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Agilent technologies high resolution microarray scanner
High expressed miRNAs in normal human placenta ( A ) HeatMap representing the top 30 high expressed miRNAs in normal human placenta. ( B ) Boxplot presenting normalized level of expression of the 866 miRNAs evaluated in normal human placenta using <t>microarray</t> miRNA expression profile. The bold line indicates de median of signal intensity of all miRNAs; the top edge represents the 75th percentile and the bottom edge the 25th percentile. Vertical bars indicate the upper and inferior limits and circles represent outlier points/samples (points 1.5 IQR above the 3rd quartile of the boxplot).
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1) Product Images from "Highly expressed placental miRNAs control key biological processes in human cancer cell lines"

Article Title: Highly expressed placental miRNAs control key biological processes in human cancer cell lines

Journal: Oncotarget

doi: 10.18632/oncotarget.25264

High expressed miRNAs in normal human placenta ( A ) HeatMap representing the top 30 high expressed miRNAs in normal human placenta. ( B ) Boxplot presenting normalized level of expression of the 866 miRNAs evaluated in normal human placenta using microarray miRNA expression profile. The bold line indicates de median of signal intensity of all miRNAs; the top edge represents the 75th percentile and the bottom edge the 25th percentile. Vertical bars indicate the upper and inferior limits and circles represent outlier points/samples (points 1.5 IQR above the 3rd quartile of the boxplot).
Figure Legend Snippet: High expressed miRNAs in normal human placenta ( A ) HeatMap representing the top 30 high expressed miRNAs in normal human placenta. ( B ) Boxplot presenting normalized level of expression of the 866 miRNAs evaluated in normal human placenta using microarray miRNA expression profile. The bold line indicates de median of signal intensity of all miRNAs; the top edge represents the 75th percentile and the bottom edge the 25th percentile. Vertical bars indicate the upper and inferior limits and circles represent outlier points/samples (points 1.5 IQR above the 3rd quartile of the boxplot).

Techniques Used: Expressing, Microarray

2) Product Images from "The Distribution of Mobile Genetic Elements (MGEs) in MRSA CC398 Is Associated with Both Host and Country"

Article Title: The Distribution of Mobile Genetic Elements (MGEs) in MRSA CC398 Is Associated with Both Host and Country

Journal: Genome Biology and Evolution

doi: 10.1093/gbe/evr092

Validation of the 62-strain Staphylococcus aureus microarray. ( A ) Clustering of triplicate microarray data generated from eight sequenced strains. Note: 1) replicate isolates cluster together and 2) isolates belonging to the same S. aureus lineage cluster more closely together than isolates from different S. aureus lineages. ( B ) Microarray heatmap showing the distribution of 60-mer oligos representing the hsdS genes. The distribution of gene variants of highly variable S. aureus genes can be investigated. An example is the hsdS genes that encode the specificity factor of the RM system and distinguish CC lineages. Staphylococcus aureus carry one or two hsdS genes, and each hsdS gene has two variable regions, TRD1 and TRD2. Horizontal lines represent 90 different 60-mer oligo probes specific to 14 TRD1 variants and 20 TRD2 variants. Isolates are represented by vertical lines and information about the lineage of each isolate is shown at the bottom of the figure. The colour in the middle depicts whether the gene variant is present in the respective isolate; red/yellow = present, black/blue = absent. The intensity of all the colors is an indicator of the total signal intensity, whereas the color is an indicator of test signal over reference signal ratio.
Figure Legend Snippet: Validation of the 62-strain Staphylococcus aureus microarray. ( A ) Clustering of triplicate microarray data generated from eight sequenced strains. Note: 1) replicate isolates cluster together and 2) isolates belonging to the same S. aureus lineage cluster more closely together than isolates from different S. aureus lineages. ( B ) Microarray heatmap showing the distribution of 60-mer oligos representing the hsdS genes. The distribution of gene variants of highly variable S. aureus genes can be investigated. An example is the hsdS genes that encode the specificity factor of the RM system and distinguish CC lineages. Staphylococcus aureus carry one or two hsdS genes, and each hsdS gene has two variable regions, TRD1 and TRD2. Horizontal lines represent 90 different 60-mer oligo probes specific to 14 TRD1 variants and 20 TRD2 variants. Isolates are represented by vertical lines and information about the lineage of each isolate is shown at the bottom of the figure. The colour in the middle depicts whether the gene variant is present in the respective isolate; red/yellow = present, black/blue = absent. The intensity of all the colors is an indicator of the total signal intensity, whereas the color is an indicator of test signal over reference signal ratio.

