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Microarray Detection Call Methodology as a Means to Identify and Compare Transcripts Expressed within Syncytial Cells from Soybean (Glycine max) Roots Undergoing Resistant and Susceptible Reactions to the Soybean Cyst Nematode (Heterodera glycines).

Klink VP, Overall CC, Alkharouf NW, Macdonald MH, Matthews BF - J. Biomed. Biotechnol. (2010)

Bottom Line: The goal was to identify genes found in specific cell populations that were eliminated by differential expression analysis due to the nature of differential expression methods.Conclusion.DCM has identified genes that are possibly cell-type specific and/or involved in important aspects of plant nematode interactions during the resistance response, revealing the uniqueness of a particular cell population at a particular point during its differentiation process.

View Article: PubMed Central - PubMed

Affiliation: Department of Biological Sciences, Harned Hall, Mississippi State University, Mississippi State, MS 39762, USA.

ABSTRACT
Background. A comparative microarray investigation was done using detection call methodology (DCM) and differential expression analyses. The goal was to identify genes found in specific cell populations that were eliminated by differential expression analysis due to the nature of differential expression methods. Laser capture microdissection (LCM) was used to isolate nearly homogeneous populations of plant root cells. Results. The analyses identified the presence of 13,291 transcripts between the 4 different sample types. The transcripts filtered down into a total of 6,267 that were detected as being present in one or more sample types. A comparative analysis of DCM and differential expression methods showed a group of genes that were not differentially expressed, but were expressed at detectable amounts within specific cell types. Conclusion. The DCM has identified patterns of gene expression not shown by differential expression analyses. DCM has identified genes that are possibly cell-type specific and/or involved in important aspects of plant nematode interactions during the resistance response, revealing the uniqueness of a particular cell population at a particular point during its differentiation process.

No MeSH data available.


Determination of probe sets to be used in the analysis. Sample 1: the particular sample under investigation (e.g., 3 dpi incompatible syncytia). Array 1: first array analyzed by DCM; Array 2: second array analyzed by DCM for a particular sample type. The word or refers to the order that the probe set measures present/marginal/absent on array 1 or array 2.
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Related In: Results  -  Collection


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fig4: Determination of probe sets to be used in the analysis. Sample 1: the particular sample under investigation (e.g., 3 dpi incompatible syncytia). Array 1: first array analyzed by DCM; Array 2: second array analyzed by DCM for a particular sample type. The word or refers to the order that the probe set measures present/marginal/absent on array 1 or array 2.

Mentions: The DCM was used to make a comparative analysis of the probe sets measuring the presence of a transcript (present transcript) within LCM-derived cell samples. The analyses would allow (1) the determination of the total number of present transcripts, (2) the determination of the numbers of present transcripts within a sample, and (3) a comparison of the present transcripts between the different sample types while estimating the differences between those samples (4) the identification of whether transcripts that are common between the two sample types under comparison had been identified in a prior differential expression analysis [26]. Only probe sets that measured detection on both arrays for a particular sample type (Figure 4) were evaluated further (see below).


Microarray Detection Call Methodology as a Means to Identify and Compare Transcripts Expressed within Syncytial Cells from Soybean (Glycine max) Roots Undergoing Resistant and Susceptible Reactions to the Soybean Cyst Nematode (Heterodera glycines).

Klink VP, Overall CC, Alkharouf NW, Macdonald MH, Matthews BF - J. Biomed. Biotechnol. (2010)

Determination of probe sets to be used in the analysis. Sample 1: the particular sample under investigation (e.g., 3 dpi incompatible syncytia). Array 1: first array analyzed by DCM; Array 2: second array analyzed by DCM for a particular sample type. The word or refers to the order that the probe set measures present/marginal/absent on array 1 or array 2.
© Copyright Policy - open-access
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2875038&req=5

fig4: Determination of probe sets to be used in the analysis. Sample 1: the particular sample under investigation (e.g., 3 dpi incompatible syncytia). Array 1: first array analyzed by DCM; Array 2: second array analyzed by DCM for a particular sample type. The word or refers to the order that the probe set measures present/marginal/absent on array 1 or array 2.
Mentions: The DCM was used to make a comparative analysis of the probe sets measuring the presence of a transcript (present transcript) within LCM-derived cell samples. The analyses would allow (1) the determination of the total number of present transcripts, (2) the determination of the numbers of present transcripts within a sample, and (3) a comparison of the present transcripts between the different sample types while estimating the differences between those samples (4) the identification of whether transcripts that are common between the two sample types under comparison had been identified in a prior differential expression analysis [26]. Only probe sets that measured detection on both arrays for a particular sample type (Figure 4) were evaluated further (see below).

Bottom Line: The goal was to identify genes found in specific cell populations that were eliminated by differential expression analysis due to the nature of differential expression methods.Conclusion.DCM has identified genes that are possibly cell-type specific and/or involved in important aspects of plant nematode interactions during the resistance response, revealing the uniqueness of a particular cell population at a particular point during its differentiation process.

View Article: PubMed Central - PubMed

Affiliation: Department of Biological Sciences, Harned Hall, Mississippi State University, Mississippi State, MS 39762, USA.

ABSTRACT
Background. A comparative microarray investigation was done using detection call methodology (DCM) and differential expression analyses. The goal was to identify genes found in specific cell populations that were eliminated by differential expression analysis due to the nature of differential expression methods. Laser capture microdissection (LCM) was used to isolate nearly homogeneous populations of plant root cells. Results. The analyses identified the presence of 13,291 transcripts between the 4 different sample types. The transcripts filtered down into a total of 6,267 that were detected as being present in one or more sample types. A comparative analysis of DCM and differential expression methods showed a group of genes that were not differentially expressed, but were expressed at detectable amounts within specific cell types. Conclusion. The DCM has identified patterns of gene expression not shown by differential expression analyses. DCM has identified genes that are possibly cell-type specific and/or involved in important aspects of plant nematode interactions during the resistance response, revealing the uniqueness of a particular cell population at a particular point during its differentiation process.

No MeSH data available.