HEK: Andreev15 Track Settings
 
Translation of 5' leaders is pervasive in genes resistant to eIF2 repression. (Andreev et al. 2015)   (All Elongating Ribosomes (Footprints) tracks)

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     Arsenite riboseq  Ribosome coverage data from elongating ribosomes (SRR1173914, SRR1173907, SRR1173913) (Andreev et al. 2015)   Schema 
     Control riboseq  Ribosome coverage data from elongating ribosomes (SRR1173905, SRR1173910, SRR1173909) (Andreev et al. 2015)   Schema 

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 coverage data from elongating ribosomes Homo sapiens(Andreev, et al. 2015)
Control_riboseq Ribosome coverage data 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. These tracks contain the uniquely mapping reads.,

References

Andreev 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