina adapters at the 3 end of the complementary strand using T4 ligase SRS10549430 Fig2f_rep1_plasmid_post.fastq Fig2f_rep1_plasmid_post.fastq OTHER OTHER PCR Illumina MiSeq SRX12594137 ExtDataFig5c_rep5_induced24h_CAN1_a1a2_12.fastq SRP341237 bp0 ExtDataFig5c_rep5_induced24h_CAN1_a1a2_12.fastq SRS10549431 ExtDataFig5c_rep5_induced24h_CAN1_a1a2_12.fastq ExtDataFig5c_rep5_induced24h_CAN1_a1a2_12.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594138 Fig5a_rep1_induced48h_Cas9-P2A-RT.fastq SRP341237 bp0 Fig5a_rep1_induced48h_Cas9-P2A-RT.fastq SRS10549432 Fig5a_rep1_induced48h_Cas9-P2A-RT.fastq Fig5a_rep1_induced48h_Cas9-P2A-RT.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594139 Fig5a_rep2_induced48h_RT-linker2-Cas9.fastq SRP341237 bp0 Fig5a_rep2_induced48h_RT-linker2-Cas9.fastq SRS10549433 Fig5a_rep2_induced48h_RT-linker2-Cas9.fastq Fig5a_rep2_induced48h_RT-linker2-Cas9.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594140 Fig5g_rep3_induced72h_HEK4_Cas9+RT.fastq SRP341237 bp0 Fig5g_rep3_induced72h_HEK4_Cas9+RT.fastq SRS10549434 Fig5g_rep3_induced72h_HEK4_Cas9+RT.fastq Fig5g_rep3_induced72h_HEK4_Cas9+RT.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594141 ExtDataFig5d_rep5_induced24h_LYP1_a1a2_12.fastq SRP341237 bp0 ExtDataFig5d_rep5_induced24h_LYP1_a1a2_12.fastq SRS10549435 ExtDataFig5d_rep5_induced24h_LYP1_a1a2_12.fastq ExtDataFig5d_rep5_induced24h_LYP1_a1a2_12.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594142 Fig4h_rep2_induced48h_Cas9+RT_a1a2_27v1.fastq SRP341237 bp0 Fig4h_rep2_induced48h_Cas9+RT_a1a2_27v1.fastq SRS10549436 Fig4h_rep2_induced48h_Cas9+RT_a1a2_27v1.fastq Fig4h_rep2_induced48h_Cas9+RT_a1a2_27v1.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594143 ExtDataFig3b_rep1_a1a2_22.fastq SRP341237 bp0 ExtDataFig3b_rep1_a1a2_22.fastq SRS10549437 ExtDataFig3b_rep1_a1a2_22.fastq ExtDataFig3b_rep1_a1a2_22.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594144 Fig5d_rep2_induced72h_EMX1_Cas9+RT.fastq SRP341237 bp0 Fig5d_rep2_induced72h_EMX1_Cas9+RT.fastq SRS10549438 Fig5d_rep2_induced72h_EMX1_Cas9+RT.fastq Fig5d_rep2_induced72h_EMX1_Cas9+RT.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594145 ExtDataFig5c_rep1_induced48h_CAN1_a1a2_27v2.fastq SRP341237 bp0 ExtDataFig5c_rep1_induced48h_CAN1_a1a2_27v2.fastq SRS10549439 ExtDataFig5c_rep1_induced48h_CAN1_a1a2_27v2.fastq ExtDataFig5c_rep1_induced48h_CAN1_a1a2_27v2.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594146 ExtDataFig5b_rep2_induced24h_FAA1_a1a2_27v2.fastq SRP341237 bp0 ExtDataFig5b_rep2_induced24h_FAA1_a1a2_27v2.fastq SRS10549442 ExtDataFig5b_rep2_induced24h_FAA1_a1a2_27v2.fastq ExtDataFig5b_rep2_induced24h_FAA1_a1a2_27v2.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594147 Fig4h_rep3_induced48h_Cas9+RT_a1a2_27v2.fastq SRP341237 bp0 Fig4h_rep3_induced48h_Cas9+RT_a1a2_27v2.fastq SRS10549440 Fig4h_rep3_induced48h_Cas9+RT_a1a2_27v2.fastq Fig4h_rep3_induced48h_Cas9+RT_a1a2_27v2.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594148 ExtDataFig5b_rep2_induced24h_FAA1_a1a2_12.fastq SRP341237 bp0 ExtDataFig5b_rep2_induced24h_FAA1_a1a2_12.fastq SRS10549441 ExtDataFig5b_rep2_induced24h_FAA1_a1a2_12.fastq ExtDataFig5b_rep2_induced24h_FAA1_a1a2_12.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594149 ExtDataFig5d_rep5_induced48h_LYP1_a1a2_12.fastq SRP341237 bp0 ExtDataFig5d_rep5_induced48h_LYP1_a1a2_12.fastq SRS10549443 ExtDataFig5d_rep5_induced48h_LYP1_a1a2_12.fastq ExtDataFig5d_rep5_induced48h_LYP1_a1a2_12.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594150 ExtDataFig5c_rep4_induced24h_CAN1_a1a2_27v2.fastq SRP341237 bp0 ExtDataFig5c_rep4_induced24h_CAN1_a1a2_27v2.fastq SRS10549444 ExtDataFig5c_rep4_induced24h_CAN1_a1a2_27v2.fastq ExtDataFig5c_rep4_induced24h_CAN1_a1a2_27v2.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594151 ExtDataFig5d_rep5_induced48h_LYP1_a1a2_27v2.fastq SRP341237 bp0 ExtDataFig5d_rep5_induced48h_LYP1_a1a2_27v2.fastq SRS10549446 ExtDataFig5d_rep5_induced48h_LYP1_a1a2_27v2.fastq ExtDataFig5d_rep5_induced48h_LYP1_a1a2_27v2.