Different crosslinking patterns by AMT–NHS and UV. (A) RNA class distribution of reads. Two UV crosslinking samples (lanes 1 and 2) were digested by 5 and 0.5 U of RNase A/T1. The last sample was the sequencing data of total RNA from non-crosslinked cells. (B) Heatmaps of H/ACA snoRNAs drawn on read per million (RPM). (C,D) Scatter plots of H/ACA snoRNA read counts from AMT–NHS in vivo crosslinking versus AMT–NHS in vitro crosslinking (C) or UV crosslinking (D). Read counts are the averages of two or three data sets with similar treatment. (E) Read coverage of snR49. The sequence motifs of snR49 are shown beneath the x-axis. (F) Box plot showing read coverage change between two types of crosslinking. Read coverage was normalized to an area of 10,000 for each H/ACA snoRNA and averaged from two or three data sets with similar treatment. Absolute changes of read count at each position of snoRNA were summed. P-value was from two-tailed t-test.
