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comparative genomic microarray protocols (Genome Explorations)

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Genome Explorations comparative genomic microarray protocols

MLST-based dendrogram showing genetic relationship of all E. faecalis isolates in this study. Small yellow highlights indicate a serotyping type strain, while black boxes designate the five most common serotypes . Arrows designate isolates used for <t>comparative</t> genomic <t>microarray</t> analysis. Abbreviations are defined as follows: ST = sequence type; CPS = capsule type; PAI = pathogenicity island fragment outlined as letter designations in (A = nuc1 ; B = cylB ; C = esp ; D = hydrolase homolog similar to xylS ; E = psaA homolog; F = gls-24 like); A red letter B indicates strains that readily transfer cytolysin via mating; Ab R = antibiotic resistance; T = tetracycline resistance; TM = tetM +; TL = tetL +; E = ermB +; VA = vanA +; VB = vanB +; G = gentamicin resistant; C = cat+ ; A = blaZ +; CBH = bile salt hydrolase; GEL = gelatinase; CYL = cytolysin. More detailed strain information is listed in .

Comparative Genomic Microarray Protocols, supplied by Genome Explorations, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/microarray+protocols/comparative+genomic+microarray+protocols/pmc01899230-227-1-10
Average 90 stars, based on 1 article reviews

comparative genomic microarray protocols - by Bioz Stars, 2026-09

90/100 stars

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1) Product Images from "Genetic Diversity among Enterococcus faecalis"

Article Title: Genetic Diversity among Enterococcus faecalis

Journal: PLoS ONE

doi: 10.1371/journal.pone.0000582

Figure Legend Snippet: MLST-based dendrogram showing genetic relationship of all E. faecalis isolates in this study. Small yellow highlights indicate a serotyping type strain, while black boxes designate the five most common serotypes . Arrows designate isolates used for comparative genomic microarray analysis. Abbreviations are defined as follows: ST = sequence type; CPS = capsule type; PAI = pathogenicity island fragment outlined as letter designations in (A = nuc1 ; B = cylB ; C = esp ; D = hydrolase homolog similar to xylS ; E = psaA homolog; F = gls-24 like); A red letter B indicates strains that readily transfer cytolysin via mating; Ab R = antibiotic resistance; T = tetracycline resistance; TM = tetM +; TL = tetL +; E = ermB +; VA = vanA +; VB = vanB +; G = gentamicin resistant; C = cat+ ; A = blaZ +; CBH = bile salt hydrolase; GEL = gelatinase; CYL = cytolysin. More detailed strain information is listed in .

Techniques Used: Microarray, Sequencing

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Significant genes of each signature were represented according to their gene function and specific role in the cell, localization and type of interaction between them. Node border color refers to cell localization, node shape to general function and node color to specific function in the cell. Edge color refers to physical interactions, biochemical interactions or to both; when not specified, a functional interaction is assumed. Upstream arrow (red) means up-regulation versus the other categories, and downstream arrow (blue) means down-regulation versus the other categories. <t>Microarray</t> data values represented here are shown in and .

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<t>Microarray</t> analysis of hUCB-MSCs from the normal and preeclampsia groups. (a) The scatter plot and MA plot show the DEGs between N3 and P3 cells. In the scatter plot, the median line indicates no difference in signal intensity between the two groups. The upper gray line indicates a twofold higher signal intensity, and the lower gray line indicates a twofold lower signal intensity for hUCB-MSCs from the preeclampsia group as compared to the normal group. In the MA plot, the median line represents N signal/P signal = 1. The upper gray line represents N signal/P signal = 2, and the lower gray line represents N signal/P signal = 0.5. N3: hUCB-MSCs at passage 3, normal pregnancy; P3: hUCB-MSCs at passage 3, preeclampsia. (b, c) Hierarchical cluster analysis of differentially expressed genes (DEGs) between N3 and P3 cells. Red represents upregulated gene clusters, and green represents downregulated gene clusters. The panels show genes up- or downregulated twofold (b) or fourfold (c) in P3 (versus N3) cells. N3: hUCB-MSCs at passage 3, normal pregnancy; P3: early hUCB-MSCs at passage 3, preeclampsia.

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Image Search Results

Journal: PLoS ONE

Article Title: Defining the Genomic Signature of Totipotency and Pluripotency during Early Human Development

doi: 10.1371/journal.pone.0062135

Figure Lengend Snippet: Significant genes of each signature were represented according to their gene function and specific role in the cell, localization and type of interaction between them. Node border color refers to cell localization, node shape to general function and node color to specific function in the cell. Edge color refers to physical interactions, biochemical interactions or to both; when not specified, a functional interaction is assumed. Upstream arrow (red) means up-regulation versus the other categories, and downstream arrow (blue) means down-regulation versus the other categories. Microarray data values represented here are shown in and .