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594152 ExtDataFig3a_rep1_a1a2_22.fastq SRP341237 bp0 ExtDataFig3a_rep1_a1a2_22.fastq SRS10549445 ExtDataFig3a_rep1_a1a2_22.fastq ExtDataFig3a_rep1_a1a2_22.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594153 Fig5h_rep3_induced72h_RNF2_Cas9.fastq SRP341237 bp0 Fig5h_rep3_induced72h_RNF2_Cas9.fastq SRS10549447 Fig5h_rep3_induced72h_RNF2_Cas9.fastq Fig5h_rep3_induced72h_RNF2_Cas9.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594154 Fig4h_rep2_induced48h_Cas9_a1a2_12.fastq SRP341237 bp0 Fig4h_rep2_induced48h_Cas9_a1a2_12.fastq SRS10549448 Fig4h_rep2_induced48h_Cas9_a1a2_12.fastq Fig4h_rep2_induced48h_Cas9_a1a2_12.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594155 Fig2f_rep2_plasmid_post.fastq SRP341237 bp0 RT-DNA prep: DBR1 to remove the branched RNA from RT-DNA, then extending the 3 end dCTP, in a reaction with terminal deoxynucleotidyl transferase (TdT); complementary strand synthesis from the extended product using Klenow Fragment with a primer containing an Illumina adapter sequence, six guanines, and a non-guanine (H) anchor. Finally, ligation of Illumina adapters at the 3 end of the complementary strand using T4 ligase SRS10549449 Fig2f_rep2_plasmid_post.fastq Fig2f_rep2_plasmid_post.fastq OTHER OTHER PCR Illumina MiSeq SRX12594156 ExtDataFig3b_rep2_a1a2_22.fastq SRP341237 bp0 ExtDataFig3b_rep2_a1a2_22.fastq SRS10549450 ExtDataFig3b_rep2_a1a2_22.fastq ExtDataFig3b_rep2_a1a2_22.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594157 Fig5a_rep1_induced48h_Cas9-linker1-RT.fastq SRP341237 bp0 Fig5a_rep1_induced48h_Cas9-linker1-RT.fastq SRS10549451 Fig5a_rep1_induced48h_Cas9-linker1-RT.fastq Fig5a_rep1_induced48h_Cas9-linker1-RT.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594158 Fig5c_rep2_induced72h_AAVS1_Cas9.fastq SRP341237 bp0 Fig5c_rep2_induced72h_AAVS1_Cas9.fastq SRS10549452 Fig5c_rep2_induced72h_AAVS1_Cas9.fastq Fig5c_rep2_induced72h_AAVS1_Cas9.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594159 ExtDataFig3c_rep3_a1a2_22.fastq SRP341237 bp0 ExtDataFig3c_rep3_a1a2_22.fastq SRS10549453 ExtDataFig3c_rep3_a1a2_22.fastq ExtDataFig3c_rep3_a1a2_22.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594160 Fig2f_rep1_plasmid_pre.fastq SRP341237 bp0 RT-DNA prep: DBR1 to remove the branched RNA from RT-DNA, then extending the 3 end dCTP, in a reaction with terminal deoxynucleotidyl transferase (TdT); complementary strand synthesis from the extended product using Klenow Fragment with a primer containing an Illumina adapter sequence, six guanines, and a non-guanine (H) anchor. Finally, ligation of Illumina adapters at the 3 end of the complementary strand using T4 ligase SRS10549454 Fig2f_rep1_plasmid_pre.fastq Fig2f_rep1_plasmid_pre.fastq OTHER OTHER PCR Illumina MiSeq SRX12594161 ExtDataFig5d_rep2_induced24h_LYP1_a1a2_12.fastq SRP341237 bp0 ExtDataFig5d_rep2_induced24h_LYP1_a1a2_12.fastq SRS10549456 ExtDataFig5d_rep2_induced24h_LYP1_a1a2_12.fastq ExtDataFig5d_rep2_induced24h_LYP1_a1a2_12.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594162 Fig5e_rep2_induced72h_FANCF_Cas9.fastq SRP341237 bp0 Fig5e_rep2_induced72h_FANCF_Cas9.fastq SRS10549455 Fig5e_rep2_induced72h_FANCF_Cas9.fastq Fig5e_rep2_induced72h_FANCF_Cas9.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594163 Fig4h_rep1_induced48h_empty_a1a2_12.fastq SRP341237 bp0 Fig4h_rep1_induced48h_empty_a1a2_12.fastq SRS10549457 Fig4h_rep1_induced48h_empty_a1a2_12.fastq Fig4h_rep1_induced48h_empty_a1a2_12.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594164 ExtDataFig5c_rep1_induced24h_CAN1_a1a2_27v2.fastq SRP341237 bp0 ExtDataFig5c_rep1_induced24h_CAN1_a1a2_27v2.fastq SRS10549458 ExtDataFig5c_rep1_induced24h_CAN1_a1a2_27v2.fastq ExtDataFig5c_rep1_induced24h_CAN1_a1a2_27v2.