Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network.

Nat Commun. 2021 Jun 2;12(1):3297. doi:10.1038/s41467-021-23143-7

Grapotte M, Saraswat M, Bessière C, Menichelli C, Ramilowski JA, Severin J, Hayashizaki Y, Itoh M, Tagami M, Murata M, Kojima-Ishiyama M, Noma S, Noguchi S, Kasukawa T, Hasegawa A, Suzuki H, Nishiyori-Sueki H, Frith MC; FANTOM consortium, Chatelain C, Carninci P, de Hoon MJL, Wasserman WW, Bréhélin L, Lecellier CH.

Cap Trap RNA-seq (CTR) seq: sequencing of CAGE cDNAs on the Nanopore platform. RT primers contain some Us and the DNA/RNA hybrids are digested with USER to shorten the tail. A BBBBBBBB UMI is present.