Techniques Used: Microarray, Generated, Variant Assay

3) Product Images from "New miRNA Profiles Accurately Distinguish Renal Cell Carcinomas and Upper Tract Urothelial Carcinomas from the Normal Kidney"

Article Title: New miRNA Profiles Accurately Distinguish Renal Cell Carcinomas and Upper Tract Urothelial Carcinomas from the Normal Kidney

Journal: PLoS ONE

doi: 10.1371/journal.pone.0091646

ROC analysis using microarray data. ROC curves of the top 30 up-regulated miRNAs in each tissue type using the microarray expression data. Of them, the miRNAs with a p
Figure Legend Snippet: ROC analysis using microarray data. ROC curves of the top 30 up-regulated miRNAs in each tissue type using the microarray expression data. Of them, the miRNAs with a p

Techniques Used: Microarray, Expressing

Correlation between microarrays and qRT-PCR. Median log 2 fold change expression levels of the 14 most up-regulated and 11 most down-regulated miRNAs between ccRCC, papRCC, chRCC and UT-UC and the normal kidney tissue, as determined by both qRT-PCR and microarray analysis. As shown in the figure, qRT-PCR and microarray results were highly compatible. The most identical results between the two techniques were those for ccRCC, which was expected due to the high sample number (Pearson’s CC = 0.778, p
Figure Legend Snippet: Correlation between microarrays and qRT-PCR. Median log 2 fold change expression levels of the 14 most up-regulated and 11 most down-regulated miRNAs between ccRCC, papRCC, chRCC and UT-UC and the normal kidney tissue, as determined by both qRT-PCR and microarray analysis. As shown in the figure, qRT-PCR and microarray results were highly compatible. The most identical results between the two techniques were those for ccRCC, which was expected due to the high sample number (Pearson’s CC = 0.778, p

Techniques Used: Quantitative RT-PCR, Expressing, Microarray

4) Product Images from "Highly expressed placental miRNAs control key biological processes in human cancer cell lines"

Article Title: Highly expressed placental miRNAs control key biological processes in human cancer cell lines

Journal: Oncotarget

doi: 10.18632/oncotarget.25264

High expressed miRNAs in normal human placenta ( A ) HeatMap representing the top 30 high expressed miRNAs in normal human placenta. ( B ) Boxplot presenting normalized level of expression of the 866 miRNAs evaluated in normal human placenta using microarray miRNA expression profile. The bold line indicates de median of signal intensity of all miRNAs; the top edge represents the 75th percentile and the bottom edge the 25th percentile. Vertical bars indicate the upper and inferior limits and circles represent outlier points/samples (points 1.5 IQR above the 3rd quartile of the boxplot).
Figure Legend Snippet: High expressed miRNAs in normal human placenta ( A ) HeatMap representing the top 30 high expressed miRNAs in normal human placenta. ( B ) Boxplot presenting normalized level of expression of the 866 miRNAs evaluated in normal human placenta using microarray miRNA expression profile. The bold line indicates de median of signal intensity of all miRNAs; the top edge represents the 75th percentile and the bottom edge the 25th percentile. Vertical bars indicate the upper and inferior limits and circles represent outlier points/samples (points 1.5 IQR above the 3rd quartile of the boxplot).

Techniques Used: Expressing, Microarray

5) Product Images from "The lysine‐specific methyltransferase KMT2C/ MLL3 regulates DNA repair components in cancer"

Article Title: The lysine‐specific methyltransferase KMT2C/ MLL3 regulates DNA repair components in cancer

