GWIPS-viz Riboseq Track Settings
 
Ribosome Profiling from GWIPS-viz   (All Expression tracks)

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Data last updated: 2016-02-11 09:48:20

Description

Ribosome profiling (ribo-seq) is a technique that takes advantage of NGS technology to sequence ribosome-protected mRNA fragments and consequently allows the locations of translating ribosomes to be determined at the entire transcriptome level (Ingolia et al., 2009).

For a more detailed description of the protocol, see Ingolia et al. (2012). For reviews on this technique and its applications, please refer to Ingolia (2014) and Michel et al. (2013).

This track displays cumulative ribo-seq data obtained from human cells under different conditions and can be used for the exploration of human genomic loci that are being translated. The values on the y-axis represent the number of ribosome footprint sequence reads at a given position. As of February 2016, the track contains data from 9 studies (see References section for details). Further details about the aggregated track and additional ribo-seq data from these and other studies including data obtained from other organisms can be found at the specialized ribo-seq browser GWIPS-viz.

Methods

For each study used to generate this track, raw fastq files were downloaded from a repository (e.g., NCBI GEO datasets). Cutadapt was used to trim the relevant adapter sequence from the reads, after which reads below 25 nt in length were discarded. The trimmed reads were aligned to ribosomal RNA using Bowtie and aligning reads were discarded. The remaining reads were then aligned to the hg38 (GRCh38) genome assembly using Bowtie. An offset of 15 nt (to infer the position of the A-site) was added to the most 5' nucleotide coordinate of each uniquely-mapped read.

The alignment files from each of the included studies were merged to generate this aggregate track.

See individual studies at GWIPS-viz for a full description of the methods of data acquisition and processing.

Credits

Thanks to Audrey Michel, Stephen Kiniry and GWIPS-viz for providing the data for this track. If you wish to cite this track, please reference:

Michel AM, Fox G, M Kiran A, De Bo C, O'Connor PB, Heaphy SM, Mullan JP, Donohue CA, Higgins DG, Baranov PV. GWIPS-viz: development of a ribo-seq genome browser. Nucleic Acids Res. 2014 Jan;42(Database issue):D859-64. PMID: 24185699; PMC: PMC3965066

References

Data

Battle A, Khan Z, Wang SH, Mitrano A, Ford MJ, Pritchard JK, Gilad Y. Impact of regulatory variation from RNA to protein. Science. 2015 Feb 6;347(6222):664-7. PMID: 25657249; PMC: PMC4507520

Cenik C, Cenik ES, Byeon GW, Grubert F, Candille SI, Spacek D, Alsallakh B, Tilgner H, Araya CL, Tang H et al. Integrative analysis of RNA, translation and protein levels reveals distinct regulatory variation across humans. Genome Res. 2015 Nov;25(11):1610-21. PMID: 26297486; PMC: PMC4617958

Elkon R, Loayza-Puch F, Korkmaz G, Lopes R, van Breugel PC, Bleijerveld OB, Altelaar AM, Wolf E, Lorenzin F, Eilers M et al. Myc coordinates transcription and translation to enhance transformation and suppress invasiveness. EMBO Rep. 2015 Dec;16(12):1723-36. PMID: 26538417; PMC: PMC4687422

Jang C, Lahens NF, Hogenesch JB, Sehgal A. Ribosome profiling reveals an important role for translational control in circadian gene expression. Genome Res 2015 Dec;25(12):1836-47. PMID: 26338483; PMC: PMC4665005

Ji Z, Song R, Regev A, Struhl K. Many lncRNAs, 5'UTRs, and pseudogenes are translated and some are likely to express functional proteins. Elife. 2015 Dec 19;4. PMID: 26687005; PMC: PMC4739776

Sidrauski C, McGeachy AM, Ingolia NT, Walter P. The small molecule ISRIB reverses the effects of eIF2α phosphorylation on translation and stress granule assembly. Elife. 2015 Feb 26;4. PMID: 25719440; PMC: PMC4341466

Tanenbaum ME, Stern-Ginossar N, Weissman JS, Vale RD. Regulation of mRNA translation during mitosis. Elife. 2015 Aug 25;4. PMID: 26305499; PMC: PMC4548207

Tirosh O, Cohen Y, Shitrit A, Shani O, Le-Trilling VT, Trilling M, Friedlander G, Tanenbaum M, Stern-Ginossar N. The transcription and translation landscapes during human cytomegalovirus infection reveal novel host-pathogen interactions. PLoS Pathog. 2015 Nov 24;11(11):e1005288. PMID: 26599541; PMC: PMC4658056

Werner A, Iwasaki S, McGourty CA, Medina-Ruiz S, Teerikorpi N, Fedrigo I, Ingolia NT, Rape M. Cell fate determination by ubiquitin-dependent regulation of translation. Nature. 2015 Sep 24;525(7570):523-7. PMID: 26399832; PMC: PMC4602398

Protocol/Technique

Ingolia NT. Ribosome profiling: new views of translation, from single codons to genome scale. Nat Rev Genet. 2014 Mar;15(3):205-13. PMID: 24468696

Ingolia NT, Brar GA, Rouskin S, McGeachy AM, Weissman JS. The ribosome profiling strategy for monitoring translation in vivo by deep sequencing of ribosome- protected mRNA fragments. Nat Protoc. 2012 Jul 26;7(8):1534-50. PMID: 22836135; PMC: PMC3535016

Ingolia NT, Ghaemmaghami S, Newman JR, Weissman JS. Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling. Science. 2009 Apr 10;324(5924):218-23. PMID: 19213877; PMC: PMC2746483

Michel AM, Baranov PV. Ribosome profiling: a Hi-Def monitor for protein synthesis at the genome-wide scale. Wiley Interdiscip Rev RNA. 2013 Sep-Oct;4(5):473-90. PMID: 23696005; PMC: PMC3823065