ArticleApplied and environmental microbiology2010
Development of a common oligonucleotide reference standard for microarray data normalization and comparison across different microbial communities.
Article in Applied and environmental microbiology, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
27 citing papers in PubMed, 78 citations in OpenAlex.
- Upper circumpolar deep water influences microbial functional gene composition and diversity along the southern Central Indian Ridge and eastern Southwest Indian Ridge.Microbiology spectrum · 2025Article
- Soil microbial functional gene dataset associated withData in brief · 2023Article
- Deciphering pH-dependent microbial taxa and functional gene co-occurrence in the coral Galaxea fascicularis.Microbial ecology · 2023Article
- Employing gene chip technology for monitoring and assessing soil heavy metal pollution.Environmental monitoring and assessment · 2021Review
- Coexistence patterns of soil methanogens are closely tied to methane generation and community assembly in rice paddies.Microbiome · 2021Article
- Functional Gene Array-Based Ultrasensitive and Quantitative Detection of Microbial Populations in Complex Communities.mSystems · 2019Article
- Acidobacteria Subgroups and Their Metabolic Potential for Carbon Degradation in Sugarcane Soil Amended With Vinasse and Nitrogen Fertilizers.Frontiers in microbiology · 2019Article
- Differential Sensitivity of Wetland-Derived Nitrogen Cycling Microorganisms to Copper Nanoparticles.ACS sustainable chemistry & engineering · 2018Article
- Elevated COFrontiers in microbiology · 2018Article
- Taxonomic and functional shifts in the beech rhizosphere microbiome across a natural soil toposequence.Scientific reports · 2017Article
- The shift of microbial communities and their roles in sulfur and iron cycling in a copper ore bioleaching system.Scientific reports · 2016Article
- Bacterial community structure and function shift across a northern boreal forest fire chronosequence.Scientific reports · 2016Article
- Microbial functional genes enriched in the Xiangjiang River sediments with heavy metal contamination.BMC microbiology · 2016Article
- Comparison of microbial taxonomic and functional shift pattern along contamination gradient.BMC microbiology · 2016Article
- Warming Alters Expressions of Microbial Functional Genes Important to Ecosystem Functioning.Frontiers in microbiology · 2016Article
- Microbial Profiling of a Suppressiveness-Induced Agricultural Soil Amended with Composted Almond Shells.Frontiers in microbiology · 2016Article
- Fungal Community Shifts in Structure and Function across a Boreal Forest Fire Chronosequence.Applied and environmental microbiology · 2015Article
- Planting increases the abundance and structure complexity of soil core functional genes relevant to carbon and nitrogen cycling.Scientific reports · 2015Article
- An integrated insight into the response of sedimentary microbial communities to heavy metal contamination.Scientific reports · 2015Article
- Over 150 years of long-term fertilization alters spatial scaling of microbial biodiversity.mBio · 2015Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors at 4 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
High-density functional gene arrays have become a powerful tool for environmental microbial detection and characterization. However, microarray data normalization and comparison for this type of microarray remain a challenge in environmental microbiology studies because some commonly used normalization methods (e.g., genomic DNA) for the study of pure cultures are not applicable. In this study, we developed a common oligonucleotide reference standard (CORS) method to address this problem. A unique 50-mer reference oligonucleotide probe was selected to co-spot with gene probes for each array feature. The complementary sequence was synthesized and labeled for use as the reference target, which was then spiked and cohybridized with each sample. The signal intensity of this reference target was used for microarray data normalization and comparison. The optimal amount or concentration were determined to be ca. 0.5 to 2.5% of a gene probe for the reference probe and ca. 0.25 to 1.25 fmol/microl for the reference target based on our evaluation with a pilot array. The CORS method was then compared to dye swap and genomic DNA normalization methods using the Desulfovibrio vulgaris whole-genome microarray, and significant linear correlations were observed. This method was then applied to a functional gene array to analyze soil microbial communities, and the results demonstrated that the variation of signal intensities among replicates based on the CORS method was significantly lower than the total intensity normalization method. The developed CORS provides a useful approach for microarray data normalization and comparison for studies of complex microbial communities.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.