Journal: EMBO Reports

doi: 10.15252/embr.201846821

KMT 2C downregulation in cancer tissue KMT2C mutations identified in our study cohort of human bladder cancers. Mutations in red are predicted to be damaging while those in black benign, according to the PolyPHEN‐2 algorithm (D and B, respectively, in Table EV1 ) 95 . Comparison of KMT2C expression in cancer/healthy matched tissue pairs ( n = 104) of the study cohort. Expression is presented as log(ratio tumor/healthy) in the y ‐axis. Data obtained from qRT–PCR analysis. P value calculated by Wilcoxon signed‐rank test. Immunofluorescence (top) and Western blot analysis (bottom) against KMT2C on representative human bladder cancers with variable KMT2C transcript levels: 11 th , 4 th , 93 rd , and 79 th percentiles for UCC30, 6, 7, and 29, respectively ( Appendix Table S2 ), from the differential expression analysis of the study cohort. Antibodies against KRT5 or KRT20 were used to stain urothelial cells and DAPI as nuclear counterstain. β‐Actin is used as loading control in Western blots. Scale bars indicate 50 μm. Comparison of KMT2C expression in human healthy and cancer tissues from bladder cancer (BC, n = 136), colorectal adenocarcinoma (COAD, n = 128), non‐small‐cell lung cancer (NSCLC, n = 341), and head and neck squamous cell carcinoma (HNSCC, n = 174) patients. For NSCLC analysis, separate cohorts from adenocarcinoma and squamous cell carcinoma were combined. Separate analysis of the two NSCLC subtypes (adenocarcinoma and squamous cell carcinoma) yielded the same results. For COAD, the y ‐axis is the log2(ratio tumor/normal) of KMT2C expression as assessed with Affymetrix microarray. All expression data were obtained from TCGA through cbioportal.org. P values calculated by Mann–Whitney U ‐test. The middle lines inside the boxes indicate the median (50 th percentile). The lower and the upper box boundaries represent the 25 th percentile and the 75 th percentile, respectively. The lower and upper whiskers extend to the lowest and highest values, respectively, within the 1.5× interquartile range (box height) from the box boundaries. Source data are available online for this figure.
Figure Legend Snippet: KMT 2C downregulation in cancer tissue KMT2C mutations identified in our study cohort of human bladder cancers. Mutations in red are predicted to be damaging while those in black benign, according to the PolyPHEN‐2 algorithm (D and B, respectively, in Table EV1 ) 95 . Comparison of KMT2C expression in cancer/healthy matched tissue pairs ( n = 104) of the study cohort. Expression is presented as log(ratio tumor/healthy) in the y ‐axis. Data obtained from qRT–PCR analysis. P value calculated by Wilcoxon signed‐rank test. Immunofluorescence (top) and Western blot analysis (bottom) against KMT2C on representative human bladder cancers with variable KMT2C transcript levels: 11 th , 4 th , 93 rd , and 79 th percentiles for UCC30, 6, 7, and 29, respectively ( Appendix Table S2 ), from the differential expression analysis of the study cohort. Antibodies against KRT5 or KRT20 were used to stain urothelial cells and DAPI as nuclear counterstain. β‐Actin is used as loading control in Western blots. Scale bars indicate 50 μm. Comparison of KMT2C expression in human healthy and cancer tissues from bladder cancer (BC, n = 136), colorectal adenocarcinoma (COAD, n = 128), non‐small‐cell lung cancer (NSCLC, n = 341), and head and neck squamous cell carcinoma (HNSCC, n = 174) patients. For NSCLC analysis, separate cohorts from adenocarcinoma and squamous cell carcinoma were combined. Separate analysis of the two NSCLC subtypes (adenocarcinoma and squamous cell carcinoma) yielded the same results. For COAD, the y ‐axis is the log2(ratio tumor/normal) of KMT2C expression as assessed with Affymetrix microarray. All expression data were obtained from TCGA through cbioportal.org. P values calculated by Mann–Whitney U ‐test. The middle lines inside the boxes indicate the median (50 th percentile). The lower and the upper box boundaries represent the 25 th percentile and the 75 th percentile, respectively. The lower and upper whiskers extend to the lowest and highest values, respectively, within the 1.5× interquartile range (box height) from the box boundaries. Source data are available online for this figure.

Techniques Used: Expressing, Quantitative RT-PCR, Immunofluorescence, Western Blot, Staining, Microarray, MANN-WHITNEY

6) Product Images from "Design and validation of an oligonucleotide microarray for the detection of genomic rearrangements associated with common hereditary cancer syndromes"

Article Title: Design and validation of an oligonucleotide microarray for the detection of genomic rearrangements associated with common hereditary cancer syndromes

Journal: Journal of Experimental & Clinical Cancer Research : CR

doi: 10.1186/s13046-014-0074-9

Diagrammatic representation of the 1900 bp deletion that starts in intron 9 of MSH2 and removes the first 94 bases of exon 10. This figure maps the locations of multiple overlapping microarray probes that can assess for LRs in this region. The MLH1/MSH2 MLPA kit (MRC-Holland, P003-C1) has only one MLPA probe in intron 10. The locations of the forward and reverse sequencing primers and the microarray probes that cover these regions are also depicted.
Figure Legend Snippet: Diagrammatic representation of the 1900 bp deletion that starts in intron 9 of MSH2 and removes the first 94 bases of exon 10. This figure maps the locations of multiple overlapping microarray probes that can assess for LRs in this region. The MLH1/MSH2 MLPA kit (MRC-Holland, P003-C1) has only one MLPA probe in intron 10. The locations of the forward and reverse sequencing primers and the microarray probes that cover these regions are also depicted.

