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TranscriptomicsWide-scale analysis of alternative polyadenylation (APA) associated with proliferation and transformation using 3'-Seq
We mapped and quantified poly(A) sites in BJ and MCF10A cells under proliferative, arrested and transformed states Two human cell lines (BJ and MCF10A) examined under proliferative, arrested and transformed states
ORGANISM(S): Homo sapiens 
2012-06-18 | E-GEOD-33592 | biostudies-arrayexpress
ProteomicsOncogene-dependent sloppiness in mRNA translation
mRNA translation is a highly conserved and tightly-controlled mechanism for protein synthesis. However, despite protein quality control mechanisms, amino-acid shortage in melanoma induces aberrant proteins by ribosomal frameshifting. The extent and the underlying mechanisms related to this phenomeno...
ORGANISM(S): Homo sapiens (Human) 
2021-09-28 | PXD022707 | Pride
Ribosomal frameshifting Cancer Tryptophan depletion Immunoprecipitation Human Translation Lc-ms/ms 
ProteomicsAnti-tumor immunity induces the presentation of aberrant peptides in melanoma
Many tumors escape by activating multiple cellular pathways that induce immunosuppression. One pivotal immune-suppressive mechanism is the production of tryptophan metabolites along the kynurenine pathway by IFNγ-induced IDO1 enzyme production 4-8. Phase III clinical trials using chemical inhibition...
ORGANISM(S): Homo sapiens (Human) 
2020-12-04 | PXD020224 | Pride
Immune recognition Proteomics Melanoma Tryptophan depletion Immunopeptidomics Aberrant peptides Lc-ms/ms 
TranscriptomicsTranscriptome-profiling (RNA-seq) and Ribosome-profiling (Ribo-seq) of BJ cells treated with Nutlin-3a, an MDM2 inhibitor, which induces p53.
We applied in parallel RNA-Seq and Ribosome-profiling analyses to immortalized human primary BJ fibroblast cells in which p53 was induced by Nutlin-3a RNA-seq, using Illumina HiSeq 2000, was applied to BJ cells treated with Nutlin-3a, at 5 timepoints: 0, 2, 4, 6, 19 hrs Ribosome profiling was applie...
ORGANISM(S): Homo sapiens 
2013-06-01 | E-GEOD-45785 | biostudies-arrayexpress
ProteomicsTryptophan depletion provokes the production and presentation of in-frame tryptophan to phenylalanine substitutions
Activated T cells secrete interferon-gamma (IFN) that triggers an intra-cellular tryptophan shortage through the activation of the Indoleamine 2,3-Dioxygenase 1 (IDO1) enzyme. Surprisingly, we here show that despite tryptophan depletion, in-frame protein synthesis bypassing tryptophan codons contin...
ORGANISM(S): Homo sapiens (Human) 
2021-12-23 | PXD028921 | Pride
Cancer Tryptophan depletion Amino acid substitution Lc-ms/ms 
TranscriptomicsGenome-wide maps of polyadenylation sites in control and PABPN1kd cells
We applied deep-sequencing based technique, 3'-Seq, to obtain comprehansive maps of poly-A sites in human cells. 3'-Seq was applied to two cell lines (U2OS and RPE-1), in control and PABPN1 knockdown cells Examination of poly-A sites in control and PABPN1kd cells (in two different cell lines)
ORGANISM(S): Homo sapiens 
2012-04-15 | E-GEOD-27452 | biostudies-arrayexpress
TranscriptomicsGenome-wide maps of polyadenylation sites in OPMD-model and control mice
We applied deep-sequencing based technique, 3'-Seq, to obtain comprehansive maps of poly-A sites in OPMD-model mice expressing trePABPN1(A17) mutant and control mice Examination of poly-A sites in control and OPMD-model mice (in two ages: 20 weeks and 12 months)
ORGANISM(S): Mus musculus 
2012-04-15 | E-GEOD-32302 | biostudies-arrayexpress
TranscriptomicsRibosome profiling of harringtonine-treated SUM1315 cells
SUM1315 were treated with harringtonine, and an untreated control sample was taken. Ribosome profiling was performed on these samples. 1 treated and 1 untreated sample
ORGANISM(S): Homo sapiens 
2016-02-17 | E-GEOD-59815 | biostudies-arrayexpress
TranscriptomicsRibosome profiling and RNA sequencing of MCF10A cells treated with torin or by serum starvation
MCF10A were either untreated, treated with torin or by starvation, to induce autophagy. RNA sequencing and ribosome profiling was performed. 1 biological replicate for each condition
ORGANISM(S): Homo sapiens 
2016-02-17 | E-GEOD-59816 | biostudies-arrayexpress
TranscriptomicsRibosome profiling on sections taken from a kidney tumor
Ribosome profiling on sections taken from a kidney tumor For two tumors: 2 sections of normal tissue and 4 samples of tumor tissue, for another two tumors 1 section of normal tissue and 1 section of tumor tissue
ORGANISM(S): Homo sapiens 
2016-02-17 | E-GEOD-59820 | biostudies-arrayexpress
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