Table 1. Strand specificity of Peregrine and ScriptSeq libraries prepared from E. coli RNA.

Prep & Treatment	rRNA	CDS	CDS w/known asRNA
Peregrine Untreated	99.77 ± 0.01	94.77 ± 0.04	86.97 ± 0.35
Peregrine DSN	99.86 ± 0.01	94.20 ± 0.23	87.17 ± 0.19
Peregrine Ribo-Zero	2.21 ± 0.09	87.15 ± 1.28	81.72 ± 1.51
ScriptSeq Untreated	99.53 ± 0.10	97.85 ± 0.19	94.04 ± 1.24
ScriptSeq Ribo-Zero	22.33 ± 4.27	97.87 ± 0.30	93.11 ± 0.92

Peregrine and ScriptSeq libraries were prepared from the same sample of E. coli K-12 total RNA, sequenced and aligned to the reference E. coli genome. Read statistics for the libraries analyzed are included in Tables S1 and S2. Reads mapping to rRNA genes, CDS, or a subset of 90 CDS from which robust antisense transcription has been observed (ref.e 24, see their Table S3) were assessed for strand specificity. Values indicate the proportion of reads mapping to the sense strand (mean ± standard deviation).