SRX18479875 Can_WT_apo_biol_rep1 SRP411155 bp0 Modified RNA was extracted from live cells using a RiboPure Bacterial RNA Purification Kit (Invitrogen, AM1925) according to manufacturer's instructions. Modification of extracted RNA was analyzed using the SHAPE-seq v2.1 workflow (Watters, K.E. et al 2016) as described previously (Dutta, D. et al. 2020) with an additional purification step where samples were size selected to 160-300 bp using the 2% Agarose Gel on the PippinHT system (Sage Science,Beverly, MA). Each sample wasanalyzedwith SPATSversion 1.9.30 SRS15953280 Sample_ReCo_Cba_WT_Apo_neg_VS_ReCo_Cba_WT_Apo_pos Can_WT_apo_biol_rep1 RNA-Seq TRANSCRIPTOMIC cDNA Illumina MiSeq SRX18479876 Can_WT_bound_biol_rep1 SRP411155 bp0 Modified RNA was extracted from live cells using a RiboPure Bacterial RNA Purification Kit (Invitrogen, AM1925) according to manufacturer's instructions. Modification of extracted RNA was analyzed using the SHAPE-seq v2.1 workflow (Watters, K.E. et al 2016) as described previously (Dutta, D. et al. 2020) with an additional purification step where samples were size selected to 160-300 bp using the 2% Agarose Gel on the PippinHT system (Sage Science,Beverly, MA). Each sample wasanalyzedwith SPATSversion 1.9.30 SRS15953281 Sample_ReCo_Cba_WT_60_neg_VS_ReCo_Cba_WT_60_pos Can_WT_bound_biol_rep1 RNA-Seq TRANSCRIPTOMIC cDNA Illumina MiSeq SRX18479877 Can_C31U_bound_biol_rep2 SRP411155 bp0 Modified RNA was extracted from live cells using a RiboPure Bacterial RNA Purification Kit (Invitrogen, AM1925) according to manufacturer's instructions. Modification of extracted RNA was analyzed using the SHAPE-seq v2.1 workflow (Watters, K.E. et al 2016) as described previously (Dutta, D. et al. 2020) with an additional purification step where samples were size selected to 160-300 bp using the 2% Agarose Gel on the PippinHT system (Sage Science,Beverly, MA). Each sample wasanalyzedwith SPATSversion 1.9.30 SRS15953282 Sample_C31U_2_Bound_neg_VS_C31U_2_Bound_pos Can_C31U_bound_biol_rep2 RNA-Seq TRANSCRIPTOMIC cDNA Illumina MiSeq SRX18479878 Can_C31U_apo_biol_rep1 SRP411155 bp0 Modified RNA was extracted from live cells using a RiboPure Bacterial RNA Purification Kit (Invitrogen, AM1925) according to manufacturer's instructions. Modification of extracted RNA was analyzed using the SHAPE-seq v2.1 workflow (Watters, K.E. et al 2016) as described previously (Dutta, D. et al. 2020) with an additional purification step where samples were size selected to 160-300 bp using the 2% Agarose Gel on the PippinHT system (Sage Science,Beverly, MA). Each sample wasanalyzedwith SPATSversion 1.9.30 SRS15953283 Sample_C31U_1_Apo_neg_VS_C31U_1_Apo_pos Can_C31U_apo_biol_rep1 RNA-Seq TRANSCRIPTOMIC cDNA Illumina MiSeq SRX18479879 Can_WT_apo_biol_rep2 SRP411155 bp0 Modified RNA was extracted from live cells using a RiboPure Bacterial RNA Purification Kit (Invitrogen, AM1925) according to manufacturer's instructions. Modification of extracted RNA was analyzed using the SHAPE-seq v2.1 workflow (Watters, K.E. et al 2016) as described previously (Dutta, D. et al. 2020) with an additional purification step where samples were size selected to 160-300 bp using the 2% Agarose Gel on the PippinHT system (Sage Science,Beverly, MA). Each sample wasanalyzedwith SPATSversion 1.9.30 SRS15953284 Sample_70_uM_1_Apo_neg_VS_70_uM_1_Apo_pos Can_WT_apo_biol_rep2 RNA-Seq TRANSCRIPTOMIC cDNA Illumina MiSeq SRX18479880 Can_WT_bound_biol_rep2 SRP411155 bp0 Modified RNA was extracted from live cells using a RiboPure Bacterial RNA Purification Kit (Invitrogen, AM1925) according to manufacturer's instructions. Modification of extracted RNA was analyzed using the SHAPE-seq v2.1 workflow (Watters, K.E. et al 2016) as described previously (Dutta, D. et al. 2020) with an additional purification step where samples were size selected to 160-300 bp using the 2% Agarose Gel on the PippinHT system (Sage Science,Beverly, MA). Each sample wasanalyzedwith SPATSversion 1.9.30 SRS15953285 Sample_70_uM_1_Bound_neg_VS_70_uM_1_bound_pos Can_WT_bound_biol_rep2 RNA-Seq TRANSCRIPTOMIC cDNA Illumina MiSeq