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

ERX2430863: 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: 26-Ribo-mRNA-seq, SD-mini rep1

SAMEA104674647 • ERS2276030 • All experiments • All runs

Organism: Saccharomyces cerevisiae

Library:

Name: 26-Ribo-mRNA-seq, SD-mini 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:

Experimental Factor: genotype: wild type genotype

Experimental Factor: compound: none

Experimental Factor: environmental stress: amino acid starvation

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

Run	# of Spots	# of Bases	Size	Published
ERR2382597	4,000,000	540M	288.2Mb	2018-03-20
ERR2382598	4,000,000	540M	266.8Mb	2018-03-20
ERR2382599	4,000,000	540M	284.6Mb	2018-03-20
ERR2382600	4,000,000	540M	265.8Mb	2018-03-20
ERR2382601	4,000,000	540M	284.5Mb	2018-03-20
ERR2382602	4,000,000	540M	274.5Mb	2018-03-20
ERR2382603	4,000,000	540M	286.6Mb	2018-03-20
ERR2382604	4,000,000	540M	280Mb	2018-03-20
ERR2382605	1,485,511	200.5M	100.5Mb	2018-03-20

ID:: 5260637

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