Project description:We optimized the SHAPE-MaP (selective 2'-hydroxyl acylation analyzed by primer extension and mutational profiling) assay to analyze structures of paired circular (circSHAPE-MaP) and linear (linearSHAPE-MaP) RNAs.
Project description:SHAPE-MaP structure probing experiment was performed on SARS-CoV-2 infected Vero or C6/36 cells at 4 days post infection with two biological replicates. For each replciate, SHAPE-MaP includes a sample treated with 2-methylnicotinic acid imidazolide acid (modified) or a minuse reagent (unmodified). NAI preferentially reacts with unpaired bases in RNA, forming acylated bases. These modifications are encoded as mutation during reverse transcripatse and library preparation. After sequencing and alignment, the reactivity profiles of 'modified' and 'unmodified' samples are used to calculate SHAPE reactivity of each base
Project description:SHAPE-MaP structure probing experiment was performed on SARS-CoV-2 infected Vero cells at 4 days post infection with two biological replicates. For each replciate, SHAPE-MaP includes a sample treated with 2-methylnicotinic acid imidazolide acid (modified) or a minue reagent (unmodified). NAI preferentially reacts with unpaired bases in RNA, forming acylated bases. These modifications are encoded as mutation during reverse transcripatse and library preparation. After sequencing and alignment, the reactivity profiles of 'modified' and 'unmodified' samples are used to calculate SHAPE reactivity of each base
Project description:A SHAPE-MaP structure probing experiment was performed on 39 firefly luciferase mRNAs containing uracil, 1-methyl-psuedouracil, or 5-methoxy-uracil. For each mRNA, SHAPE-MaP includes a sample treated with 1M6 ('MOD'), a minus reagent ('NC'), and a denatured control ('DEN'). The 1M6 reagent preferenctially reacts with unpaired bases in RNA and subsequently induces mutations during the reverse transcription step of library preparation. After sequencing and alignment, the 'mutational profiles' of the 'p', 'm', and 'd' samples are used to calculate the SHAPE reactivity of each base.