Myeloma:Wiita 2013 Track Settings
 
Global cellular response to chemotherapy-induced apoptosis. (Wiita et al. 2013)   (All Elongating Ribosomes (A-site) tracks)

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     0h MM1S untreated ribosome footprint  Ribosome Profiles of elongating ribosomes from Homo sapiens (Wiita et al. 2013)   Schema 
     1  Ribosome Profiles of elongating ribosomes from Homo sapiens (Wiita et al. 2013)   Schema 
     12h MM1S 20nM bortezomib ribosome footprint  Ribosome Profiles of elongating ribosomes from Homo sapiens (Wiita et al. 2013)   Schema 
     3h MM1S 20nM bortezomib ribosome footprint  Ribosome Profiles of elongating ribosomes from Homo sapiens (Wiita et al. 2013)   Schema 
     6h MM1S 20nM bortezomib ribosome footprint  Ribosome Profiles of elongating ribosomes from Homo sapiens (Wiita et al. 2013)   Schema 
     9h MM1S 20nM bortezomib ribosome footprint  Ribosome Profiles of elongating ribosomes from Homo sapiens (Wiita et al. 2013)   Schema 
    

Description

We examined MM1.S myeloma cells exposed to 20 nM bortezomib across a time course with independent samples of poly(A) mRNA and ribosome footprints isolated at each of six time points (0h (untreated), 1.5h, 3h, 6h, 9h, 12h). Sequencing was performed on a Illumina HiSeq 2000 with single-end.

Methods

Raw sequence data were obtained from NCBI FTP directory(SRP027015). Data from the following samples were processed:

12h_MM1S_20nM_bortezomib_ribosome_footprint Ribosome profiling data from Homo sapiens(Wiita, et al. 2013)
0h_MM1S_untreated_ribosome_footprint Ribosome profiling data from Homo sapiens(Wiita, et al. 2013)
6h_MM1S_20nM_bortezomib_ribosome_footprint Ribosome profiling data from Homo sapiens(Wiita, et al. 2013)
3h_MM1S_20nM_bortezomib_ribosome_footprint Ribosome profiling data from Homo sapiens(Wiita, et al. 2013)
9h_MM1S_20nM_bortezomib_ribosome_footprint Ribosome profiling data from Homo sapiens(Wiita, et al. 2013)
1 Ribosome profiling data from Homo sapiens(Wiita, et al. 2013)

Adapter sequences had already been removed from reads. 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 these tracks contains the uniquely mapping reads.An offset of 15 nucleotides was then used to get the corresponding A-site of each read.

References

Wiita AP, Ziv E, Wiita PJ, Urisman A, Julien O, Burlingame AL, Weissman JS, Wells JA (2013) Global cellular response to chemotherapy-induced apoptosis. . Elife. 2013 Oct 29;2:e01236. doi: 10.7554/eLife.01236. Research Support, N.I.H., Extramural; Research Support, Non-U.S. Gov't