Del et al. 2022 (PRJNA731473)
General Details
Title | Phospho-RNA sequencing with CircAID-p-seq |
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Organism | |
Number of Samples | 12 |
Release Date | 2021/05/20 00:00 |
Sequencing Types | |
Protocol Details |
Study Links
GWIPS-viz | Trips-Viz | RiboCrypt |
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Visit RiboCrypt |
Repository Details
SRA | SRP320668 |
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ENA | SRP320668 |
GEO | |
BioProject | PRJNA731473 |
Publication
Title | |
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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) | ||
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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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