Illumina MiSeq sequencing; Genome-Wide Translation Profiling by Ribos... - SRA

ERX2430828: Illumina MiSeq sequencing; Genome-Wide Translation Profiling by Ribosome-Bound tRNA Capture
3 ILLUMINA (Illumina MiSeq) runs: 9.2M spots, 1.2G bases, 513.1Mb downloads

Design: Genome-Wide Translation Profiling by Ribosome-Bound tRNA Capture

Submitted by: RIKEN Brain Science Institute

Study: Genome-Wide Translation Profiling by Ribosome-Bound tRNA Capture

PRJEB25491 • ERP107411 • All experiments • All runs

show Abstracthide Abstract

In the ribosome complex, tRNA is a critical element of mRNA translation. We reported a new technology for profiling ribosome-embedded tRNAs and their modifications. With the method, we generated a comprehensive survey of the quanity and quality of intra-ribosomal tRNAs (Ribo-tRNA-seq). Ribo-tRNA-seq can provide new insights on translation control mechanism in diverse biological contexts.

Sample: 41-mRNA-seq, 2mM H2O2 rep3

SAMEA104674612 • ERS2275995 • All experiments • All runs

Organism: Saccharomyces cerevisiae

Library:

Name: 41-mRNA-seq, 2mM H2O2 rep3_s

Instrument: Illumina MiSeq

Strategy: RNA-Seq

Source: TRANSCRIPTOMIC

Selection: Oligo-dT

Layout: SINGLE

Construction protocol: Wild-type, BY4741, Yeast cells were treated with or without stresses before a 2-min treatment of cycloheximide. Cells were quickly frozen in liquid nitrogen for at least 5 mins and fragmented with metal beads under frozen condition. The yeast cell was cultured in YPD medium at 30 degree The treatment of the stresses was 1 hour, except amino acid starvation, SD-mini, which the treatment time was 20 mins. 3AT means 3-Amino-1,2,4-triazole, is a competitive inhibitor of the product of the HIS3 gene. The treatment is 100mM for 1hr in histidine depletion medium. The final concentration of 4EGI-1 treatment is 100uM for 1hr. Total RNA was extracted by phenol/chloroform method. tRNA molecular and mRNA fragments were recycling for library generation. Check the details of the protocol in Chen and Tanaka, Cell Reports 2018.

Experiment attributes: (show all 4 attributes...) (hide...)

Experimental Factor: genotype: wild type genotype

Experimental Factor: compound: hydrogen peroxide

Experimental Factor: dose: 2

Experimental Factor: environmental stress: none

Runs: 3 runs, 9.2M spots, 1.2G bases, 513.1Mb

Run	# of Spots	# of Bases	Size	Published
ERR2382553	4,000,000	544M	223.3Mb	2018-03-20
ERR2382554	4,000,000	544M	223.2Mb	2018-03-20
ERR2382555	1,186,852	161.4M	66.6Mb	2018-03-20

ID:: 5260602

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