Techniques Used: Microarray, Multiplex Ligation-dependent Probe Amplification, Sequencing

Targeted microarray result demonstrating a partial deletion of exon 10 in MSH2 at the A) gene level and B) probe level. Vertical yellow lines represent MSH2 exons. Individual probes are represented by the black dots. Probe clusters for exons devoid of LRs are shown to center at the 0 horizontal line, which represents two allelic copies. The cluster of microarray probes spanning the 5’ portion of MSH2 exon 10 probe centers at approximately −0.75, indicating the presence of a partial deletion of this exon.
Figure Legend Snippet: Targeted microarray result demonstrating a partial deletion of exon 10 in MSH2 at the A) gene level and B) probe level. Vertical yellow lines represent MSH2 exons. Individual probes are represented by the black dots. Probe clusters for exons devoid of LRs are shown to center at the 0 horizontal line, which represents two allelic copies. The cluster of microarray probes spanning the 5’ portion of MSH2 exon 10 probe centers at approximately −0.75, indicating the presence of a partial deletion of this exon.

Techniques Used: Microarray

7) Product Images from "Lassa and Marburg viruses elicit distinct host transcriptional responses early after infection"

Article Title: Lassa and Marburg viruses elicit distinct host transcriptional responses early after infection

Journal: BMC Genomics

doi: 10.1186/1471-2164-15-960

Clustering of microarray samples. Each point corresponds to an RNA sample, and their distances represent how similar they are based on applying Multidimensional Scaling to the microarray expression values of 16 genes: 4 common response genes (MX1, OAS1, IFI44L and CXCL10), 4 Marburg-specific response genes (HSPA1B, IGJ, HSPA1L and BIRC3) and 4 Lassa-specific response genes (SIGLEC1, TNK2, TNFSF10 and NR4A2). Lassa- and Marburg-infected samples are shown in increasingly darker shades of blue and red, respectively.
Figure Legend Snippet: Clustering of microarray samples. Each point corresponds to an RNA sample, and their distances represent how similar they are based on applying Multidimensional Scaling to the microarray expression values of 16 genes: 4 common response genes (MX1, OAS1, IFI44L and CXCL10), 4 Marburg-specific response genes (HSPA1B, IGJ, HSPA1L and BIRC3) and 4 Lassa-specific response genes (SIGLEC1, TNK2, TNFSF10 and NR4A2). Lassa- and Marburg-infected samples are shown in increasingly darker shades of blue and red, respectively.

Techniques Used: Microarray, Expressing, Infection

8) Product Images from "Expressed miRNAs target feather related mRNAs involved in cell signaling, cell adhesion and structure during chicken epidermal development"

Article Title: Expressed miRNAs target feather related mRNAs involved in cell signaling, cell adhesion and structure during chicken epidermal development

Journal: Gene

doi: 10.1016/j.gene.2016.06.027

(a) Graphically displays the number of differentially expressed miRNA genes for all 14 comparison groups. (b) Illustrates a hierarchical clustering dendrogram of the biological replicates grouped by their respective microarray sample and based on the
Figure Legend Snippet: (a) Graphically displays the number of differentially expressed miRNA genes for all 14 comparison groups. (b) Illustrates a hierarchical clustering dendrogram of the biological replicates grouped by their respective microarray sample and based on the

Techniques Used: Microarray

9) Product Images from "Deciphering the response of Mycobacterium smegmatis to nitrogen stress using bipartite active modules"

Article Title: Deciphering the response of Mycobacterium smegmatis to nitrogen stress using bipartite active modules

Journal: BMC Genomics

doi: 10.1186/1471-2164-14-436

Changes in the mycobacterial transcriptome in response to nitrogen stress. Significant gene expression response is observed upon external nitrogen depletion. Very few genes display changes in expression until external depletion, where approximately 1000 genes are differentially expressed in nitrogen limiting and not nitrogen excess environments. Up-regulated genes are represented by black bars and down regulated genes represented by grey bars. Microarray expression data was obtained from three independent biological replicates. The concentration of ammonium (mM) in the external medium is represented by a grey dashed line with closed triangles.
Figure Legend Snippet: Changes in the mycobacterial transcriptome in response to nitrogen stress. Significant gene expression response is observed upon external nitrogen depletion. Very few genes display changes in expression until external depletion, where approximately 1000 genes are differentially expressed in nitrogen limiting and not nitrogen excess environments. Up-regulated genes are represented by black bars and down regulated genes represented by grey bars. Microarray expression data was obtained from three independent biological replicates. The concentration of ammonium (mM) in the external medium is represented by a grey dashed line with closed triangles.

Techniques Used: Expressing, Microarray, Concentration Assay

10) Product Images from "Single-Round Patterned DNA Library Microarray Aptamer Lead Identification"

Article Title: Single-Round Patterned DNA Library Microarray Aptamer Lead Identification

Journal: Journal of Analytical Methods in Chemistry

doi: 10.1155/2015/137489

Microarray performance of the top 15 ranked potential thrombin binders of PT2 compared to controls. Inset: close-up view of the intensities of the top 5 ranked sequences compared to the negative control. Error bars represent standard deviation of replicates of fluorescence values obtained from a 2 h incubation of 100 nM Cy3-thrombin with the microarray at 20°C.
Figure Legend Snippet: Microarray performance of the top 15 ranked potential thrombin binders of PT2 compared to controls. Inset: close-up view of the intensities of the top 5 ranked sequences compared to the negative control. Error bars represent standard deviation of replicates of fluorescence values obtained from a 2 h incubation of 100 nM Cy3-thrombin with the microarray at 20°C.

