Dataset features

Specifications


Application: RNA-seq analysis
Number of samples: 8
Release date: Jul 18 2015
Last update date: Nov 5 2015
Access: Public
Dataset link Codon usage influences the local rate of translation elongation to regulate co-translational protein folding

Experimental Protocol


For sample 1 and 2, ribosome-protected fragments (RPF) and mRNA sequencing from WT Neurospora transcriptome were extracted to examine the residence time of each codon to understand the decoding rate. For sample 3 and 4, RPFs of the fully optimized (OPT) Firefly luciferase as well as the chimera [(2-423)OPT-(424-550)WT] Firefly luciferase, both of which were individually targeted to the his3 locus, were extracted to monitor the codon-regulated translational kinetics in vivo. For sample 5-8, RPFs were extracted from in vitro translation reactions covering the OPT construct and three chimera construts: N-OP, (2-223)OPT-(224-550)WT; M-OP, (2-223)WT-(224-423)OPT-(424-550)WT; C-OP (2-423)WT-(424-550)OPT. The RPF reads were compared to each other to monitor the translational kinetics in vitro.

Repositories


GEO

GSE71032

ENA

SRP061262

BioProject

PRJNA290152

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Contact


Yunkun Dang