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

ERX2430803: Illumina MiSeq sequencing; Genome-Wide Translation Profiling by Ribosome-Bound tRNA Capture
7 ILLUMINA (Illumina MiSeq) runs: 26.7M spots, 3.6G bases, 1.4Gb 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: 38-Ribo-mRNA-seq, 0.5mM H2O2 rep1

SAMEA104674587 • ERS2275970 • All experiments • All runs

Organism: Saccharomyces cerevisiae

Library:

Name: 38-Ribo-mRNA-seq, 0.5mM H2O2 rep1_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: 0.5

Experimental Factor: environmental stress: none

Runs: 7 runs, 26.7M spots, 3.6G bases, 1.4Gb

Run	# of Spots	# of Bases	Size	Published
ERR2382507	4,000,000	544M	218.5Mb	2018-03-20
ERR2382508	4,000,000	544M	223.2Mb	2018-03-20
ERR2382509	4,000,000	544M	219Mb	2018-03-20
ERR2382510	4,000,000	544M	221.6Mb	2018-03-20
ERR2382511	4,000,000	544M	223.9Mb	2018-03-20
ERR2382512	4,000,000	544M	218.1Mb	2018-03-20
ERR2382513	2,663,103	362.2M	148.8Mb	2018-03-20

ID:: 5260577

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