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| Status |
Public on Oct 01, 2008 |
| Title |
A method of stripping custom microarrays |
| Platform organisms |
Caenorhabditis elegans; Drosophila melanogaster; Danio rerio; Homo sapiens; Mus musculus; Rattus norvegicus |
| Sample organisms |
Homo sapiens; synthetic construct |
| Experiment type |
Non-coding RNA profiling by array
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| Summary |
Our genome wide analyses of microRNA expression profiles involve the hybridization of fluorescently labeled RNA samples to custom made, DNA microarrays based on the GAPSII coated slides. We describe a simple and effective method to regenerate such custom microarrays. Our protocol entails the use of a very low concentration of sodium hydroxide in a low salt buffer to strip RNA molecules from the arrays. The solution is also capable of removing DNA molecules hybridized to the slides, while preserving the slide coating and printed DNA probes. Slides can be stripped and reused at least twice without significantly sacrificing data quality.
Keywords: expression study, new vs. stripped array comparison
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| Overall design |
There are two stripping conditions in this study (1mM NaOH and 2mM NaOH in SSC buffer). For 1mM NaOH treatment, new, once-, twice-, and triple-stripped arrays are studies. For 2mM NaOH treatment, new and once-stripped arrays are measured.
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| Contributor(s) |
Zeng Y, Zhang X |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
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| Submission date |
Jan 29, 2008 |
| Last update date |
Mar 19, 2012 |
| Contact name |
Xiaoxiao Zhang |
| E-mail(s) |
zhang688@umn.edu
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| Organization name |
University of Minnesota
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| Street address |
312 Church St. SE
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| City |
Minneapolis |
| ZIP/Postal code |
55455 |
| Country |
USA |
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| Platforms (1) |
| GPL6432 |
University of Minnesota nematode, fruit fly, zebrafish, mouse, rat, and human miRNA array 1K version 1 |
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| Samples (6)
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| GSM260382 |
293T New A, 1mM NaOH treatment |
| GSM260383 |
Rehybridization after stripped once, 1mM NaOH treatment |
| GSM260384 |
Rehybridization after stripped twice, 1mM NaOH treatment |
| GSM260385 |
Rehybridization after stripped three times, 1mM NaOH treatment |
| GSM260386 |
293T New B, 2mM NaOH treatment |
| GSM260387 |
Rehybridization after stripped once, 2mM NaOH treatment |
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| Relations |
| BioProject |
PRJNA108525 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE10305_RAW.tar |
490.0 Kb |
(http)(custom) |
TAR (of TXT) |
| Processed data included within Sample table |
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