Description Ribosome profiles of elongating ribosomes from normal and neoplastic human brain tissue (Gonzalez et al. 2014) Methods
Raw sequence data were obtained from NCBI SRA database (Series GSE51424). Data from the following samples were processed:
| GSM1495244 | Normal Human RiboProfiling A |
| GSM1495245 | Normal Human RiboProfiling B |
| GSM1495246 | Normal Human RiboProfiling C |
| GSM1495247 | Tumour Human RiboProfiling A |
| GSM1495248 | Tumour Human RiboProfiling B |
Cutadapt was used to trim the adaptor sequence "CTGTAGGCACCAT" from reads, after which reads below 25 nucleotides in length were discarded. An alignment to ribosomal RNA was then performed using Bowtie, and aligning reads were discarded. Finally, an alignment to the hg19 genome assembly was performed using Bowtie, and this track contains the uniquely mapping reads that align to the A-site (using an offset of 15nt).
References
Gonzalez, C., Sims, J., Hornstein, N., Mela, A., Garcia, F., Lei, L., Gass, D., Amendolara, B., Bruce, J., Canoll, P. and Sims, P. (2014). Ribosome Profiling Reveals a Cell-Type-Specific Translational Landscape in Brain Tumors. Journal of Neuroscience, 34(33), pp.10924-10936.
|
|