HCT116: Fijalkowska17 Track Settings
 
eIF1 modulates the recognition of suboptimal translation initiation sites and steers gene expression via uORFs. (Fijalkowska et al. 2017)   (All Elongating Ribosomes (A-site) tracks)

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     Ribosome profiling of control HCT116 cells treated with cycloheximide  Ribosome profiles from elongating ribosomes (SRR4293696) (Fijalkowska et al. 2017)   Schema 
     Ribosome profiling of HCT116 cells upon eIF1 knockdown treated with cycloheximide  Ribosome profiles from elongating ribosomes (SRR4293694) (Fijalkowska et al. 2017)   Schema 

Description

Description fromGSE87328: Ribosome profiling and mRNA sequening of human HCT116 cells upon eIF1 knockdown and in control conditions.

Methods

Raw sequence data were obtainedfrom NCBI FTP directory(SRP090415). Data from the following samples were processed:

Ribosome_profiling_of_control_HCT116_cells_treated_with_cycloheximide Ribosome profiles from elongating ribosomes Homo sapiens(Fijalkowska, et al. 2017)
Ribosome_profiling_of_HCT116_cells_upon_eIF1_knockdown_treated_with_cycloheximide Ribosome profiles from elongating ribosomes Homo sapiens(Fijalkowska, et al. 2017)

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 15 nucleotides was then used to get the corresponding A-site of each read.These tracks contain the uniquely mapping reads.,

References

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.