Techniques Used: Microarray, Negative Control, Standard Deviation, Fluorescence, Incubation

11) Product Images from "Linking Microbial Community and Catabolic Gene Structures during the Adaptation of Three Contaminated Soils under Continuous Long-Term Pollutant Stress"

Article Title: Linking Microbial Community and Catabolic Gene Structures during the Adaptation of Three Contaminated Soils under Continuous Long-Term Pollutant Stress

Journal: Applied and Environmental Microbiology

doi: 10.1128/AEM.03482-15

Microarray hybridization profiles of CZE soil samples. Soils were incubated for 90 days in the presence of benzene or BTEX or without the addition of contaminants (control), and probes showing hybridization in at least one sample of the respective soil
Figure Legend Snippet: Microarray hybridization profiles of CZE soil samples. Soils were incubated for 90 days in the presence of benzene or BTEX or without the addition of contaminants (control), and probes showing hybridization in at least one sample of the respective soil

Techniques Used: Microarray, Hybridization, Incubation

Microarray hybridization profiles of BRA soil samples. Soils were incubated for 90 days in the presence of benzene or BTEX or without the addition of contaminants (control), and probes showing hybridization in at least one sample of the respective soil
Figure Legend Snippet: Microarray hybridization profiles of BRA soil samples. Soils were incubated for 90 days in the presence of benzene or BTEX or without the addition of contaminants (control), and probes showing hybridization in at least one sample of the respective soil

Techniques Used: Microarray, Hybridization, Incubation

Microarray hybridization profiles of SUI soil samples. Soils were incubated for 90 days in the presence of benzene or BTEX or without the addition of contaminants (control), and probes showing hybridization in at least one sample of the respective soil
Figure Legend Snippet: Microarray hybridization profiles of SUI soil samples. Soils were incubated for 90 days in the presence of benzene or BTEX or without the addition of contaminants (control), and probes showing hybridization in at least one sample of the respective soil

Techniques Used: Microarray, Hybridization, Incubation

12) Product Images from "Insights into the prevalence and underlying causes of clonal variation through transcriptomic analysis in Pichia pastoris"

Article Title: Insights into the prevalence and underlying causes of clonal variation through transcriptomic analysis in Pichia pastoris

Journal: Applied Microbiology and Biotechnology

doi: 10.1007/s00253-017-8317-2

Downregulation of expression of genes in the autophagy pathway of CV7(L) compared to wild-type. Microarray data was mapped using KEGG Mapper Search Colour pathway. Green boxes indicate organism-specific pathways. Blue boxes show genes that are significantly downregulated. The figure was generated using the KEGG Mapper Search Colour pathway programme (Kanehisa and Goto 2000 ; Kanehisa et al. 2012 )
Figure Legend Snippet: Downregulation of expression of genes in the autophagy pathway of CV7(L) compared to wild-type. Microarray data was mapped using KEGG Mapper Search Colour pathway. Green boxes indicate organism-specific pathways. Blue boxes show genes that are significantly downregulated. The figure was generated using the KEGG Mapper Search Colour pathway programme (Kanehisa and Goto 2000 ; Kanehisa et al. 2012 )

Techniques Used: Expressing, Microarray, Generated

13) Product Images from "Intestinal CD103+CD11b− dendritic cells restrain colitis via IFN-γ-induced anti-inflammatory response in epithelial cells"

Article Title: Intestinal CD103+CD11b− dendritic cells restrain colitis via IFN-γ-induced anti-inflammatory response in epithelial cells