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594165 ExtDataFig5c_rep2_induced24h_CAN1_a1a2_12.fastq SRP341237 bp0 ExtDataFig5c_rep2_induced24h_CAN1_a1a2_12.fastq SRS10549459 ExtDataFig5c_rep2_induced24h_CAN1_a1a2_12.fastq ExtDataFig5c_rep2_induced24h_CAN1_a1a2_12.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594166 Fig4d_rep3_a1a2_12.fastq SRP341237 bp0 Fig4d_rep3_a1a2_12.fastq SRS10549460 Fig4d_rep3_a1a2_12.fastq Fig4d_rep3_a1a2_12.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594167 ExtDataFig5b_rep2_induced48h_FAA1_a1a2_27v2.fastq SRP341237 bp0 ExtDataFig5b_rep2_induced48h_FAA1_a1a2_27v2.fastq SRS10549462 ExtDataFig5b_rep2_induced48h_FAA1_a1a2_27v2.fastq ExtDataFig5b_rep2_induced48h_FAA1_a1a2_27v2.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594168 Fig5f_rep2_induced72h_HEK3_Cas9+RT.fastq SRP341237 bp0 Fig5f_rep2_induced72h_HEK3_Cas9+RT.fastq SRS10549461 Fig5f_rep2_induced72h_HEK3_Cas9+RT.fastq Fig5f_rep2_induced72h_HEK3_Cas9+RT.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594169 Fig4h_rep2_induced24h_Cas9+RT_a1a2_12.fastq SRP341237 bp0 Fig4h_rep2_induced24h_Cas9+RT_a1a2_12.fastq SRS10549463 Fig4h_rep2_induced24h_Cas9+RT_a1a2_12.fastq Fig4h_rep2_induced24h_Cas9+RT_a1a2_12.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594170 Fig5g_rep3_induced72h_HEK4_Cas9.fastq SRP341237 bp0 Fig5g_rep3_induced72h_HEK4_Cas9.fastq SRS10549464 Fig5g_rep3_induced72h_HEK4_Cas9.fastq Fig5g_rep3_induced72h_HEK4_Cas9.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594171 Fig4d_rep7_a1a2_22.fastq SRP341237 bp0 Fig4d_rep7_a1a2_22.fastq SRS10549465 Fig4d_rep7_a1a2_22.fastq Fig4d_rep7_a1a2_22.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594172 ExtDataFig5b_rep5_induced24h_FAA1_a1a2_12.fastq SRP341237 bp0 ExtDataFig5b_rep5_induced24h_FAA1_a1a2_12.fastq SRS10549466 ExtDataFig5b_rep5_induced24h_FAA1_a1a2_12.fastq ExtDataFig5b_rep5_induced24h_FAA1_a1a2_12.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594173 Fig4h_rep3_induced24h_empty_a1a2_12.fastq SRP341237 bp0 Fig4h_rep3_induced24h_empty_a1a2_12.fastq SRS10549467 Fig4h_rep3_induced24h_empty_a1a2_12.fastq Fig4h_rep3_induced24h_empty_a1a2_12.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594174 Fig2b_rep1_plasmid_post.fastq SRP341237 bp0 RT-DNA prep: DBR1 to remove the branched RNA from RT-DNA, then extending the 3 end dCTP, in a reaction with terminal deoxynucleotidyl transferase (TdT); complementary strand synthesis from the extended product using Klenow Fragment with a primer containing an Illumina adapter sequence, six guanines, and a non-guanine (H) anchor. Finally, ligation of Illumina adapters at the 3 end of the complementary strand using T4 ligase SRS10549468 Fig2b_rep1_plasmid_post.fastq Fig2b_rep1_plasmid_post.fastq OTHER OTHER PCR Illumina MiSeq SRX12594175 Fig2c_rep3_RTDNA.fastq SRP341237 bp0 RT-DNA prep: DBR1 to remove the branched RNA from RT-DNA, then extending the 3 end dCTP, in a reaction with terminal deoxynucleotidyl transferase (TdT); complementary strand synthesis from the extended product using Klenow Fragment with a primer containing an Illumina adapter sequence, six guanines, and a non-guanine (H) anchor. Finally, ligation of Illumina adapters at the 3 end of the complementary strand using T4 ligase SRS10549469 Fig2c_rep3_RTDNA.fastq Fig2c_rep3_RTDNA.fastq OTHER OTHER PCR Illumina MiSeq SRX12594176 Fig4d_rep7_a1a2_12.fastq SRP341237 bp0 Fig4d_rep7_a1a2_12.fastq SRS10549470 Fig4d_rep7_a1a2_12.fastq Fig4d_rep7_a1a2_12.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594177 Fig5c_rep3_induced72h_AAVS1_Cas9+RT.fastq SRP341237 bp0 Fig5c_rep3_induced72h_AAVS1_Cas9+RT.fastq SRS10549472 Fig5c_rep3_induced72h_AAVS1_Cas9+RT.fastq Fig5c_rep3_induced72h_AAVS1_Cas9+RT.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594178 Fig4h_rep2_induced24h_RT_a1a2_12.fastq SRP341237 bp0 Fig4h_rep2_induced24h_RT_a1a2_12.fastq SRS10549471 Fig4h_rep2_induced24h_RT_a1a2_12.fastq Fig4h_rep2_induced24h_RT_a1a2_12.