Description fromGSE87328: Ribosome profiling and mRNA sequening of human HCT116 cells upon eIF1 knockdown and in control conditions.
Raw sequence data were obtainedfrom NCBI FTP directory(SRP090415).
Data from the following samples were processed:
Adapter sequence CTGTAGGCACCATCAAT 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 12 nucleotides was then used to get the corresponding P-site of each read.These tracks contain the uniquely mapping reads.,
| Ribosome_profiling_of_control_HCT116_cells_lactimidomycin ||Ribosome profiles from initiating ribosomes Homo sapiens(Fijalkowska, et al. 2017) |
| Ribosome_profiling_of_HCT116_cells_upon_eIF1_knockdown_lactimidomycin ||Ribosome profiles from initiating ribosomes Homo sapiens(Fijalkowska, et al. 2017) |
Fijalkowska D, Verbruggen S, Ndah E, Jonckheere V, Menschaert G, Van Damme P (2017) eIF1 modulates the recognition of suboptimal translation initiation sites and steers gene expression via uORFs. .Nucleic Acids Res. 2017 Jul 27;45(13):7997-8013. doi: 10.1093/nar/gkx469.