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

ERX2430823: Illumina MiSeq sequencing; Genome-Wide Translation Profiling by Ribosome-Bound tRNA Capture
9 ILLUMINA (Illumina MiSeq) runs: 33.5M spots, 4.5G bases, 2.3Gb 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: 18-Ribo-mRNA-seq, 2mM H2O2 rep2, 9 files

SAMEA104674607 • ERS2275990 • All experiments • All runs

Organism: Saccharomyces cerevisiae

Library:

Name: 18-Ribo-mRNA-seq, 2mM H2O2 rep2, 9 files_s

Instrument: Illumina MiSeq

Strategy: RNA-Seq

Source: TRANSCRIPTOMIC

Selection: other

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: 9 runs, 33.5M spots, 4.5G bases, 2.3Gb

Run	# of Spots	# of Bases	Size	Published
ERR2382537	4,000,000	540M	289.1Mb	2018-03-20
ERR2382538	4,000,000	540M	280Mb	2018-03-20
ERR2382539	4,000,000	540M	287.9Mb	2018-03-20
ERR2382540	4,000,000	540M	289.3Mb	2018-03-20
ERR2382541	4,000,000	540M	283.6Mb	2018-03-20
ERR2382542	4,000,000	540M	276.1Mb	2018-03-20
ERR2382543	4,000,000	540M	285.5Mb	2018-03-20
ERR2382544	4,000,000	540M	283.3Mb	2018-03-20
ERR2382545	1,496,055	202M	100.3Mb	2018-03-20

ID:: 5260597

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