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594179 Fig5h_rep2_induced72h_RNF2_Cas9.fastq SRP341237 bp0 Fig5h_rep2_induced72h_RNF2_Cas9.fastq SRS10549473 Fig5h_rep2_induced72h_RNF2_Cas9.fastq Fig5h_rep2_induced72h_RNF2_Cas9.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594180 ExtDataFig5d_rep6_induced48h_LYP1_a1a2_27v2.fastq SRP341237 bp0 ExtDataFig5d_rep6_induced48h_LYP1_a1a2_27v2.fastq SRS10549474 ExtDataFig5d_rep6_induced48h_LYP1_a1a2_27v2.fastq ExtDataFig5d_rep6_induced48h_LYP1_a1a2_27v2.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594181 ExtDataFig5b_rep3_induced24h_FAA1_a1a2_12.fastq SRP341237 bp0 ExtDataFig5b_rep3_induced24h_FAA1_a1a2_12.fastq SRS10549475 ExtDataFig5b_rep3_induced24h_FAA1_a1a2_12.fastq ExtDataFig5b_rep3_induced24h_FAA1_a1a2_12.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594182 Fig5e_rep2_induced72h_FANCF_Cas9+RT.fastq SRP341237 bp0 Fig5e_rep2_induced72h_FANCF_Cas9+RT.fastq SRS10549476 Fig5e_rep2_induced72h_FANCF_Cas9+RT.fastq Fig5e_rep2_induced72h_FANCF_Cas9+RT.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594183 ExtDataFig5b_rep4_induced48h_FAA1_a1a2_27v2.fastq SRP341237 bp0 ExtDataFig5b_rep4_induced48h_FAA1_a1a2_27v2.fastq SRS10549477 ExtDataFig5b_rep4_induced48h_FAA1_a1a2_27v2.fastq ExtDataFig5b_rep4_induced48h_FAA1_a1a2_27v2.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594184 Fig5h_rep1_induced72h_RNF2_Cas9+RT.fastq SRP341237 bp0 Fig5h_rep1_induced72h_RNF2_Cas9+RT.fastq SRS10549478 Fig5h_rep1_induced72h_RNF2_Cas9+RT.fastq Fig5h_rep1_induced72h_RNF2_Cas9+RT.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594185 Fig4d_rep1_a1a2_22.fastq SRP341237 bp0 Fig4d_rep1_a1a2_22.fastq SRS10549479 Fig4d_rep1_a1a2_22.fastq Fig4d_rep1_a1a2_22.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594186 Fig5d_rep3_induced72h_EMX1_Cas9+RT.fastq SRP341237 bp0 Fig5d_rep3_induced72h_EMX1_Cas9+RT.fastq SRS10549480 Fig5d_rep3_induced72h_EMX1_Cas9+RT.fastq Fig5d_rep3_induced72h_EMX1_Cas9+RT.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594187 Fig4h_rep1_induced24h_Cas9_a1a2_12.fastq SRP341237 bp0 Fig4h_rep1_induced24h_Cas9_a1a2_12.fastq SRS10549481 Fig4h_rep1_induced24h_Cas9_a1a2_12.fastq Fig4h_rep1_induced24h_Cas9_a1a2_12.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594188 Fig4h_rep1_induced24h_Cas9+RT_a1a2_27v2.fastq SRP341237 bp0 Fig4h_rep1_induced24h_Cas9+RT_a1a2_27v2.fastq SRS10549482 Fig4h_rep1_induced24h_Cas9+RT_a1a2_27v2.fastq Fig4h_rep1_induced24h_Cas9+RT_a1a2_27v2.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594189 ExtDataFig5d_rep4_induced24h_LYP1_a1a2_12.fastq SRP341237 bp0 ExtDataFig5d_rep4_induced24h_LYP1_a1a2_12.fastq SRS10549483 ExtDataFig5d_rep4_induced24h_LYP1_a1a2_12.fastq ExtDataFig5d_rep4_induced24h_LYP1_a1a2_12.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594190 Fig5a_rep2_induced48h_Cas9-linker1-RT.fastq SRP341237 bp0 Fig5a_rep2_induced48h_Cas9-linker1-RT.fastq SRS10549484 Fig5a_rep2_induced48h_Cas9-linker1-RT.fastq Fig5a_rep2_induced48h_Cas9-linker1-RT.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594191 Fig2f_rep3_RTDNA_PCRd.fastq SRP341237 bp0 RT-DNA prep: DBR1 to remove the branched RNA from RT-DNA, then extending the 3 end dCTP, in a reaction with terminal deoxynucleotidyl transferase (TdT); complementary strand synthesis from the extended product using Klenow Fragment with a primer containing an Illumina adapter sequence, six guanines, and a non-guanine (H) anchor. Finally, ligation of Illumina adapters at the 3 end of the complementary strand using T4 ligase SRS10549485 Fig2f_rep3_RTDNA_PCRd.fastq Fig2f_rep3_RTDNA_PCRd.fastq OTHER OTHER PCR Illumina MiSeq SRX12594192 Fig5e_rep1_induced72h_FANCF_Cas9+RT.fastq SRP341237 bp0 Fig5e_rep1_induced72h_FANCF_Cas9+RT.fastq SRS10549486 Fig5e_rep1_induced72h_FANCF_Cas9+RT.fastq Fig5e_rep1_induced72h_FANCF_Cas9+RT.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594193 ExtDataFig5c_rep5_induced48h_CAN1_a1a2_12.fastq SRP341237 bp0 ExtDataFig5c_rep5_induced48h_CAN1_a1a2_12.fastq SRS10549487 ExtDataFig5c_rep5_induced48h_CAN1_a1a2_12.fastq ExtDataFig5c_rep5_induced48h_CAN1_a1a2_12.