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E-GEOD-60752 - Time resolved ribosome profiling study of oxygen and glucose deprivation of rat pheochromocytoma cells

Status
Released on 10 April 2015, last updated on 19 August 2015
Organism
Rattus norvegicus
Samples (16)
Protocols (2)
Description
Oxygen and glucose metabolism plays a pivotal role in many (patho)physiological conditions. In particular, oxygen and glucose deprivation (OGD) occurs during ischemia and stroke, resulting in extensive tissue injury and cell death. We applied time-resolved ribosome profiling technique to assess early events at the level of gene expression in rat pheochromocytoma PC12 cells during short-term OGD. Most substantial alterations in transcripts levels and their translation were seen to occur in the first 20 minutes of OGD. The rapid adaptation of translation apparatus to OGD is global and involves altered elongation and initiation rates. We also observed salient and reproducible alterations in ribosome densities of individual mRNAs such as increased translation of particular upstream Open Reading Frames (uORFs); induced site-specific arrests of the ribosomes and synthesis of extended protein isoforms. Ribosome profiling (with mRNA-seq sequencing) was carried out at 0,20,40 and 60 minutes of OGD. Two biological replicates were used.
Experiment type
RNA-seq of coding RNA 
Contacts
Pavel V Baranov <p.baranov@ucc.ie>, Alexander V Zhdanov, Dmitry B Papkovsky, Dmitry E Andreev, Ivan N Shatsky, Patrick B O’Connor, Ruslan I Dmitriev
Citation
Oxygen and glucose deprivation induces widespread alterations in mRNA translation within 20 minutes. Andreev DE, O'Connor PB, Zhdanov AV, Dmitriev RI, Shatsky IN, Papkovsky DB, Baranov PV.
MINSEQE
Exp. designProtocolsVariablesProcessedSeq. reads
Files
Investigation descriptionE-GEOD-60752.idf.txt
Sample and data relationshipE-GEOD-60752.sdrf.txt
Processed data (1)E-GEOD-60752.processed.1.zip
Additional data (1)E-GEOD-60752.additional.1.zip
Links