NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Series GSE39641 Query DataSets for GSE39641
Status Public on Oct 01, 2012
Title Genome-Wide Study Based On Abasic Site Revealed Selective RNA Oxidation In Neuro 2a Cells
Organism Mus musculus
Experiment type Expression profiling by array
Summary To investigate selectivity of mRNA oxidation, total RNA and oxidized RNA isolated from Neuro 2a cells before and after H2O2 treatment were employed for microarray analysis. It was found that selective oxidation of mRNA already occurs under normal culture conditions but was increased by H2O2, especially in a subset of mRNAs related to certain functions. Moreover, mRNA oxidation level is also related to its abundance or stability (half-life time). This shows for the first time that mRNA oxidation is associated with RNA homeostasis including function, stability and abundance depending on cellular redox status in a genome-wide scale.
 
Overall design Neuro 2a cells received hydrogen peroxide treatment or no treatment as a control. Samples were applied for RNA extraction and ARP labeling, which could bind with apurinic/apyrimidinic sites, and then a pull-down process to isolate oxidized RNA. Total RNA and oxidized RNA were used for subsequent transcriptomic profiling.

4 types of samples were analyzed:
Basal-total: untreated N2a cells labeled with ARP, but not processed for the pull-down assay.
Ox-total: hydrogen peroxide-treated N2a cells labeled with ARP, but not processed for the pull-down assay.
Basal-ARP: untreated N2a cells labeled with ARP, and processed for the pull-down assay. ARP-derivatized RNA, which is also oxidized RNA, was concentrated and used for the microarray analysis.
Ox-ARP: hydrogen peroxide-treated N2a cells labeled with ARP, and processed for the pull-down assay. ARP-derivatized RNA, which is also oxidized RNA, was concentrated and used for the microarray analysis.
 
Contributor(s) Han S, Tanaka M, Brucklacher RM, Yan H, Mitschelen M, Farley JA, Freeman WM, Sonntag WE
Citation missing Has this study been published? Please login to update or notify GEO.
Submission date Jul 25, 2012
Last update date Jun 14, 2018
Contact name Penn State COM
Organization name Penn State College of Medicine
Department Genome Sciences Facility
Street address 500 University Drive
City Hershey
State/province PA
ZIP/Postal code 17033
Country USA
 
Platforms (1)
GPL6885 Illumina MouseRef-8 v2.0 expression beadchip
Samples (16)
GSM973557 Basal-total, rep1
GSM973558 Basal-total, rep2
GSM973559 Basal-total, rep3
Relations
BioProject PRJNA171312

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

Supplementary file Size Download File type/resource
GSE39641_RAW.tar 3.1 Mb (http)(custom) TAR
GSE39641_non-normalized.txt.gz 2.6 Mb (ftp)(http) TXT
Raw data are available on Series record
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap