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_no_drug_treatment | Ribosome profiles from elongating ribosomes Homo sapiens(Chen, et al. 2020) |
| Cardiomyocyte_no_drug_treatment | Ribosome profiles from elongating 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 15 nucleotides was then used to get the corresponding A-site of each read.These tracks contain the uniquely mapping reads.,ReferencesChen 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 …
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