Journal: Mucosal Immunology

doi: 10.1038/mi.2015.64

Transcriptome of colon dendritic cell (DC) subsets. ( a ) Sorting strategy for colon DC isolation. Large intestines obtained from 8 mice, either control (steady state (SS)) or dextran sodium sulfate (DSS) treated (day 4 DSS), were pooled and lamina propria (LP) cells were isolated. Procedure was repeated three times independently. Following CD11c high MHCII + DC subsets were sorted and analyzed in a gene expression microarray: (1) CD103 + CD11b − , (2) CD103 + CD11b + , and (3) CD103 − CD11b + . ( b ) Transcript heat map of the ∼640 genes that are at least twofold differentially expressed in one comparison (red: upregulated; green: downregulated). Clustering was performed using Pearson's correlation and complete linkage. Heat map was z -score normalized by row. ( c ) XY plot of the first two components of a principal component analysis (PCA) of all six groups (SS 1–3 and DSS 1–3). ( d ) Heat map showing differential expression of selected genes involved in DC development and function; heat map was generated as described in b .
Figure Legend Snippet: Transcriptome of colon dendritic cell (DC) subsets. ( a ) Sorting strategy for colon DC isolation. Large intestines obtained from 8 mice, either control (steady state (SS)) or dextran sodium sulfate (DSS) treated (day 4 DSS), were pooled and lamina propria (LP) cells were isolated. Procedure was repeated three times independently. Following CD11c high MHCII + DC subsets were sorted and analyzed in a gene expression microarray: (1) CD103 + CD11b − , (2) CD103 + CD11b + , and (3) CD103 − CD11b + . ( b ) Transcript heat map of the ∼640 genes that are at least twofold differentially expressed in one comparison (red: upregulated; green: downregulated). Clustering was performed using Pearson's correlation and complete linkage. Heat map was z -score normalized by row. ( c ) XY plot of the first two components of a principal component analysis (PCA) of all six groups (SS 1–3 and DSS 1–3). ( d ) Heat map showing differential expression of selected genes involved in DC development and function; heat map was generated as described in b .

Techniques Used: Isolation, Mouse Assay, Expressing, Microarray, Generated

14) Product Images from "Identification of candidate long non-coding RNAs in response to myocardial infarction"

Article Title: Identification of candidate long non-coding RNAs in response to myocardial infarction

Journal: BMC Genomics

doi: 10.1186/1471-2164-15-460

Quantitative assessment of lncRNAs in the heart. Expression of the top 10 lncRNAs identified as differentially expressed between MI and sham-operated mice in microarray experiments was quantified using quantitative RT-PCR, first (A) in the derivation group of 8 mice (4 sham and 4 MI), and then (B) in an independent validation group of 16 mice (8 sham and 8 MI). LncRNAs expression is shown relative to GAPDH (log scale). *P
Figure Legend Snippet: Quantitative assessment of lncRNAs in the heart. Expression of the top 10 lncRNAs identified as differentially expressed between MI and sham-operated mice in microarray experiments was quantified using quantitative RT-PCR, first (A) in the derivation group of 8 mice (4 sham and 4 MI), and then (B) in an independent validation group of 16 mice (8 sham and 8 MI). LncRNAs expression is shown relative to GAPDH (log scale). *P

Techniques Used: Expressing, Mouse Assay, Microarray, Quantitative RT-PCR

Microarray analysis. Cardiac transcriptome of 4 sham-operated mice and 4 MI mice (derivation group) was characterized 24 hours after surgery using microarrays. A . Principal component analysis showing the ability of gene expression data to discriminate MI mice from sham-operated mice. B . M-A plot showing the distribution of the genes in the dataset. The vertical axis displays log2 transformed-fold change and the horizontal axis displays the average signal of each gene. C . Heatmap of differentially expressed genes. For B and C, red color indicates genes up-regulated in MI mice and green color indicates genes down-regulated in MI mice compared to sham mice. Black color indicates genes with comparable expression between MI and sham mice. Significance threshold was 2-fold with a q-value
Figure Legend Snippet: Microarray analysis. Cardiac transcriptome of 4 sham-operated mice and 4 MI mice (derivation group) was characterized 24 hours after surgery using microarrays. A . Principal component analysis showing the ability of gene expression data to discriminate MI mice from sham-operated mice. B . M-A plot showing the distribution of the genes in the dataset. The vertical axis displays log2 transformed-fold change and the horizontal axis displays the average signal of each gene. C . Heatmap of differentially expressed genes. For B and C, red color indicates genes up-regulated in MI mice and green color indicates genes down-regulated in MI mice compared to sham mice. Black color indicates genes with comparable expression between MI and sham mice. Significance threshold was 2-fold with a q-value

Techniques Used: Microarray, Mouse Assay, Expressing, Transformation Assay

Effect of MI on lncRNAs expression in the heart. Microarrays performed with the 4 MI and 4 sham-operated mice (Derivation group) were mined for lncRNAs data. A . Analytical pipeline used to identify microarray probes recognizing lncRNAs. B . Percentage of probes on the microarray corresponding to mRNA and lncRNA transcripts. C . Heat-map of lncRNAs differentially expressed between MI and sham mice with a threshold fold-change of 2-fold and a q-value
Figure Legend Snippet: Effect of MI on lncRNAs expression in the heart. Microarrays performed with the 4 MI and 4 sham-operated mice (Derivation group) were mined for lncRNAs data. A . Analytical pipeline used to identify microarray probes recognizing lncRNAs. B . Percentage of probes on the microarray corresponding to mRNA and lncRNA transcripts. C . Heat-map of lncRNAs differentially expressed between MI and sham mice with a threshold fold-change of 2-fold and a q-value