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594194 Fig5a_rep3_induced48h_Cas9-linker2-RT.fastq SRP341237 bp0 Fig5a_rep3_induced48h_Cas9-linker2-RT.fastq SRS10549488 Fig5a_rep3_induced48h_Cas9-linker2-RT.fastq Fig5a_rep3_induced48h_Cas9-linker2-RT.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594195 ExtDataFig5c_rep4_induced24h_CAN1_a1a2_12.fastq SRP341237 bp0 ExtDataFig5c_rep4_induced24h_CAN1_a1a2_12.fastq SRS10549489 ExtDataFig5c_rep4_induced24h_CAN1_a1a2_12.fastq ExtDataFig5c_rep4_induced24h_CAN1_a1a2_12.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594196 Fig5g_rep2_induced72h_HEK4_Cas9+RT.fastq SRP341237 bp0 Fig5g_rep2_induced72h_HEK4_Cas9+RT.fastq SRS10549490 Fig5g_rep2_induced72h_HEK4_Cas9+RT.fastq Fig5g_rep2_induced72h_HEK4_Cas9+RT.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594197 Fig5a_rep3_induced48h_RT-linker1-Cas9.fastq SRP341237 bp0 Fig5a_rep3_induced48h_RT-linker1-Cas9.fastq SRS10549491 Fig5a_rep3_induced48h_RT-linker1-Cas9.fastq Fig5a_rep3_induced48h_RT-linker1-Cas9.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594198 Fig4d_rep5_a1a2_22.fastq SRP341237 bp0 Fig4d_rep5_a1a2_22.fastq SRS10549492 Fig4d_rep5_a1a2_22.fastq Fig4d_rep5_a1a2_22.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594199 ExtDataFig5a_rep3_induced48h_TRP2_a1a2_12.fastq SRP341237 bp0 ExtDataFig5a_rep3_induced48h_TRP2_a1a2_12.fastq SRS10549494 ExtDataFig5a_rep3_induced48h_TRP2_a1a2_12.fastq ExtDataFig5a_rep3_induced48h_TRP2_a1a2_12.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594200 ExtDataFig5d_rep1_induced48h_LYP1_a1a2_12.fastq SRP341237 bp0 ExtDataFig5d_rep1_induced48h_LYP1_a1a2_12.fastq SRS10549493 ExtDataFig5d_rep1_induced48h_LYP1_a1a2_12.fastq ExtDataFig5d_rep1_induced48h_LYP1_a1a2_12.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594201 ExtDataFig5a_rep3_induced24h_TRP2_a1a2_27v2.fastq SRP341237 bp0 ExtDataFig5a_rep3_induced24h_TRP2_a1a2_27v2.fastq SRS10549495 ExtDataFig5a_rep3_induced24h_TRP2_a1a2_27v2.fastq ExtDataFig5a_rep3_induced24h_TRP2_a1a2_27v2.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594202 ExtDataFig3a_rep3_a1a2_12.fastq SRP341237 bp0 ExtDataFig3a_rep3_a1a2_12.fastq SRS10549496 ExtDataFig3a_rep3_a1a2_12.fastq ExtDataFig3a_rep3_a1a2_12.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594203 Fig5f_rep1_induced72h_HEK3_Cas9.fastq SRP341237 bp0 Fig5f_rep1_induced72h_HEK3_Cas9.fastq SRS10549497 Fig5f_rep1_induced72h_HEK3_Cas9.fastq Fig5f_rep1_induced72h_HEK3_Cas9.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594204 Fig5a_rep1_induced48h_RT-linker1-Cas9.fastq SRP341237 bp0 Fig5a_rep1_induced48h_RT-linker1-Cas9.fastq SRS10549498 Fig5a_rep1_induced48h_RT-linker1-Cas9.fastq Fig5a_rep1_induced48h_RT-linker1-Cas9.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594205 Fig5d_rep1_induced72h_EMX1_Cas9.fastq SRP341237 bp0 Fig5d_rep1_induced72h_EMX1_Cas9.fastq SRS10549499 Fig5d_rep1_induced72h_EMX1_Cas9.fastq Fig5d_rep1_induced72h_EMX1_Cas9.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594206 Fig5a_rep3_induced48h_Cas9-P2A-RT.fastq SRP341237 bp0 Fig5a_rep3_induced48h_Cas9-P2A-RT.fastq SRS10549500 Fig5a_rep3_induced48h_Cas9-P2A-RT.fastq Fig5a_rep3_induced48h_Cas9-P2A-RT.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594207 ExtDataFig5d_rep3_induced48h_LYP1_a1a2_27v2.fastq SRP341237 bp0 ExtDataFig5d_rep3_induced48h_LYP1_a1a2_27v2.fastq SRS10549501 ExtDataFig5d_rep3_induced48h_LYP1_a1a2_27v2.fastq ExtDataFig5d_rep3_induced48h_LYP1_a1a2_27v2.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594208 Fig4h_rep3_induced48h_Cas9+RT_a1a2_27v1.fastq SRP341237 bp0 Fig4h_rep3_induced48h_Cas9+RT_a1a2_27v1.fastq SRS10549502 Fig4h_rep3_induced48h_Cas9+RT_a1a2_27v1.fastq Fig4h_rep3_induced48h_Cas9+RT_a1a2_27v1.