Unknown,Transcriptomics,Genomics,Proteomics

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Expression profiling data from mid-log phase cultures of wild type Vibrio campbellii BAA-1116


ABSTRACT: 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 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).

ORGANISM(S): Vibrio harveyi ATCC BAA-1116

SUBMITTER: Baochuan Lin 

PROVIDER: E-GEOD-20960 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Identification of non-coding RNAs in environmental vibrios.

Silveira Ana Cristina G ACG   Robertson Kelly L KL   Lin Baochuan B   Wang Zheng Z   Vora Gary J GJ   Vasconcelos Ana Tereza R ATR   Thompson Fabiano L FL  

Microbiology (Reading, England) 20100506 Pt 8


The discovery of non-coding RNA (ncRNA) has been mainly limited to laboratory model systems and human pathogenic bacteria. In this study, we begin to explore the ncRNA diversity in four recently sequenced environmental Vibrio species (Vibrio alginolyticus 40B, Vibrio communis 1DA3, Vibrio mimicus VM573 and Vibrio campbellii BAA-1116) by performing in silico searches using Infernal and Rfam for the identification of putative ncRNA-encoding genes. This search method resulted in the identification  ...[more]

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