Latif et al. 2015 (PRJNA269272)

General Details

Title Ribosome profiling of E. coli K-12 MG1655 MOPS rich media with 0.2% glucose
Organism Escherichia coli str. K-12 substr. MG1655
Number of Samples 2
Release Date 2014/12/04 00:00
Sequencing Types
Protocol Details

Study Links

Repository Details

SRA SRP050548
ENA SRP050548
GEO
BioProject PRJNA269272

Publication

Title
Authors Latif H,Szubin R,Tan J,Brunk E,Lechner A,Zengler K,Palsson BO
Journal BioTechniques
Publication Date 2015 Jun
Abstract Ribosome profiling is a powerful tool for characterizing in vivo protein translation at the genome scale, with multiple applications ranging from detailed molecular mechanisms to systems-level predictive modeling. Though highly effective, this intricate technique has yet to become widely used in the microbial research community. Here we present a streamlined ribosome profiling protocol with reduced barriers to entry for microbial characterization studies. Our approach provides simplified alternatives during harvest, lysis, and recovery of monosomes and also eliminates several time-consuming steps, in particular size-selection steps during library construction. Furthermore, the abundance of rRNAs and tRNAs in the final library is drastically reduced. Our streamlined workflow enables greater throughput, cuts the time from harvest to the final library in half (down to 3-4 days), and generates a high fraction of informative reads, all while retaining the high quality standards of the existing protocol.
PMC
PMID 26054770
DOI
Run Accession Study Accession Scientific Name Cell Line Library Type Treatment GWIPS-viz Trips-Viz RiboCrypt Reads BAM BigWig (F) BigWig (R)
SRR1693437 PRJNA269272 Escherichia coli
SRR1693438 PRJNA269272 Escherichia coli
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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