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594209 ExtDataFig5c_rep1_induced48h_CAN1_a1a2_12.fastq SRP341237 bp0 ExtDataFig5c_rep1_induced48h_CAN1_a1a2_12.fastq SRS10549503 ExtDataFig5c_rep1_induced48h_CAN1_a1a2_12.fastq ExtDataFig5c_rep1_induced48h_CAN1_a1a2_12.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594210 ExtDataFig5c_rep2_induced24h_CAN1_a1a2_27v2.fastq SRP341237 bp0 ExtDataFig5c_rep2_induced24h_CAN1_a1a2_27v2.fastq SRS10549504 ExtDataFig5c_rep2_induced24h_CAN1_a1a2_27v2.fastq ExtDataFig5c_rep2_induced24h_CAN1_a1a2_27v2.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594211 ExtDataFig5b_rep1_induced48h_FAA1_a1a2_27v2.fastq SRP341237 bp0 ExtDataFig5b_rep1_induced48h_FAA1_a1a2_27v2.fastq SRS10549505 ExtDataFig5b_rep1_induced48h_FAA1_a1a2_27v2.fastq ExtDataFig5b_rep1_induced48h_FAA1_a1a2_27v2.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594212 ExtDataFig5b_rep6_induced48h_FAA1_a1a2_12.fastq SRP341237 bp0 ExtDataFig5b_rep6_induced48h_FAA1_a1a2_12.fastq SRS10549506 ExtDataFig5b_rep6_induced48h_FAA1_a1a2_12.fastq ExtDataFig5b_rep6_induced48h_FAA1_a1a2_12.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594213 Fig4h_rep2_induced48h_Cas9+RT_a1a2_27v2.fastq SRP341237 bp0 Fig4h_rep2_induced48h_Cas9+RT_a1a2_27v2.fastq SRS10549507 Fig4h_rep2_induced48h_Cas9+RT_a1a2_27v2.fastq Fig4h_rep2_induced48h_Cas9+RT_a1a2_27v2.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594214 Fig5g_rep2_induced72h_HEK4_Cas9.fastq SRP341237 bp0 Fig5g_rep2_induced72h_HEK4_Cas9.fastq SRS10549508 Fig5g_rep2_induced72h_HEK4_Cas9.fastq Fig5g_rep2_induced72h_HEK4_Cas9.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594215 Fig2c_rep1_plasmid_post.fastq SRP341237 bp0 RT-DNA prep: DBR1 to remove the branched RNA from RT-DNA, then extending the 3 end dCTP, in a reaction with terminal deoxynucleotidyl transferase (TdT); complementary strand synthesis from the extended product using Klenow Fragment with a primer containing an Illumina adapter sequence, six guanines, and a non-guanine (H) anchor. Finally, ligation of Illumina adapters at the 3 end of the complementary strand using T4 ligase SRS10549509 Fig2c_rep1_plasmid_post.fastq Fig2c_rep1_plasmid_post.fastq OTHER OTHER PCR Illumina MiSeq SRX12594216 Fig4d_rep3_a1a2_22.fastq SRP341237 bp0 Fig4d_rep3_a1a2_22.fastq SRS10549510 Fig4d_rep3_a1a2_22.fastq Fig4d_rep3_a1a2_22.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594217 ExtDataFig3c_rep1_a1a2_12.fastq SRP341237 bp0 ExtDataFig3c_rep1_a1a2_12.fastq SRS10549511 ExtDataFig3c_rep1_a1a2_12.fastq ExtDataFig3c_rep1_a1a2_12.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594218 Fig4h_rep1_induced24h_Cas9+RT_a1a2_12.fastq SRP341237 bp0 Fig4h_rep1_induced24h_Cas9+RT_a1a2_12.fastq SRS10549512 Fig4h_rep1_induced24h_Cas9+RT_a1a2_12.fastq Fig4h_rep1_induced24h_Cas9+RT_a1a2_12.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594219 Fig4h_rep1_induced48h_RT_a1a2_12.fastq SRP341237 bp0 Fig4h_rep1_induced48h_RT_a1a2_12.fastq SRS10549513 Fig4h_rep1_induced48h_RT_a1a2_12.fastq Fig4h_rep1_induced48h_RT_a1a2_12.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594220 Fig5e_rep3_induced72h_FANCF_Cas9.fastq SRP341237 bp0 Fig5e_rep3_induced72h_FANCF_Cas9.fastq SRS10549514 Fig5e_rep3_induced72h_FANCF_Cas9.fastq Fig5e_rep3_induced72h_FANCF_Cas9.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594221 ExtDataFig5b_rep4_induced24h_FAA1_a1a2_12.fastq SRP341237 bp0 ExtDataFig5b_rep4_induced24h_FAA1_a1a2_12.fastq SRS10549515 ExtDataFig5b_rep4_induced24h_FAA1_a1a2_12.fastq ExtDataFig5b_rep4_induced24h_FAA1_a1a2_12.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594222 ExtDataFig5c_rep3_induced24h_CAN1_a1a2_12.fastq SRP341237 bp0 ExtDataFig5c_rep3_induced24h_CAN1_a1a2_12.fastq SRS10549516 ExtDataFig5c_rep3_induced24h_CAN1_a1a2_12.fastq ExtDataFig5c_rep3_induced24h_CAN1_a1a2_12.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594223 ExtDataFig5d_rep6_induced24h_LYP1_a1a2_27v2.fastq SRP341237 bp0 ExtDataFig5d_rep6_induced24h_LYP1_a1a2_27v2.fastq SRS10549517 ExtDataFig5d_rep6_induced24h_LYP1_a1a2_27v2.fastq ExtDataFig5d_rep6_induced24h_LYP1_a1a2_27v2.