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Techniques: Functional Assay, Microarray

Comparison of mRNA expression in seven candidate genes between TPCH test (n = 30, microarray) and training set (n = 62 qRT-PCR data), with two public microarray datasets of lung tissue samples (Spira et al , , n = 34; and Golpon et al , n = 10) . Fold change represents mean expression ratio of moderate versus mild emphysema (TPCH training set), severe/mild emphysema versus normal (Spira et al ), or severe emphysema versus normal samples (Golpon et al ). The absence of a bar indicates the gene was not represented on the microarray platform.

Journal: Respiratory Research

Article Title: Expression profiling identifies genes involved in emphysema severity

doi: 10.1186/1465-9921-10-81

Figure Lengend Snippet: Comparison of mRNA expression in seven candidate genes between TPCH test (n = 30, microarray) and training set (n = 62 qRT-PCR data), with two public microarray datasets of lung tissue samples (Spira et al , , n = 34; and Golpon et al , n = 10) . Fold change represents mean expression ratio of moderate versus mild emphysema (TPCH training set), severe/mild emphysema versus normal (Spira et al ), or severe emphysema versus normal samples (Golpon et al ). The absence of a bar indicates the gene was not represented on the microarray platform.

Article Snippet: Lung and universal reference RNA (Stratagene, La Jolla, CA, USA) was reverse transcribed, labeled with Cy5 and Cy3 (Amersham/GE Healthcare, Buckinghamshire, England) respectively and co-hybridized onto a 22K Operon V2.1 Human Genome Oligo Microarray chip http://www.operon.com containing 21,329 70 mer probes representing ~14,200 named transcripts printed by the British Columbia Gene Array Facility http://www.microarray.prostatecentre.com .

Techniques: Expressing, Microarray, Quantitative RT-PCR

Microarray analysis of hUCB-MSCs from the normal and preeclampsia groups. (a) The scatter plot and MA plot show the DEGs between N3 and P3 cells. In the scatter plot, the median line indicates no difference in signal intensity between the two groups. The upper gray line indicates a twofold higher signal intensity, and the lower gray line indicates a twofold lower signal intensity for hUCB-MSCs from the preeclampsia group as compared to the normal group. In the MA plot, the median line represents N signal/P signal = 1. The upper gray line represents N signal/P signal = 2, and the lower gray line represents N signal/P signal = 0.5. N3: hUCB-MSCs at passage 3, normal pregnancy; P3: hUCB-MSCs at passage 3, preeclampsia. (b, c) Hierarchical cluster analysis of differentially expressed genes (DEGs) between N3 and P3 cells. Red represents upregulated gene clusters, and green represents downregulated gene clusters. The panels show genes up- or downregulated twofold (b) or fourfold (c) in P3 (versus N3) cells. N3: hUCB-MSCs at passage 3, normal pregnancy; P3: early hUCB-MSCs at passage 3, preeclampsia.

Journal: Stem Cells International

Article Title: Comparative Analysis of Human Umbilical Cord Blood-Derived Mesenchymal Stem Cells between Preeclampsia and Normal Pregnant Women

doi: 10.1155/2020/8403192

Figure Lengend Snippet: Microarray analysis of hUCB-MSCs from the normal and preeclampsia groups. (a) The scatter plot and MA plot show the DEGs between N3 and P3 cells. In the scatter plot, the median line indicates no difference in signal intensity between the two groups. The upper gray line indicates a twofold higher signal intensity, and the lower gray line indicates a twofold lower signal intensity for hUCB-MSCs from the preeclampsia group as compared to the normal group. In the MA plot, the median line represents N signal/P signal = 1. The upper gray line represents N signal/P signal = 2, and the lower gray line represents N signal/P signal = 0.5. N3: hUCB-MSCs at passage 3, normal pregnancy; P3: hUCB-MSCs at passage 3, preeclampsia. (b, c) Hierarchical cluster analysis of differentially expressed genes (DEGs) between N3 and P3 cells. Red represents upregulated gene clusters, and green represents downregulated gene clusters. The panels show genes up- or downregulated twofold (b) or fourfold (c) in P3 (versus N3) cells. N3: hUCB-MSCs at passage 3, normal pregnancy; P3: early hUCB-MSCs at passage 3, preeclampsia.

Article Snippet: The standard protocol used for sample preparation and microarray processing is available from Agilent Technologies.

Techniques: Microarray

Network analysis of senescence-related differentially expressed genes (DEGs). Genes represented by a large circle are senescence-related differentially expressed genes (DEGs) obtained from microarray analysis. Red ones are genes related with senescence as well as cell aging. FDR: false discovery rate.

Journal: Stem Cells International

Article Title: Comparative Analysis of Human Umbilical Cord Blood-Derived Mesenchymal Stem Cells between Preeclampsia and Normal Pregnant Women

doi: 10.1155/2020/8403192

Figure Lengend Snippet: Network analysis of senescence-related differentially expressed genes (DEGs). Genes represented by a large circle are senescence-related differentially expressed genes (DEGs) obtained from microarray analysis. Red ones are genes related with senescence as well as cell aging. FDR: false discovery rate.

Article Snippet: The standard protocol used for sample preparation and microarray processing is available from Agilent Technologies.

Techniques: Microarray