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| Status |
Public on Mar 01, 2008 |
| Title |
Correlation of microRNA levels during hypoxia with predicted target mRNAs through genome-wide microarray analysis |
| Platform organisms |
Homo sapiens; Mus musculus; Rattus norvegicus |
| Sample organism |
Homo sapiens |
| Experiment type |
Expression profiling by array
Non-coding RNA profiling by array
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| Summary |
three replicates of HT29 cells per conditionwere grown under normoxic and hypoxic conditions. RNA and miRNA was extracted from each replicate and run on the GPL570 and GPL5106 arrays respectively.
Low levels of oxygen in tissues, seen in situations such as chronic lung disease, necrotic tumors, and high altitude exposures, initiate a signaling pathway that results in active transcription of genes possessing a hypoxia response element (HRE). To identify changes induced by hypoxia and determine whether miRNA may have effects on gene expression, we conducted mRNA- and miRNA-array-based analysis on HT29 cells, and developed methods for the comparative analysis of these data sets. To date, no studies have examined the effects of an environmental perturbation on miRNA levels and their relationship to gene expression. Comparison of miRNAs with the expression of their predicted targets indicated a lower level of concordance than expected. We did, however, find preliminary evidence of combinatorial regulation of mRNA expression by miRNA. The methods described here for comparative analysis of miRNA and mRNA profiling will be useful for better understanding genome wide regulatory responsiveness, and to refine miRNA predictive algorithms under development for that purpose.
Keywords: miRNA, hypoxia, HT29, cystic fibrosis
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| Overall design |
Two group experiment (noroxia and hypoxia) three replicates per condition
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| Contributor(s) |
Page GP |
| Citation(s) |
18474670, 19320992 |
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| Submission date |
Oct 04, 2007 |
| Last update date |
Aug 20, 2019 |
| Contact name |
Grier Page |
| E-mail(s) |
gpage@uab.edu
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| Phone |
205-934-4930
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| Organization name |
University of Alabama at Birmingham
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| Street address |
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| City |
Birmingham |
| State/province |
AL |
| ZIP/Postal code |
35294 |
| Country |
USA |
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| Platforms (2) |
| GPL570 |
[HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array |
| GPL5106 |
mirVANA miRNA Bioarray V2 |
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| Samples (12)
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| GSM234653 |
Human hypoxia 1 (miRNA array) |
| GSM234654 |
Human hypoxia 2 (miRNA array) |
| GSM234655 |
Human hypoxia 3 (miRNA array) |
| GSM234656 |
Human normoxia 1 (Affymetrix U133 2.0) |
| GSM234657 |
Human normoxia 2 (Affymetrix U133 2.0) |
| GSM234658 |
Human normoxia 3 (Affymetrix U133 2.0) |
| GSM234659 |
Human hypoxia 1 (Affymetrix U133 2.0) |
| GSM234660 |
Human hypoxia 2 (Affymetrix U133 2.0) |
| GSM234661 |
Human hypoxia 3 (Affymetrix U133 2.0) |
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| Relations |
| BioProject |
PRJNA102837 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE9234_RAW.tar |
27.5 Mb |
(http)(custom) |
TAR (of CEL, GPR) |
| Processed data included within Sample table |
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