Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

JIR1201, JIR1212, JIR1244, JIR1461, JIR1474, JIR3209, JIR3350, JIR3356 and JIR3528 genomic arrays

ABSTRACT: Comparing the genetic content of strains JIR1201, JIR1212, JIR1244, JIR1461, JIR1474, JIR3209, JIR3350, JIR3356 and JIR3528 to wild-type strain JIR3356. Comparison of JIR3356 with itself to eliminate any variation that may occur with the technique. This experiment should not produce any statistically significant expression changes. Two biological replicates were analysed per strain, which included a dye swap. Raw data was compiled using IMAGENE. Normalisation and statistical analysis was undertaken using BASE. Statistics were performed using the Wilcoxon signed ranked test.

ORGANISM(S): Dichelobacter nodosus

SUBMITTER: J Songer

PROVIDER: E-GEOD-5157 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Genome sequence and identification of candidate vaccine antigens from the animal pathogen Dichelobacter nodosus.

Myers Garry S A GS Parker Dane D Al-Hasani Keith K Kennan Ruth M RM Seemann Torsten T Ren Qinghu Q Badger Jonathan H JH Selengut Jeremy D JD Deboy Robert T RT Tettelin Hervé H Boyce John D JD McCarl Victoria P VP Han Xiaoyan X Nelson William C WC Madupu Ramana R Mohamoud Yasmin Y Holley Tara T Fedorova Nadia N Khouri Hoda H Bottomley Steven P SP Whittington Richard J RJ Adler Ben B Songer J Glenn JG Rood Julian I JI Paulsen Ian T IT

Nature biotechnology 20070429 5

Dichelobacter nodosus causes ovine footrot, a disease that leads to severe economic losses in the wool and meat industries. We sequenced its 1.4-Mb genome, the smallest known genome of an anaerobe. It differs markedly from small genomes of intracellular bacteria, retaining greater biosynthetic capabilities and lacking any evidence of extensive ongoing genome reduction. Comparative genomic microarray studies and bioinformatic analysis suggested that, despite its small size, almost 20% of the geno ...[more]

PMID: 17468768

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Project description:MicroRNAs (miRNAs) in body fluids are candidate diagnostics for a variety of conditions and diseases, including breast cancer. One premise for using extracellular miRNAs to diagnose disease is the notion that the abundance of the miRNAs in body fluids reflects their abundance in the abnormal cells causing the disease. As a result, the search for such diagnostics in body fluids has focused on miRNAs that are abundant in the cells of origin. Here we report that released miRNAs do not necessarily reflect the abundance of miRNA in the cell of origin. We find that release of miRNAs from cells into blood, milk and ductal fluids is selective and that the selection of released miRNAs may correlate with malignancy. In particular, the bulk of miR-451 and miR-1246 produced by malignant mammary epithelial cells was released, but the majority of these miRNAs produced by non-malignant mammary epithelial cells was retained. Our findings suggest the existence of a cellular selection mechanism for miRNA release and indicate that the extracellular and cellular miRNA profiles differ. This selective release of miRNAs is an important consideration for the identification of circulating miRNAs as biomarkers of disease. miRNA microarrays were screened by LC Sciences. One microgram of MCF7 cellular RNA preparation was labeled with Cy3, and one microgram of the extracellular RNA samples was labeled with Cy5. In brief, the RNA was labeled with Cy5 or Cy3 and hybridized to LCSciences standard arrays for mature miRNA of all species available in the Sanger miRBase database (Release 12.0). The data were analyzed including background subtraction, using a LOWESS (locally weighted regression) method on the background-subtracted data. Only transcripts with a signal intensity higher than 3X (background SD) and spot CV<0.5. CV was calculated by (SD)/(signal intensity), and in which repeating probes on the array produced signals from at least 50% of the repeating probes are above detection level.

Dataset Information

JIR1201, JIR1212, JIR1244, JIR1461, JIR1474, JIR3209, JIR3350, JIR3356 and JIR3528 genomic arrays

Publications

Genome sequence and identification of candidate vaccine antigens from the animal pathogen Dichelobacter nodosus.

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