Hsu et al. 2016 (PRJNA321201)

General Details

Title Buffer composition affects ribosome footprint precision in Arabidopsis root and shoot
Organism
Number of Samples 8
Release Date 2016/05/10 00:00
Sequencing Types
Protocol Details

Study Links

Repository Details

SRA SRP074779
ENA SRP074779
GEO GSE81295
BioProject PRJNA321201

Publication

Title
Authors Hsu PY, Calviello L, Wu HL, Li FW, Rothfels CJ, Ohler U, Benfey PN
Journal Proceedings of the National Academy of Sciences of the United States of America
Publication Date 2016 Nov 8
Abstract Deep sequencing of ribosome footprints (ribosome profiling) maps and quantifies mRNA translation. Because ribosomes decode mRNA every 3 nt, the periodic property of ribosome footprints could be used to identify novel translated ORFs. However, due to the limited resolution of existing methods, the 3-nt periodicity is observed mostly in a global analysis, but not in individual transcripts. Here, we report a protocol applied to Arabidopsis that maps over 90% of the footprints to the main reading frame and thus offers super-resolution profiles for individual transcripts to precisely define translated regions. The resulting data not only support many annotated and predicted noncanonical translation events but also uncover small ORFs in annotated noncoding RNAs and pseudogenes. A substantial number of these unannotated ORFs are evolutionarily conserved, and some produce stable proteins. Thus, our study provides a valuable resource for plant genomics and an efficient optimization strategy for ribosome profiling in other organisms.
PMC PMC5111709
PMID 27791167
DOI
Run Accession Study Accession Scientific Name Cell Line Library Type Treatment GWIPS-viz Trips-Viz Reads BAM BigWig (F) BigWig (R)
SRR3495992 PRJNA321201 Arabidopsis thaliana 0.0 Ribo-Seq 0.0
SRR3495993 PRJNA321201 Arabidopsis thaliana 0.0 Ribo-Seq 0.0
SRR3495994 PRJNA321201 Arabidopsis thaliana 0.0 Ribo-Seq 0.0
SRR3495995 PRJNA321201 Arabidopsis thaliana 0.0 Ribo-Seq 0.0
SRR3495996 PRJNA321201 Arabidopsis thaliana 0.0 Ribo-Seq 0.0
SRR3495997 PRJNA321201 Arabidopsis thaliana 0.0 Ribo-Seq 0.0
SRR3495998 PRJNA321201 Arabidopsis thaliana 0.0 Ribo-Seq 0.0
SRR3495999 PRJNA321201 Arabidopsis thaliana 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)

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