Del et al. 2022 (PRJNA731473)

General Details

Title Phospho-RNA sequencing with CircAID-p-seq
Organism
Number of Samples 12
Release Date 2021/05/20 00:00
Sequencing Types
Protocol Details

Study Links

Repository Details

SRA SRP320668
ENA SRP320668
GEO
BioProject PRJNA731473

Publication

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 RiboCrypt Reads BAM BigWig (F) BigWig (R)
SRR14602119 PRJNA731473 Homo sapiens HEK293 circAID-p-seq Cycloheximide
SRR14602120 PRJNA731473 Homo sapiens HEK293 RNA-Seq Cycloheximide
SRR14602122 PRJNA731473 Homo sapiens HEK293 RNA-Seq chx_harr
SRR14602123 PRJNA731473 Homo sapiens circAID-p-seq untreated
SRR14602124 PRJNA731473 Homo sapiens circAID-p-seq untreated
SRR14602126 PRJNA731473 Homo sapiens Ribo-Seq untreated
SRR14602127 PRJNA731473 Mus musculus Ribo-Seq untreated
SRR14602129 PRJNA731473 Mus musculus circAID-p-seq Cycloheximide
SRR14602131 PRJNA731473 Mus musculus circAID-p-seq chx_harr
SRR14602133 PRJNA731473 Mus musculus Ribo-Seq untreated
SRR14602134 PRJNA731473 Mus musculus Ribo-Seq untreated
SRR14602135 PRJNA731473 Mus musculus Ribo-Seq untreated
Run Accession Study Accession Scientific Name Cell Line Library Type Treatment GWIPS-viz Trips-Viz RiboCrypt Reads BAM BigWig (F) BigWig (R)

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