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. MethodsRaw 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
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