Datasets

Title	Testing conditions for ribosome profiling in Drosophila melanogaster
Organism
Number of Samples	5
Release Date	2021/02/09 00:00
Sequencing Types
Protocol Details

Title
Authors	Douka K,Agapiou M,Birds I,Aspden JL
Journal	Frontiers in molecular biosciences
Publication Date	2021
Abstract	Our understanding of mRNA translation and its regulation has been transformed by the development of ribosome profiling. This approach relies upon RNase footprinting of translating ribosomes in a precise manner to generate an accurate snapshot of ribosome positions with nucleotide resolution. Here we tested a variety of conditions, which contribute to the preciseness of ribosome footprinting and therefore the success of ribosome profiling. We found that NaCl concentration, RNaseI source, RNaseI amount, and temperature of footprinting all contributed to the quality of ribosome footprinting in human neuroblastoma SH-SY5Y cells. These ideal conditions for footprinting also improved footprint quality when used with Drosophila melanogaster S2 cells. Footprinting under the same conditions generated different footprints sizes and framing patterns in human and D. melanogaster cells. We also found that treatment of S2 cells with cycloheximide prior to footprinting impacted the distribution of footprints across ORFs, without affecting overall read length distribution and framing pattern, as previously found in other organisms. Together our results indicate that a variety of factors affect ribosome footprint quality and the nature of precise footprinting varies across species. Copyright © 2022 Douka, Agapiou, Birds and Aspden.
PMC	PMC8822167
PMID	35145996
DOI

Douka et al. 2022 (PRJNA700841)