Figure 3

TGIRT-seq of ribo-depleted fragmented UHRR with ERCC spike-ins using the NTT and NTC adapters. TGIRT-seq libraries were prepared in triplicate for each adapter and sequenced on an Illumina NextSeq 500 to obtain 58–105 million 75-nt paired-end reads, which were mapped to a human reference genomic (Ensembl GRCh38) modified to include additional rRNA repeats (Methods and Supplementary Table S1). The datasets were used to generate stacked bar graphs showing the percentages of: (A) read-pairs that mapped concordantly in the annotated orientation to different categories of genomic features; (B) small ncRNA reads that mapped to different classes of small ncRNAs; (C) protein-coding gene reads that mapped to the sense or antisense strand; (D) bases in protein-coding gene reads that mapped to coding sequences (CDS), introns, 5′- and 3′-untranslated regions (UTRs), and intergenic regions. The name of the dataset is indicated below. (E) Aggregate nucleotide frequencies at the beginning of Read 1 (5′-RNA end; positions 1 to 14) and Read 2 (3′-RNA end; positions −1 to −14) in combined datasets for technical replicates obtained by TGIRT-seq of fragmented UHRR plus ERCC spike-ins with either the NTC or NTT adapter (datasets NTC-F1 to F3 and NTT-F1 to F3, respectively).