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594224 ExtDataFig3b_rep3_a1a2_12.fastq SRP341237 bp0 ExtDataFig3b_rep3_a1a2_12.fastq SRS10549518 ExtDataFig3b_rep3_a1a2_12.fastq ExtDataFig3b_rep3_a1a2_12.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594225 ExtDataFig3a_rep4_a1a2_12.fastq SRP341237 bp0 ExtDataFig3a_rep4_a1a2_12.fastq SRS10549519 ExtDataFig3a_rep4_a1a2_12.fastq ExtDataFig3a_rep4_a1a2_12.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594226 ExtDataFig1c_rep1_RTDNA_TdTprep.fastq SRP341237 bp0 RT-DNA prep: DBR1 to remove the branched RNA from RT-DNA, then extending the 3 end dCTP, in a reaction with terminal deoxynucleotidyl transferase (TdT); complementary strand synthesis from the extended product using Klenow Fragment with a primer containing an Illumina adapter sequence, six guanines, and a non-guanine (H) anchor. Finally, ligation of Illumina adapters at the 3 end of the complementary strand using T4 ligase SRS10549520 ExtDataFig1c_rep1_RTDNA_TdTprep.fastq ExtDataFig1c_rep1_RTDNA_TdTprep.fastq OTHER OTHER PCR Illumina MiSeq SRX12594227 ExtDataFig5b_rep2_induced48h_FAA1_a1a2_12.fastq SRP341237 bp0 ExtDataFig5b_rep2_induced48h_FAA1_a1a2_12.fastq SRS10549521 ExtDataFig5b_rep2_induced48h_FAA1_a1a2_12.fastq ExtDataFig5b_rep2_induced48h_FAA1_a1a2_12.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594228 Fig5f_rep3_induced72h_HEK3_Cas9+RT.fastq SRP341237 bp0 Fig5f_rep3_induced72h_HEK3_Cas9+RT.fastq SRS10549522 Fig5f_rep3_induced72h_HEK3_Cas9+RT.fastq Fig5f_rep3_induced72h_HEK3_Cas9+RT.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594229 ExtDataFig5b_rep4_induced24h_FAA1_a1a2_27v2.fastq SRP341237 bp0 ExtDataFig5b_rep4_induced24h_FAA1_a1a2_27v2.fastq SRS10549523 ExtDataFig5b_rep4_induced24h_FAA1_a1a2_27v2.fastq ExtDataFig5b_rep4_induced24h_FAA1_a1a2_27v2.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594230 ExtDataFig5d_rep3_induced24h_LYP1_a1a2_12.fastq SRP341237 bp0 ExtDataFig5d_rep3_induced24h_LYP1_a1a2_12.fastq SRS10549524 ExtDataFig5d_rep3_induced24h_LYP1_a1a2_12.fastq ExtDataFig5d_rep3_induced24h_LYP1_a1a2_12.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594231 ExtDataFig5a_rep1_induced24h_TRP2_a1a2_12.fastq SRP341237 bp0 ExtDataFig5a_rep1_induced24h_TRP2_a1a2_12.fastq SRS10549525 ExtDataFig5a_rep1_induced24h_TRP2_a1a2_12.fastq ExtDataFig5a_rep1_induced24h_TRP2_a1a2_12.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594232 Fig4h_rep3_induced24h_RT_a1a2_12.fastq SRP341237 bp0 Fig4h_rep3_induced24h_RT_a1a2_12.fastq SRS10549527 Fig4h_rep3_induced24h_RT_a1a2_12.fastq Fig4h_rep3_induced24h_RT_a1a2_12.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594233 ExtDataFig3c_rep2_a1a2_12.fastq SRP341237 bp0 ExtDataFig3c_rep2_a1a2_12.fastq SRS10549526 ExtDataFig3c_rep2_a1a2_12.fastq ExtDataFig3c_rep2_a1a2_12.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594234 Fig4h_rep2_induced24h_empty_a1a2_12.fastq SRP341237 bp0 Fig4h_rep2_induced24h_empty_a1a2_12.fastq SRS10549528 Fig4h_rep2_induced24h_empty_a1a2_12.fastq Fig4h_rep2_induced24h_empty_a1a2_12.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594235 ExtDataFig5c_rep6_induced48h_CAN1_a1a2_12.fastq SRP341237 bp0 ExtDataFig5c_rep6_induced48h_CAN1_a1a2_12.fastq SRS10549529 ExtDataFig5c_rep6_induced48h_CAN1_a1a2_12.fastq ExtDataFig5c_rep6_induced48h_CAN1_a1a2_12.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594236 Fig2b_rep3_RTDNA.fastq SRP341237 bp0 RT-DNA prep: DBR1 to remove the branched RNA from RT-DNA, then extending the 3 end dCTP, in a reaction with terminal deoxynucleotidyl transferase (TdT); complementary strand synthesis from the extended product using Klenow Fragment with a primer containing an Illumina adapter sequence, six guanines, and a non-guanine (H) anchor. Finally, ligation of Illumina adapters at the 3 end of the complementary strand using T4 ligase SRS10549530 Fig2b_rep3_RTDNA.fastq Fig2b_rep3_RTDNA.fastq OTHER OTHER PCR Illumina MiSeq SRX12594237 Fig5c_rep2_induced72h_AAVS1_Cas9+RT.fastq SRP341237 bp0 Fig5c_rep2_induced72h_AAVS1_Cas9+RT.fastq SRS10549531 Fig5c_rep2_induced72h_AAVS1_Cas9+RT.fastq Fig5c_rep2_induced72h_AAVS1_Cas9+RT.