Description Description fromGSE70802: Cells expressing either DDX3 WT or R534H variant were treated with or without sodium arsenite and lysed in the presence of cyclohexime. Ribosome-protected mRNA fragments after RNase I treatment were recovered and sequenced.
Methods Raw sequence data were obtainedfrom NCBI FTP directory(SRP060676).
Data from the following samples were processed:
| DDX3_WT_ribosome_profiling | Ribosome profiles from elongating ribosomes Homo sapiens(Oh, et al. 2016) |
| DDX3_WT_ribosome_profiling_with_sodium_arsenite | Ribosome profiles from elongating ribosomes Homo sapiens(Oh, et al. 2016) |
| Rluc_control_ribosome_profiling | Ribosome profiles from elongating ribosomes Homo sapiens(Oh, et al. 2016) |
| DDX3_R534H_ribosome_profiling_with_sodium_arsenite | Ribosome profiles from elongating ribosomes Homo sapiens(Oh, et al. 2016) |
| DDX3_R534H_ribosome_profiling | Ribosome profiles from elongating ribosomes Homo sapiens(Oh, et al. 2016) |
| Rluc_control_ribosome_profiling_with_sodium_arsenite | Ribosome profiles from elongating ribosomes Homo sapiens(Oh, et al. 2016) |
Adapter sequence AGATCGGAAGAGCACAC and CAGATCGGAAGAGCACA 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.
An offset of 15 nucleotides was then used to get the corresponding A-site of each read.These tracks contain the uniquely mapping reads.,ReferencesOh S, Flynn RA, Floor SN, Purzner J, Martin L, Do BT, Schubert S, Vaka D, Morrissy S, Li Y, Kool M, Hovestadt V, Jones DT, Northcott PA, Risch T, Warnatz HJ, Yaspo ML, Adams CM, Leib RD, Breese M, Marra MA, Malkin D, Lichter P, Doudna JA, Pfister SM, Taylor MD, Chang HY, Cho YJ (2016) Medulloblastoma-associated DDX3 variant selectively alters the translational response to stress. .Oncotarget. 2016 May 10;7(19):28169-82. doi: 10.18632/oncotarget.8612.
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