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Genomic in vitro transcription and Nanopore direct RNA sequencing of a human B-Lymphocyte cell line

Tzadikario, T.; Akeson, S.; Esfahani, N. G.; Stein, A.; Choudhary, U.; Amar, K.; Jain, M.

2025-04-27 genomics
10.1101/2025.04.25.650674 bioRxiv
Show abstract

Genomic DNA used as a template for in vitro transcription of RNA can serve as a true negative control for RNA modification detection in Nanopore direct RNA sequencing (DRS) data. We generated DRS for IVT RNA composed of canonical nucleotides using genomic DNA templates. We applied Dorado modification calling models to these data, which allowed for the calculation of 9-mer specific false positive rates for a set of RNA modifications. These false positive rates capture the complete set of 9-mer sequence contexts and can be applied to a broad range of experimental conditions. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=104 SRC="FIGDIR/small/650674v1_ufig1.gif" ALT="Figure 1"> View larger version (21K): org.highwire.dtl.DTLVardef@66765aorg.highwire.dtl.DTLVardef@e435e5org.highwire.dtl.DTLVardef@8e7c01org.highwire.dtl.DTLVardef@6f44b6_HPS_FORMAT_FIGEXP M_FIG C_FIG Graphical description of a method for In-Vitro Transcription and sequencing of genomic material.

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"Similar papers" are the closest papers from that journal in the model's embedding space. They show what the match is built on, but the ranking comes mostly from a classifier over the whole training set, not from these examples alone.