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Series GSE89017 Query DataSets for GSE89017
Status Public on Jul 06, 2018
Title Genome-wide analysis of 8-oxoguanine DNA glycosylase-1 after oxidative stress exposure
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary We report the application of ChIP-Sequencing for profiling genome-wide distribution of 8-oxoguanine DNA glycosylase1 (OGG1, a DNA base excision repair protein), after oxidative stress exposure mediated by glucose oxidase (GOx) of cells. By obtaining an average of over 18 million of total reads per sample and over 19.5 million of unique reads per sample from chromatin immunoprecipitated DNA, we generated genome-wide chromatin-state maps of HEK293 cells. We performed gene ontology and functional pathway analysis of genes associated with peaks to identify regions of the genomes (e.g. promoter, introns, etc) where the peaks tend to occur. The results show that OGG1 is primarily associated with promoter regions in vicinity of transcription factor binding sites 5' of transcription start sites (TSS). This pattern of distribution occurs in spite of genome-wide oxidative modifications of guanines (primarily 8-oxoG). OGG1 increased significantly at regulatory regions of CXC-, CC- chemokines, cytokines and growth factors. In controls, the DNA was chromatin immunoprecipitated using antibody to NF-κB/RelA. As expected NF-κB was enriched on gene regulatory regions including those of proinflammatory,cell proliferation ones. These and other data derived from further analysis, suggest that OGG1 modulates gene expression in coordination with NF-κB.
Overall design FLAG-tagged OGG1 expressing HEK293 cells were stimulated with GOx (1 µU) for 0, 15, 30 and 60 min. After GOx exposure, protein-DNA complexes were crosslinked using formalin according to standard Millipore® protocol. DNA was sheared with 10-sec pulses using a Cole-Parmer GEX 130 ultrasonic processor (average 300 bp) and chromatin was immunoprecipitated (IP) with antibody to FLAG or anti-RelA/p65 antibody and IPs were collected using G-agarose beads (Millipore Corporation). After extraction, the DNA was subjected to high-throughput sequencing using Solexa/Illumina genome analyzer (Ambry Genetics).
Contributor(s) Aguilera-Aguirre L, Boldogh I
Citation(s) 29940424
Submission date Oct 21, 2016
Last update date May 15, 2019
Contact name Istvan Boldogh
Department Microbiology & Immunology
Street address 301 UNIVERSITY BLVD.
City Galveston
State/province Texas
ZIP/Postal code 77555
Country USA
Platforms (1)
GPL15433 Illumina HiSeq 1000 (Homo sapiens)
Samples (8)
GSM2357433 Flag-OGG1-Con-2
GSM2357434 Flag-OGG1-GOX-15-1
GSM2357435 Flag-OGG1-GOX-30-1
BioProject PRJNA349805
SRA SRP091905

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Supplementary file Size Download File type/resource
GSE89017_RAW.tar 386.2 Mb (http)(custom) TAR (of TDF)
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Raw data are available in SRA
Processed data provided as supplementary file

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