RNA libraries were prepared using the Direct RNA Sequencing kit (SQK-RNA002). Sequencing was performed on the Oxford Nanopore PromethION P24 sequencer using the FLO-PRO002 flow cell. Sequencing was performed using MinKNOW v.22.03.4 and MinKNOW Core v.5.0.0 with a pore scan frequency of 1.5 h, active channel selection set to on and reserved pores set to on. Libraries were run for 72 h. Basecalling was performed using Bream v.7.0.9 and Guppy v.6.0.7. Data processing was performed on an Ubuntu 20.04 system. Sequencing was performed by the BioMicro Center at Massachusetts Institute of Technology. Computational analysis of long-read direct RNA-seq data Individual passing FASTQ files from the same sample were merged to generate a single FASTQ file per sample. Except in the case of JAFFAL17 v.2.2 and v.2.3, all mouse data analyses were performed using reference files from GENCODE58 release M28 (GRCm39), and all human data analyses were performed using reference files from GENCODE Release 43 (GRCh38.p13). For JAFFAL, matched reference files were downloaded from the UCSC genome browser59 and prepared using the instructions provided on the JAFFAL wiki (https://github.com/Oshlack/JAFFA/wiki). Genomic alignments for NanoPlot60 v.1.42.0 were performed using Minimap261 v.2.24 with the parameters -ax splice -uf -k14 and aligned reads were processed...

Chemical modifications in DNA enable hidden messages for secure data transmission. Here, authors develop DeepSME, a nanopore sequencing and deep-learning framework that conceals data into DNA using 5-...

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