SRX18479881 Can_C17U_apo_biol_rep1 SRP411155 bp0 Modified RNA was extracted from live cells using a RiboPure Bacterial RNA Purification Kit (Invitrogen, AM1925) according to manufacturer's instructions. Modification of extracted RNA was analyzed using the SHAPE-seq v2.1 workflow (Watters, K.E. et al 2016) as described previously (Dutta, D. et al. 2020) with an additional purification step where samples were size selected to 160-300 bp using the 2% Agarose Gel on the PippinHT system (Sage Science,Beverly, MA). Each sample wasanalyzedwith SPATSversion 1.9.30 SRS15953286 Sample_C17U_1_Apo _neg_VS_C17U_1_Apo_pos_2 Can_C17U_apo_biol_rep1 RNA-Seq TRANSCRIPTOMIC cDNA Illumina MiSeq SRX18479882 Can_C17U_bound_biol_rep1 SRP411155 bp0 Modified RNA was extracted from live cells using a RiboPure Bacterial RNA Purification Kit (Invitrogen, AM1925) according to manufacturer's instructions. Modification of extracted RNA was analyzed using the SHAPE-seq v2.1 workflow (Watters, K.E. et al 2016) as described previously (Dutta, D. et al. 2020) with an additional purification step where samples were size selected to 160-300 bp using the 2% Agarose Gel on the PippinHT system (Sage Science,Beverly, MA). Each sample wasanalyzedwith SPATSversion 1.9.30 SRS15953287 Sample_C17U_1_Bound_neg_VS_C17U_1_Bound_pos_2 Can_C17U_bound_biol_rep1 RNA-Seq TRANSCRIPTOMIC cDNA Illumina MiSeq SRX18479883 Can_C17U_apo_biol_rep2 SRP411155 bp0 Modified RNA was extracted from live cells using a RiboPure Bacterial RNA Purification Kit (Invitrogen, AM1925) according to manufacturer's instructions. Modification of extracted RNA was analyzed using the SHAPE-seq v2.1 workflow (Watters, K.E. et al 2016) as described previously (Dutta, D. et al. 2020) with an additional purification step where samples were size selected to 160-300 bp using the 2% Agarose Gel on the PippinHT system (Sage Science,Beverly, MA). Each sample wasanalyzedwith SPATSversion 1.9.30 SRS15953288 Sample_C17U_2_Apo_neg_VS_C17U_2_Apo_pos Can_C17U_apo_biol_rep2 RNA-Seq TRANSCRIPTOMIC cDNA Illumina MiSeq SRX18479884 Can_C17U_bound_biol_rep2 SRP411155 bp0 Modified RNA was extracted from live cells using a RiboPure Bacterial RNA Purification Kit (Invitrogen, AM1925) according to manufacturer's instructions. Modification of extracted RNA was analyzed using the SHAPE-seq v2.1 workflow (Watters, K.E. et al 2016) as described previously (Dutta, D. et al. 2020) with an additional purification step where samples were size selected to 160-300 bp using the 2% Agarose Gel on the PippinHT system (Sage Science,Beverly, MA). Each sample wasanalyzedwith SPATSversion 1.9.30 SRS15953289 Sample_C17U_2_Bound_neg_VS_C17U_2_Bound_pos Can_C17U_bound_biol_rep2 RNA-Seq TRANSCRIPTOMIC cDNA Illumina MiSeq SRX18479885 Can_C31U_bound_biol_rep1 SRP411155 bp0 Modified RNA was extracted from live cells using a RiboPure Bacterial RNA Purification Kit (Invitrogen, AM1925) according to manufacturer's instructions. Modification of extracted RNA was analyzed using the SHAPE-seq v2.1 workflow (Watters, K.E. et al 2016) as described previously (Dutta, D. et al. 2020) with an additional purification step where samples were size selected to 160-300 bp using the 2% Agarose Gel on the PippinHT system (Sage Science,Beverly, MA). Each sample wasanalyzedwith SPATSversion 1.9.30 SRS15953290 Sample_C31U_1_Bound_neg_VS_C31U_1_Bound_pos Can_C31U_bound_biol_rep1 RNA-Seq TRANSCRIPTOMIC cDNA Illumina MiSeq SRX18479886 Can_C31U_apo_biol_rep2 SRP411155 bp0 Modified RNA was extracted from live cells using a RiboPure Bacterial RNA Purification Kit (Invitrogen, AM1925) according to manufacturer's instructions. Modification of extracted RNA was analyzed using the SHAPE-seq v2.1 workflow (Watters, K.E. et al 2016) as described previously (Dutta, D. et al. 2020) with an additional purification step where samples were size selected to 160-300 bp using the 2% Agarose Gel on the PippinHT system (Sage Science,Beverly, MA). Each sample wasanalyzedwith SPATSversion 1.9.30 SRS15953291 Sample_C31U_2_Apo_neg_VS_C31U_2_Apo_pos Can_C31U_apo_biol_rep2 RNA-Seq TRANSCRIPTOMIC cDNA Illumina MiSeq