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Series GSE60752 Query DataSets for GSE60752
Status Public on Apr 10, 2015
Title Time resolved ribosome profiling study of oxygen and glucose deprivation of rat pheochromocytoma cells
Organism Rattus norvegicus
Experiment type Expression profiling by high throughput sequencing
Summary 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.
 
Overall design Ribosome profiling (with mRNA-seq sequencing) was carried out at 0,20,40 and 60 minutes of OGD. Two biological replicates were used.
 
Contributor(s) Andreev DE, O’Connor PB, Zhdanov AV, Dmitriev RI, Shatsky IN, Papkovsky DB, Baranov PV
Citation(s) 25943107
Submission date Aug 26, 2014
Last update date May 15, 2019
Contact name Pavel V Baranov
E-mail(s) p.baranov@ucc.ie
Organization name University College Cork
Department Biochemistry and Cell Biology
Lab Lapti
Street address Western Gateway Building, UCC
City Cork
State/province Co. Cork
ZIP/Postal code NA
Country Ireland
 
Platforms (1)
GPL14844 Illumina HiSeq 2000 (Rattus norvegicus)
Samples (16)
GSM1487097 0 min. OGD, ribo-seq, replicate #1
GSM1487098 0 min. OGD, mRNA-seq, replicate #1
GSM1487099 20 min. OGD, ribo-seq, replicate #1
Relations
BioProject PRJNA259424
SRA SRP045777

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

Supplementary file Size Download File type/resource
GSE60752_RAW.tar 3.5 Mb (http)(custom) TAR (of CSV)
GSE60752_supplementary_data.xls.gz 5.1 Mb (ftp)(http) XLS
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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