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| Status |
Public on Jun 01, 2010 |
| Title |
Expression profiling data from mid-log phase cultures of wild type Vibrio campbellii BAA-1116 |
| Organism |
Vibrio campbellii CAIM 519 = NBRC 15631 = ATCC 25920 |
| Experiment type |
Expression profiling by array
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| Summary |
Small RNA and regulatory RNA discovery has been based on (i) computational predictions mainly in intergenic regions, (ii) microarray experiments, (iii) shotgun cloning of cDNA libraries, (iv) classical cloning of abundant small RNAs after size fractionation in polyacrylamide gels and (v) copurification with proteins like Hfq, CsrA and RNA polymerase.
In this study, we attempted to experimentally validate in silico small and regulatory RNA predictions for V. campbellii BAA-1116 using a microarray expression profiling strategy. Specifically, we investigated transcripts from mid-log phase cultures grown in nutrient rich media and examined their hybridization to tiled probes targeting annotated V. campbellii BAA-1116 intergenic regions.
Keywords: small RNA discovery
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| Overall design |
Five replicates of wild type V. campbellii BAA-1116 were grown to Mid-log phase, and total RNA was extracted from 1.0E+9 cells. Messenger RNA was isolated from the total RNA extracts treated with DNase, labeled with biotin, fragmented and hybridized to V. campbellii BAA-1116 whole genome microarray (520694F, Affymetrix).
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| Contributor(s) |
Lin B, Silverira AC, Roberson KL, Vasconcelos AT, Thompson FL, Wang Z, Vora GJ |
| Citation(s) |
20447992 |
| |
| Submission date |
Mar 19, 2010 |
| Last update date |
Mar 22, 2012 |
| Contact name |
Baochuan Lin |
| E-mail(s) |
[email protected]
|
| Phone |
202-767-0289
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| Organization name |
US Naval Research Laboratory
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| Department |
Center for Bio/Molecular Science & Engineering
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| Street address |
4555 Overlook Avenue, S. W.
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| City |
Washington |
| State/province |
DC |
| ZIP/Postal code |
20375 |
| Country |
USA |
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| Platforms (1) |
| GPL10230 |
[Vharveyis520694F] US Naval Research Laboratory V campbellii BAA-1116 whole genome microarray |
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| Samples (5)
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| Relations |
| BioProject |
PRJNA124521 |
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