MCF7: LoayzaPuch16 Track Settings
 
Tumour-specific proline vulnerability uncovered by differential ribosome codon reading. (LoayzaPuch et al. 2016)   (All Elongating Ribosomes (Footprints) tracks)

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     MCF7 IP150 RP  Ribosome coverage data from elongating ribosomes (SRR2873688) (LoayzaPuch et al. 2016)   Schema 
     MCF7 IP50 RP  Ribosome coverage data from elongating ribosomes (SRR2873687) (LoayzaPuch et al. 2016)   Schema 
     MCF7 SG RP  Ribosome coverage data from elongating ribosomes (SRR2873686) (LoayzaPuch et al. 2016)   Schema 

Description

Description fromGSE74511: 1 sucrose gradient sample, 2 immunoprecipitation samples in two concentrations of beads

Methods

Raw sequence data were obtainedfrom NCBI FTP directory(SRP065530). Data from the following samples were processed:

MCF7_SG_RP Ribosome coverage data from elongating ribosomes Homo sapiens(LoayzaPuch, et al. 2016)
MCF7_IP50_RP Ribosome coverage data from elongating ribosomes Homo sapiens(LoayzaPuch, et al. 2016)
MCF7_IP150_RP Ribosome coverage data from elongating ribosomes Homo sapiens(LoayzaPuch, et al. 2016)

Adapter sequence TGGAATTCTCGGGTGCC was removed from reads using Cutadapt An alignment to ribosomal RNA was performed using Bowtie, and aligning reads were discarded. An alignment to the hg38 genome assembly was performed using Bowtie, and reads below 25 nt were discarded. These tracks contain the uniquely mapping reads.,

References

Loayza-Puch F, Rooijers K, Buil LC, Zijlstra J, Oude Vrielink JF, Lopes R, Ugalde AP, van Breugel P, Hofland I, Wesseling J, van Tellingen O, Bex A, Agami R (2016) Tumour-specific proline vulnerability uncovered by differential ribosome codon reading. .Nature. 2016 Feb 25;530(7591):490-4. doi: 10.1038/nature16982. Epub 2016 Feb 15. Research Support, Non-U.S. Govt