Description Description fromGSE55195: Ribosome profiling of sodium arsenite treated cells for examination of translational response to induction of eIF2 phosphoylation
Methods Raw sequence data were obtainedfrom NCBI FTP directory(SRP038695).
Data from the following samples were processed:
| Arsenite_riboseq | Ribosome profiles from elongating ribosomes Homo sapiens(Andreev, et al. 2015) |
| Control_riboseq | Ribosome profiles from elongating ribosomes Homo sapiens(Andreev, et al. 2015) |
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.,ReferencesAndreev DE, "OConnor PB", Fahey C, Kenny EM, Terenin IM, Dmitriev SE, Cormican P, Morris DW, Shatsky IN, Baranov PV (2015) Translation of 5' leaders is pervasive in genes resistant to eIF2 repression. .Elife. 2015 Jan 26;4:e03971. doi: 10.7554/eLife.03971. Research Support, Non-U.S. Govt
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