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 profiles from elongating ribosomes Homo sapiens(Park, et al. 2017) |
| RPF_293T_controltreated | Ribosome profiles 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.
An offset of 15 nucleotides was then used to get the corresponding A-site of each read.These tracks contain the uniquely mapping reads.,ReferencesPark 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.
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