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Series GSE93854 Query DataSets for GSE93854
Status Public on Jan 22, 2020
Title Adaptation of human cells to protein synthesis errors
Organism Homo sapiens
Experiment type Expression profiling by array
Summary Protein synthesis is a highly regulated process and maintenance of its fidelity is essential to life. Alterations in the components of the protein synthesis machinery, namely RNAs, aminoacyl-tRNA synthetases (aaRS) or tRNA modifying enzymes, increase the level of protein synthesis errors (PSE), and are associated with several conditions, from cancer to neurodegeneration. Still, the cause-effect mechanisms remain to be elucidated in many conditions. In order to have a global picture of how human cells respond and adapt in culture we created stable HEK293 cell lines that express mutant tRNAs. For this, we modified the anticodon of a human serine transfer RNA (tRNASer), to incorporate the amino acid serine (Ser) at various non-cognate sites and overexpressed the wild type tRNASer to evaluate the effects of tRNA misexpression. DNA microarrays were then performed to identify the transcriptional deregulation induced by PSE of cells in culture at different time points (cells passages).
Overall design HEK293 cells were stably transfected with a plasmid carrying modified tRNAs and five cell lines were created; Mock (empty plasmid, our control), tRNASer(S) (carrying the wild type serine tRNA); tRNASer(A) (carrying a serine tRNA with Alanine anticodon); tRNASer(L) (carrying a serine tRNA with Leucine anticodon) and tRNASer(H) (carrying a serine tRNA with Histidine anticodon). After the creation of stable cell lines (designed passage 1, P1), cells were kept in culture dishes and subcultured ever 3 days using the same dilution (1/6) until passage 30. Three biological replicates of each of the five cell lines was extracted at three time points; P1 (cells passage 1, after the creation of the stable cell lines); P15 (cells passage 15, an intermediary time point) and P30 (cells passage 30, end of evolution experiment). All 45 samples were hybridized in Sure Print G3 Human Gene Expression 8x60k v2 microarrays (Agilent Technologies, Cat.G4851B).
Contributor(s) Varanda AS, Santos M, Soares A, Oliveira C, Santos MS
Citation(s) 31570039
Submission date Jan 19, 2017
Last update date Jan 25, 2020
Contact name Ana Sofia Varanda
Organization name University of Aveiro
Department Health Sciences
Lab iBiMED
Street address Campus Universitário Santiago
City Aveiro
ZIP/Postal code 3810-193
Country Portugal
Platforms (1)
GPL17077 Agilent-039494 SurePrint G3 Human GE v2 8x60K Microarray 039381 (Probe Name version)
Samples (45)
GSM2463946 HEK293_tRNA_emptyplasmid_control_P1_rep1
GSM2463947 HEK293_tRNA_emptyplasmid_control_P1_rep2
GSM2463948 HEK293_tRNA_emptyplasmid_control_P1_rep3
BioProject PRJNA362604

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SOFT formatted family file(s) SOFTHelp
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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE93854_RAW.tar 138.4 Mb (http)(custom) TAR (of TXT)
Processed data included within Sample table

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