Journal: Nucleic Acids Research

Article Title: PBOX-sRNA-seq uncovers novel features of miRNA modification and identifies selected 5′-tRNA fragments bearing 2′- O -modification

doi: 10.1093/nar/gkae537

Figure Lengend Snippet: PBOX-sRNA-seq successfully captures 2′-O-modified sRNAs from highly degraded RNA samples. ( A ) RIN values of total RNAs extracted from samples before (T0) and after defrost. T10 and T15 indicate 10 and 15 min of defrost, respectively. RIN values were measured using Qsep100 analyzer with RNA Cartridge Kit (R1). The magenta peak <3 min is a low-size marker (20-nt) and the 18S and 28S rRNA peaks are delineated by red and green dotted lines, respectively. ( B ) Agarose gel electrophoresis analysis of total RNA integrity. ( C ) Quality control analysis of sRNA libraries using a Qsep100 analyzer with a standard cartridge (S2). Magenta peaks represent low-size (20 bp, left) and large-size markers (1000 bp, right). PCR products without insertions are 119 bp, whereas those with sRNAs (21–24 nt) are approximately 143 bp. Results from technical replicate 1 were shown here. Similar results were obtained in technical replicate 2 . ( D ) Size distribution and genomic classification of 14–35 nt mapped reads from conventional sRNA-seq and PBOX-sRNA-seq datasets. The data are the mean of two technical replicates, with the Pearson correlation coefficient ( R ) also provided.

Article Snippet: Libraries were purified using Monarch PCR & DNA kit (NEB, USA) and then assessed for concentration and size via the Qubit dsDNA HS kit (Thermo Fisher) and Qsep100 analyzer with S2 cartridge kit (Bioptic, C105201), respectively.

Techniques: Modification, Marker, Agarose Gel Electrophoresis, Control