Description

Description fromGSE114794: Ribosome occupancy and mRNAs levels in transformed and non-transformed cells cultured for i) 30 minutes under complete (Ctrl) or glutamine-free (NoQ) DMEM medium, and ii) 4 hours under complete (Ctrl), glucose-free (NoG), glutamine-free (NoQ), cysteine/cystine-free (NoCys) or leucine, isoleucine, valine (NoBCAA)-free DMEM medium. The translation efficiency (TE) was calculated as the log2 ratio of RPKM measured by ribosome profiling over RPKM measured by RNA-seq. Differences in ribosome occupancy (RO) and TE between the metabolic stress condition and the reference sample (either TAM or EtOH cells grown in complete DMEM) were used to examine the transcriptional and translational changes, respectively. The ribosome profiling and RNA sequencing experiments were performed in duplicate with the exception of RNA-seq at 30 minutes (single experiments), ribosome profiling in cysteine/cystine-deprived EtOH cells (triplicate experiments), and the Torin1 ribosome profiling and RNA-seq (single experiment). The complete dataset comprises the raw (.fastq) and processed (RPKM) files of all 57 high-throughput sequenced samples.

Methods

Raw sequence data were obtainedfrom NCBI FTP directory(SRP148767). Data from the following samples were processed:

References

Gameiro PA, Struhl K (2018) Nutrient Deprivation Elicits a Transcriptional and Translational Inflammatory Response Coupled to Decreased Protein Synthesis. .Cell Rep. 2018 Aug 7;24(6):1415-1424. doi: 10.1016/j.celrep.2018.07.021.