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Sara Davis

Publications and source records attributed to Sara Davis.

5 recordsLinked to original sources
PubMed2005

A method for determining zygosity of transgenic zebrafish by TaqMan real-time PCR.

When producing a genetically modified organism, intended genes are often integrated into a target genome by random insertions. Subsequently, it is often desirable to know the gene copy number of the transgenic organism and the zygosity of its offspring. Because of the random insertions, the estimation can be made only by quantitative measurement of the genes. Even though TaqMan real-time PCR has been used in gene expression analysis, it is routinely used to quantify differences larger than twofold or more than one PCR cycle. In this study, we employed TaqMan quantitative PCR to determine zygosity of transgenic fluorescent zebrafish in which a homozygote and a hemizygote differ by only twofold. We measured relative quantities of the transgene by taking the threshold cycle (Ct) of both the transgene and an internal control zebrafish genomic DNA. Using scatterplots and statistical inference, we demonstrated that homozygotes and hemizygotes could be differentiated unambiguously when multiple measurements were taken. We discuss the relationship between the repetitive measurements and TaqMan precision with a statistical model. The result illustrates that the method can be extended to some areas that require even higher precision such as determining the polyploidy of an organism.

Animals↗
PubMed2004

A method for gene expression analysis by oligonucleotide arrays from minute biological materials.

Gene expression profiling has been widely used in identifying differentially expressed genes. One of the most popular formats is oligonucleotide array. A limitation of oligonucleotide arrays is the requirement of relatively large amounts of biological starting materials for gene expression analysis. We have developed a simple method for gene expression profiling from very small amounts of biological material by combining exponential (PCR) and linear (T7 RNA polymerase) amplification. By modifying the widely used SMART protocol, we combined T7 promoter ligation and PCR amplification in one step and generated around 0.5 microg of PCRcDNA from 30 ng of total RNA in a single PCR. The PCRcDNA was in vitro transcribed by T7 RNA polymerase to generate complementary RNA (cRNA), which then was used to hybridize Affymetrix GeneChips. Our results demonstrated a linear correlation between the PCR amplification and the conventional linear amplification in gene expression ratios of individual transcript species between two different RNA preparations. The method was further validated by TaqMan reactions. Moreover, both linear and PCR methods showed some inherent bias as to which transcripts were detected, suggesting that using both in parallel may provide a more comprehensive coverage of the transcriptome present in a given sample.

Base Sequence↗
PubMed2004

A method for cross-species gene expression analysis with high-density oligonucleotide arrays.

DNA microarrays have been widely used in gene expression analysis of biological processes. Due to a lack of sequence information, the applications have been largely restricted to humans and a few model organisms. Presented within this study are results of the cross-species hybridization with Affymetrix human high-density oligonucleotide arrays or GeneChip using distantly related mammalian species; cattle, pig and dog. Based on the unique feature of the Affymetrix GeneChip where every gene is represented by multiple probes, we hypothesized that sequence conservation within mammals is high enough to generate sufficient signals from some of the probes for expression analysis. We demonstrated that while overall hybridization signals are low for cross-species hybridization, a few probes of most genes still generated signals equivalent to the same-species hybridization. By masking the poorly hybridized probes electronically, the remaining probes provided reliable data for gene expression analysis. We developed an algorithm to select the reliable probes for analysis utilizing the match/mismatch feature of GeneChip. When comparing gene expression between two tissues using the selected probes, we found a linear correlation between the cross-species and same-species hybridization. In addition, we validated cross-species hybridization results by quantitative PCR using randomly selected genes. The method shown herein could be applied to both plant and animal research.

Algorithms↗
PubMed2004

Enhanced sensitivity RNA gel loading buffer that enables efficient RNA separation on native gels.

RNA gel analysis is essential for quality assessment of RNA preparations for subsequent analysis such as microarrays and real-time PCRs. The routinely used standard electrophoresis of RNA through formaldehyde-containing agarose gels is not only labor-intensive and time-consuming, but also involves sizeable quantities of hazardous materials. Above all, it is not sensitive, requiring more than 1 microgram of RNA for the assay. Current gene expression profiling with microarrays and real-time PCR often involves limiting amounts of RNA. It is therefore important to have a more sensitive way to analyze RNA. Here we report an improved ethidium bromide-based RNA gel analysis system with our Superload buffer that increases sensitivity to 12.5 ng of total RNA and allows RNA analysis on a regular native Tris-acetate EDTA (TAE) agarose gel.

Animals↗