Datasets

Title	Phospho-RNA sequencing with CircAID-p-seq
Organism
Number of Samples	5
Release Date	2021/05/20 00:00
Sequencing Types
Protocol Details

Title
Authors	Del Piano A, Kecman T, Schmid M, Barbieri R, Brocchieri L, Tornaletti S, Firrito C, Minati L, Bernabo P, Signoria I, Lauria F, Gillingwater TH, Viero G, Clamer M
Journal	Nucleic acids research
Publication Date	2022 Feb 28
Abstract	Most RNA footprinting approaches that require ribonuclease cleavage generate RNA fragments bearing a phosphate or cyclic phosphate group at their 3' end. Unfortunately, current library preparation protocols rely only on a 3' hydroxyl group for adaptor ligation or poly-A tailing. Here, we developed circAID-p-seq, a PCR-free library preparation for selective 3' phospho-RNA sequencing. As a proof of concept, we applied circAID-p-seq to ribosome profiling, which is based on sequencing of RNA fragments protected by ribosomes after endonuclease digestion. CircAID-p-seq, combined with the dedicated computational pipeline circAidMe, facilitates accurate, fast and highly efficient sequencing of phospho-RNA fragments from eukaryotic cells and tissues. We used circAID-p-seq to portray ribosome occupancy in transcripts, providing a versatile and PCR-free strategy to possibly unravel any endogenous 3'-phospho RNA molecules. © The Author(s) 2021. Published by Oxford University Press on behalf of Nucleic Acids Research.
PMC	PMC8887461
PMID	34850942
DOI

Run Accession	Study Accession	Scientific Name	Cell Line	Library Type	Treatment	GWIPS-viz	Trips-Viz	Reads	BAM	BigWig (F)	BigWig (R)
SRR14602122	PRJNA731473	Homo sapiens	HEK293	RNA-Seq	0.0
SRR14602126	PRJNA731473	Homo sapiens	HEK293	Ribo-Seq	0.0
SRR14602133	PRJNA731473	Mus musculus	0.0	Ribo-Seq	0.0
SRR14602134	PRJNA731473	Mus musculus	0.0	Ribo-Seq	0.0
SRR14602135	PRJNA731473	Mus musculus	0.0	Ribo-Seq	0.0
Run Accession	Study Accession	Scientific Name	Cell Line	Library Type	Treatment	GWIPS-viz	Trips-Viz	Reads	BAM	BigWig (F)	BigWig (R)

Del et al. 2022 (PRJNA731473)