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Selective Translation Complex Profiling Reveals Staged Initiation and Co-translational Assembly of Initiation Factor Complexes (Wagner et al. 2020)   (All Small Ribosomal Subunits (Footprints) tracks)

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     human eIF3b bound 40S  Ribosome profiles from elongating ribosomes (SRR10315322) (Wagner et al. 2020)   Schema 
     human unselected 40S  Ribosome profiles from elongating ribosomes (SRR10315321, SRR10315320) (Wagner et al. 2020)   Schema 

Description

Description fromGSE139131: 2 replicates for 40S and 80S TCP-seq, 1 replicate for eIF3b bound 40S Sel-TCP-seq and mRNA

Methods

Raw sequence data were obtainedfrom NCBI FTP directory(SRP226389). Data from the following samples were processed:

human_eIF3b_bound_40S Ribosome profiles from elongating ribosomes Homo sapiens(Wagner, et al. 2020)
human_unselected_80S Ribosome profiles from elongating ribosomes Homo sapiens(Wagner, et al. 2020)
human_unselected_40S Ribosome profiles from elongating ribosomes Homo sapiens(Wagner, et al. 2020)

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 18 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

Wagner S., Herrmannovxc3xa1 A., Hronovxc3xa1 V., Gunixc5xa1ovxc3xa1 S., Sen N.D., Hannan R.D., Hinnebusch A.G., Shirokikh N.E., Preiss T., Valxc3xa1xc5xa1ek L.S. (2020) Selective Translation Complex Profiling Reveals Staged Initiation and Co-translational Assembly of Initiation Factor Complexes.Translational control targeting the initiation phase is central to the regulation of gene expression. Understanding all of its aspects requires substantial technological advancements. Here we modified yeast translation complex profile sequencing (TCP-seq), related to ribosome profiling, and adapted …