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Series GSE148377 Query DataSets for GSE148377
Status Public on Oct 13, 2020
Title Profiling of 8-oxoG RNA modifications reveals strong functional network relationships in bronchial epitheilium following exposure to formaldehyde
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary Recent studies have highlighted the association between oxidative stress-inducing chemicals and diseases such as Alzheimer’s disease and cancer. While chemicals like formaldehyde are known causative agents of disease and overall negatively impact human health, their mechanisms of action remain unclear. Recent development of antibodies that target oxidized RNA nucleotides and advances in RNA-sequencing technology enable the isolation and identification of differentially oxidized transcripts. In this study, oxidation-specific immunoprecipitation is combined with RNA-sequencing to detect transcripts that are enriched in oxidized nucleotides following direct exposure of 1 ppm formaldehyde to human BEAS-2B lung cells using an air-liquid interface exposure system. Results from this analysis suggest a functional role of the oxidized transcripts in signaling pathways regulating cellular proliferation, migration, and programmed cell death. By combining direct cell-exposure systems, oxidized-RNA immunoprecipitation, RNA-sequencing technologies, and network analyses, detection of specifically oxidized molecular markers could be used to further characterize biological responses to external stressors and identify targets for drug development toward therapies for complex diseases.
 
Overall design Examination of transcript abundance from two biological replicates of lung cell RNA isolated by immunoprecipitation relative to total RNA following exposure to either clean air or 1ppm formaldehyde for two hours
 
Contributor(s) Gonzalez JC, Sherman MW, Wang DS, Chuvalo-Abrahm JC, Hildebrandt Ruiz L, Contreras LM
Citation(s) 33024153
Submission date Apr 09, 2020
Last update date Oct 13, 2020
Contact name Lydia M Contreras
Organization name University of Texas at Austin
Department Chemical Engineering
Street address 200 E Dean Keeton St,
City Austin
State/province TX
ZIP/Postal code 78712
Country USA
 
Platforms (1)
GPL20301 Illumina HiSeq 4000 (Homo sapiens)
Samples (8)
GSM4466622 S1: Clean Air Input RNA
GSM4466623 S2: Clean Air Input RNA
GSM4466624 S3: Formaldehyde Air Input RNA
Relations
BioProject PRJNA624094
SRA SRP255876

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
GSE148377_DESeq2-CA_IP.txt.gz 3.9 Mb (ftp)(http) TXT
GSE148377_DESeq2-FA_IP.txt.gz 3.9 Mb (ftp)(http) TXT
GSE148377_DESeq2-Input.txt.gz 3.2 Mb (ftp)(http) TXT
GSE148377_RAW.tar 24.2 Mb (http)(custom) TAR (of TXT)
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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