ArticleNucleic acids research2010
Beyond Affymetrix arrays: expanding the set of known hybridization isotherms and observing pre-wash signal intensities.
Article in Nucleic acids research, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 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
17 citing papers in PubMed.
- A Novel Method That Allows SNP Discrimination with 160:1 Ratio for Biosensors Based on DNA-DNA Hybridization.Biosensors · 2021Article
- Gene Meter: Accurate abundance calculations of gene expression.Communicative & integrative biology · 2017Article
- Introduction to sequencing the brain transcriptome.International review of neurobiology · 2014Review
- Single-stranded DNA catalyzes hybridization of PCR-products to microarray capture probes.PloS one · 2014Article
- A revised design for microarray experiments to account for experimental noise and uncertainty of probe response.PloS one · 2014Article
- Physico-chemical foundations underpinning microarray and next-generation sequencing experiments.Nucleic acids research · 2013Review
- Genes, behavior and next-generation RNA sequencing.Genes, brain, and behavior · 2013Review
- Modeling the diagnostic criteria for alcohol dependence with genetic animal models.Current topics in behavioral neurosciences · 2013Review
- Probing hybridization parameters from microarray experiments: nearest-neighbor model and beyond.Nucleic acids research · 2012Article
- Identification of non-specific hybridization using an empirical equation fitted to non-equilibrium dissociation curves.Journal of microbiological methods · 2012Article
- From hybridization theory to microarray data analysis: performance evaluation.BMC bioinformatics · 2011Article
- ArrayInitiative - a tool that simplifies creating custom Affymetrix CDFs.BMC bioinformatics · 2011Article
- Was the Scanner Calibration Slide used for its intended purpose?BMC bioinformatics · 2011Article
- Evaluating gene expression in C57BL/6J and DBA/2J mouse striatum using RNA-Seq and microarrays.PloS one · 2011Article
- Accurate estimates of microarray target concentration from a simple sequence-independent Langmuir model.PloS one · 2010Article
- Scanner calibration revisited.BMC bioinformatics · 2010Article
- Washing scaling of GeneChip microarray expression.BMC bioinformatics · 2010Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Microarray hybridization studies have attributed the nonlinearity of hybridization isotherms to probe saturation and post-hybridization washing. Both processes are thought to distort 'true' target abundance because immobilized probes are saturated with excess target and stringent washing removes loosely bound targets. Yet the paucity of studies aimed at understanding hybridization and dissociation makes it difficult to align physicochemical theory to microarray results. To fill the void, we first examined hybridization isotherms generated on different microarray platforms using a ribosomal RNA target and then investigated hybridization signals at equilibrium and after stringent wash. Hybridization signal at equilibrium was achieved by treating the microarray with isopropanol, which prevents nucleic acids from dissolving into solution. Our results suggest that (i) the shape of hybridization isotherms varied by microarray platform with some being hyperbolic or linear, and others following a power-law; (ii) at equilibrium, fluorescent signal of different probes hybridized to the same target were not similar even with excess of target and (iii) the amount of target removed by stringent washing depended upon the hybridization time, the probe sequence and the presence/absence of nonspecific targets. Possible physicochemical interpretations of the results and future studies are discussed.
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.