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.,ReferencesWagner 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 …
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