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mTORC1 Balances Cellular Amino Acid Supply with Demand for Protein Synthesis through Post-transcriptional Control of ATF4. (Park et al. 2017)   (All Elongating Ribosomes (Footprints) tracks)

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     RPF 293T controltreated  Ribosome coverage data from elongating ribosomes (SRR5413155, SRR5413156) (Park et al. 2017)   Schema 
     RPF 293T torin 1treated  Ribosome coverage data from elongating ribosomes (SRR5413158, SRR5413157) (Park et al. 2017)   Schema 

Description

Description fromGSE97384: RNA-seq analysis of wild-type and ATF4-null HEK293T cells treated with Torin 1 or tunicamycin for 6 h, and ribosome profiling analysis of HEK293T cells treated with Torin 1 for 24 h.

Methods

Raw sequence data were obtainedfrom NCBI FTP directory(SRP103009). Data from the following samples were processed:

RPF_293T_torin_1treated Ribosome coverage data from elongating ribosomes Homo sapiens(Park, et al. 2017)
RPF_293T_controltreated Ribosome coverage data from elongating ribosomes Homo sapiens(Park, et al. 2017)

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 25nt were discarded. These tracks contain the uniquely mapping reads.,

References

Park Y, Reyna-Neyra A, Philippe L, Thoreen CC (2017) mTORC1 Balances Cellular Amino Acid Supply with Demand for Protein Synthesis through Post-transcriptional Control of ATF4. .Cell Rep. 2017 May 9;19(6):1083-1090. doi: 10.1016/j.celrep.2017.04.042.