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Pervasive functional translation of noncanonical human open reading frames (Chen et al. 2020)   (All Initiating Ribosomes (P-site) tracks)

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     Cardiomyocyte ribosome profiling harr  Ribosome profiles from initiating ribosomes (SRR9113063) (Chen et al. 2020)   Schema 
     iPSC ribosome profiling harr  Ribosome profiles from initiating ribosomes (SRR9113062) (Chen et al. 2020)   Schema 

Description

Description fromGSE131650: Paired RNA-seq and ribosome profiling sequencing data for human induced pluripotent stem cells (iPSCs) and iPSC-derived cardiomyocytes, either with or without the translational inhibitor harringtonine. Three replicates are availble for the no drug treatment samples.

Methods

Raw sequence data were obtainedfrom NCBI FTP directory(SRP199285). Data from the following samples were processed:

iPSC_harr Ribosome profiles from initiating ribosomes Homo sapiens(Chen, et al. 2020)
Cardiomyocyte_harr Ribosome profiles from initiating ribosomes Homo sapiens(Chen, et al. 2020)

Adapter sequences had already been removed from reads. 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.,

References

Chen Chen, Andreas-David Brunner, J Zachery Cogan, James K Nuxc3xb1ez, Alexander P Fields, Britt Adamson, Daniel N Itzhak, Jason Y Li, Matthias Mann, Manuel D Leonetti, Jonathan S Weissman (2020) Pervasive functional translation of noncanonical human open reading frames.Ribosome profiling has revealed pervasive but largely uncharacterized translation outside of canonical coding sequences (CDSs). In this work, we exploit a systematic CRISPR-based screening strategy to identify hundreds of noncanonical CDSs that are essential for cellular growth and whose disruption …