A scientist wants to analyze the transcriptome of Escherichia coli. To do so, he grows E. coli in a flask, takes a sample from the culture, and extracts the nucleic acids from the sample. She then uses an enzyme called DNase to remove the DNA, leaving only RNA. The RNA is then converted to complementary DNA (cDNA) using a reverse transcriptase. This cDNA, which is more stable than the RNA from which it was synthesized, is broken into small fragments (< 400 bp), and these fragments are then sequenced. The resulting transcriptome dataset (RNASeq) contains millions of sequence fragments corresponding to the transcripts from the original sample. However, upon reviewing his lab notes, the researcher notices he did not add the recommended amount of DNase. He suspects that his dataset may contain sequences originating from DNA, in addition to those from RNA. Describe two patterns that he could look for in the data to confirm that the sequence data reflect RNA, rather than the DNA from which the RNA was transcribed. For each, describe why such a pattern would be expected for RNA, but not DNA. Note: the E. coli genome has been sequenced in its entirety, i.e., the sequences of all genes and other genetic elements are known, as is the location of these features on the chromosome.

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