Techniques Used: Expressing, Mouse Assay, Microarray

Correlation between lncRNAs and remodeling genes. Microarray data from the derivation group of 4 sham-operated and 4 MI mice were used in these analyses. A . Networks indicating the strength of the correlation between the lncRNAs MIRT1 and MIRT2 and 38 coding genes known to be involved in remodeling (“remodeling genes”). Remodeling genes differentially expressed between sham-operated and MI mice are coloured, with darker colour indicating a strong differential expression. Red colour indicates a higher level of expression in MI mice compared to sham-operated mice. Remodeling genes unaffected by MI are in white circles. A q-value
Figure Legend Snippet: Correlation between lncRNAs and remodeling genes. Microarray data from the derivation group of 4 sham-operated and 4 MI mice were used in these analyses. A . Networks indicating the strength of the correlation between the lncRNAs MIRT1 and MIRT2 and 38 coding genes known to be involved in remodeling (“remodeling genes”). Remodeling genes differentially expressed between sham-operated and MI mice are coloured, with darker colour indicating a strong differential expression. Red colour indicates a higher level of expression in MI mice compared to sham-operated mice. Remodeling genes unaffected by MI are in white circles. A q-value

Techniques Used: Microarray, Mouse Assay, Expressing

15) Product Images from "Single-Round Patterned DNA Library Microarray Aptamer Lead Identification"

Article Title: Single-Round Patterned DNA Library Microarray Aptamer Lead Identification

Journal: Journal of Analytical Methods in Chemistry

doi: 10.1155/2015/137489

Microarray performance of the top 15 ranked potential thrombin binders of PT2 compared to controls. Inset: close-up view of the intensities of the top 5 ranked sequences compared to the negative control. Error bars represent standard deviation of replicates of fluorescence values obtained from a 2 h incubation of 100 nM Cy3-thrombin with the microarray at 20°C.
Figure Legend Snippet: Microarray performance of the top 15 ranked potential thrombin binders of PT2 compared to controls. Inset: close-up view of the intensities of the top 5 ranked sequences compared to the negative control. Error bars represent standard deviation of replicates of fluorescence values obtained from a 2 h incubation of 100 nM Cy3-thrombin with the microarray at 20°C.

Techniques Used: Microarray, Negative Control, Standard Deviation, Fluorescence, Incubation

16) Product Images from "Carbon availability triggers the decomposition of plant litter and assimilation of nitrogen by an ectomycorrhizal fungus"

Article Title: Carbon availability triggers the decomposition of plant litter and assimilation of nitrogen by an ectomycorrhizal fungus

Journal: The ISME Journal

doi: 10.1038/ismej.2013.91

Transcriptional responses in the mycelium of P. involutus when grown in organic matter (OM) extracts, with or without glucose (G) and with or without NH 4 + (N) as shown by microarray analysis. ( a ) Principal component analysis (PCA) was performed on the expression levels of 10 443 transcripts out of 11 528 analyzed on the DNA microarray that had a false-discovery rate of q ⩽0.01. MMN, minimum Melin–Norkrans (that is, mineral nutrient) medium. n =3, except for MMN ( n =6); each point in the PCA represents a replicate. ( b ) Differentially expressed genes in OM versus MMN. The scatter plots show the intensity of the normalized and log 2 -transformed hybridization signals. The diagonal line ( y = x ) shows genes with near identical hybridization signals. The lines at y = x +1 and y = x −1 correspond to a log 2 relative expression between the OM substrates and MMN of +0.5 and −0.5, respectively. The numbers of genes upregulated more than twofold ( q ⩽0.01) are shown in parentheses. ( c ) The numbers of transcripts in various functional categories that were upregulated more than twofold ( q ⩽0.01) in pairwise comparisons of transcription levels after growth in media containing OM versus MMN. The total numbers of transcripts annotated to each functional category among the 11 528 probe sequences are given in parentheses. The significance of the enrichments are shown in Supplementary Table S3 .
Figure Legend Snippet: Transcriptional responses in the mycelium of P. involutus when grown in organic matter (OM) extracts, with or without glucose (G) and with or without NH 4 + (N) as shown by microarray analysis. ( a ) Principal component analysis (PCA) was performed on the expression levels of 10 443 transcripts out of 11 528 analyzed on the DNA microarray that had a false-discovery rate of q ⩽0.01. MMN, minimum Melin–Norkrans (that is, mineral nutrient) medium. n =3, except for MMN ( n =6); each point in the PCA represents a replicate. ( b ) Differentially expressed genes in OM versus MMN. The scatter plots show the intensity of the normalized and log 2 -transformed hybridization signals. The diagonal line ( y = x ) shows genes with near identical hybridization signals. The lines at y = x +1 and y = x −1 correspond to a log 2 relative expression between the OM substrates and MMN of +0.5 and −0.5, respectively. The numbers of genes upregulated more than twofold ( q ⩽0.01) are shown in parentheses. ( c ) The numbers of transcripts in various functional categories that were upregulated more than twofold ( q ⩽0.01) in pairwise comparisons of transcription levels after growth in media containing OM versus MMN. The total numbers of transcripts annotated to each functional category among the 11 528 probe sequences are given in parentheses. The significance of the enrichments are shown in Supplementary Table S3 .