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594238 Fig4h_rep1_induced48h_Cas9+RT_a1a2_27v2.fastq SRP341237 bp0 Fig4h_rep1_induced48h_Cas9+RT_a1a2_27v2.fastq SRS10549532 Fig4h_rep1_induced48h_Cas9+RT_a1a2_27v2.fastq Fig4h_rep1_induced48h_Cas9+RT_a1a2_27v2.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594239 Fig5a_rep1_induced48h_RT-linker2-Cas9.fastq SRP341237 bp0 Fig5a_rep1_induced48h_RT-linker2-Cas9.fastq SRS10549533 Fig5a_rep1_induced48h_RT-linker2-Cas9.fastq Fig5a_rep1_induced48h_RT-linker2-Cas9.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594240 ExtDataFig5d_rep6_induced48h_LYP1_a1a2_12.fastq SRP341237 bp0 ExtDataFig5d_rep6_induced48h_LYP1_a1a2_12.fastq SRS10549534 ExtDataFig5d_rep6_induced48h_LYP1_a1a2_12.fastq ExtDataFig5d_rep6_induced48h_LYP1_a1a2_12.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594241 ExtDataFig1c_rep2_RTDNA_TdTprep.fastq SRP341237 bp0 RT-DNA prep: DBR1 to remove the branched RNA from RT-DNA, then extending the 3 end dCTP, in a reaction with terminal deoxynucleotidyl transferase (TdT); complementary strand synthesis from the extended product using Klenow Fragment with a primer containing an Illumina adapter sequence, six guanines, and a non-guanine (H) anchor. Finally, ligation of Illumina adapters at the 3 end of the complementary strand using T4 ligase SRS10549535 ExtDataFig1c_rep2_RTDNA_TdTprep.fastq ExtDataFig1c_rep2_RTDNA_TdTprep.fastq OTHER OTHER PCR Illumina MiSeq SRX12594242 Fig4d_rep2_a1a2_22.fastq SRP341237 bp0 Fig4d_rep2_a1a2_22.fastq SRS10549536 Fig4d_rep2_a1a2_22.fastq Fig4d_rep2_a1a2_22.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594243 ExtDataFig5a_rep3_induced48h_TRP2_a1a2_27v2.fastq SRP341237 bp0 ExtDataFig5a_rep3_induced48h_TRP2_a1a2_27v2.fastq SRS10549537 ExtDataFig5a_rep3_induced48h_TRP2_a1a2_27v2.fastq ExtDataFig5a_rep3_induced48h_TRP2_a1a2_27v2.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594244 Fig4h_rep3_induced48h_Cas9_a1a2_12.fastq SRP341237 bp0 Fig4h_rep3_induced48h_Cas9_a1a2_12.fastq SRS10549538 Fig4h_rep3_induced48h_Cas9_a1a2_12.fastq Fig4h_rep3_induced48h_Cas9_a1a2_12.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594245 Fig5c_rep3_induced72h_AAVS1_Cas9.fastq SRP341237 bp0 Fig5c_rep3_induced72h_AAVS1_Cas9.fastq SRS10549539 Fig5c_rep3_induced72h_AAVS1_Cas9.fastq Fig5c_rep3_induced72h_AAVS1_Cas9.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594246 Fig4d_rep6_a1a2_22.fastq SRP341237 bp0 Fig4d_rep6_a1a2_22.fastq SRS10549540 Fig4d_rep6_a1a2_22.fastq Fig4d_rep6_a1a2_22.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594247 ExtDataFig1c_rep3_RTDNA_TdTprep.fastq SRP341237 bp0 RT-DNA prep: DBR1 to remove the branched RNA from RT-DNA, then extending the 3 end dCTP, in a reaction with terminal deoxynucleotidyl transferase (TdT); complementary strand synthesis from the extended product using Klenow Fragment with a primer containing an Illumina adapter sequence, six guanines, and a non-guanine (H) anchor. Finally, ligation of Illumina adapters at the 3 end of the complementary strand using T4 ligase SRS10549541 ExtDataFig1c_rep3_RTDNA_TdTprep.fastq ExtDataFig1c_rep3_RTDNA_TdTprep.fastq OTHER OTHER PCR Illumina MiSeq SRX12594248 ExtDataFig5d_rep3_induced24h_LYP1_a1a2_27v2.fastq SRP341237 bp0 ExtDataFig5d_rep3_induced24h_LYP1_a1a2_27v2.fastq SRS10549542 ExtDataFig5d_rep3_induced24h_LYP1_a1a2_27v2.fastq ExtDataFig5d_rep3_induced24h_LYP1_a1a2_27v2.fastq AMPLICON GENOMIC PCR Illumina MiSeq SRX12594249 Fig5f_rep3_induced72h_HEK3_Cas9.fastq SRP341237 bp0 Fig5f_rep3_induced72h_HEK3_Cas9.fastq SRS10549543 Fig5f_rep3_induced72h_HEK3_Cas9.fastq Fig5f_rep3_induced72h_HEK3_Cas9.fastq AMPLICON GENOMIC PCR Illumina MiSeq