Description fromGSE111866: We performed ribosome profiling (RIBO-seq) and transcriptome profiling (RNA-seq) on MCF-7 cells
Raw sequence data were obtainedfrom NCBI FTP directory(SRP135757).
Data from the following samples were processed:
Adapter sequence ATCTCGTATGCCGTCT and AGATCGGAAGAGCACAC 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.,
| MCF7_RIBOseq ||Ribosome profiles from elongating ribosomes Homo sapiens(Lauria, et al. 2018) |
Lauria F, Tebaldi T, Bernabxc3xb2 P, Groen EJN, Gillingwater TH, Viero G (2018) riboWaltz: Optimization of ribosome P-site positioning in ribosome profiling data. .PLoS Comput Biol. 2018 Aug 13;14(8):e1006169. doi: 10.1371/journal.pcbi.1006169. eCollection 2018 Aug.