Techniques Used: Microarray, Expressing, Transformation Assay, Hybridization, Functional Assay

17) Product Images from "Changes in tear biomarker levels in keratoconus after corneal collagen crosslinking"

Article Title: Changes in tear biomarker levels in keratoconus after corneal collagen crosslinking

Journal: Molecular Vision

doi:

Antibody microarrays customized. A : Specific device for analyzing four microarrays simultaneously. B,C : Spotting pattern for the 24-subarray format. D : Representative image of the arrays showing the distribution of the standard calibration curve and samples. Only one microarray slide contains a standard calibration curve (left column) and the fluorescence acquisition for 16 tear samples (Microarray 1). Other slices (Microarrays 2–4) show the fluorescence for 24 tear samples. Fluorescence scans of the microarray multiplex assays were acquired at 633 nm.
Figure Legend Snippet: Antibody microarrays customized. A : Specific device for analyzing four microarrays simultaneously. B,C : Spotting pattern for the 24-subarray format. D : Representative image of the arrays showing the distribution of the standard calibration curve and samples. Only one microarray slide contains a standard calibration curve (left column) and the fluorescence acquisition for 16 tear samples (Microarray 1). Other slices (Microarrays 2–4) show the fluorescence for 24 tear samples. Fluorescence scans of the microarray multiplex assays were acquired at 633 nm.

Techniques Used: Microarray, Fluorescence, Multiplex Assay

18) Product Images from "Comprehensive analysis of tobacco pollen transcriptome unveils common pathways in polar cell expansion and underlying heterochronic shift during spermatogenesis"

Article Title: Comprehensive analysis of tobacco pollen transcriptome unveils common pathways in polar cell expansion and underlying heterochronic shift during spermatogenesis

Journal: BMC Plant Biology

doi: 10.1186/1471-2229-12-24

Quantitative RT-PCR validation of microarray gene expression . Relative expression levels of selected genes determined at mature pollen (MP) and at four stages of pollen-tube growth (4, 13, 24 and 48 h of cultivation). On the secondary axis, corresponding normalized expression signal at two pollen stages (MP and PT4) derived from microarray chip hybridization. The tobacco 18S RNA gene was used to normalize obtained Ct values to compute relative expression levels at each stage of the pollen gametophyte development.
Figure Legend Snippet: Quantitative RT-PCR validation of microarray gene expression . Relative expression levels of selected genes determined at mature pollen (MP) and at four stages of pollen-tube growth (4, 13, 24 and 48 h of cultivation). On the secondary axis, corresponding normalized expression signal at two pollen stages (MP and PT4) derived from microarray chip hybridization. The tobacco 18S RNA gene was used to normalize obtained Ct values to compute relative expression levels at each stage of the pollen gametophyte development.

Techniques Used: Quantitative RT-PCR, Microarray, Expressing, Derivative Assay, Chromatin Immunoprecipitation, Hybridization

19) Product Images from "Global transcriptional response of Caulobacter crescentus to iron availability"

Article Title: Global transcriptional response of Caulobacter crescentus to iron availability

Journal: BMC Genomics

doi: 10.1186/1471-2164-14-549

Overview of iron-responsive and Fur-regulated genes in C. crescentus identified by microarray analyses. The Venn diagrams were constructed using the number of up- and down-regulated genes from experiments comparing wild type cells exposed to iron-limiting versus iron-replete conditions or comparing fur mutant strain versus wild type strain both in iron-replete condition. The complete set of the genes belonging to each group is listed in Tables 1 , 2 , 3 , 4 and Additional file 1 : Table S1. The upstream region of these genes (−200 to +50 bp relative to the start codon) were searched for sequence motifs using the MEME tool. A 19-pb palindromic motif, corresponding to the Fur binding site, was exclusively found in the group of genes regulated by both iron and Fur.
Figure Legend Snippet: Overview of iron-responsive and Fur-regulated genes in C. crescentus identified by microarray analyses. The Venn diagrams were constructed using the number of up- and down-regulated genes from experiments comparing wild type cells exposed to iron-limiting versus iron-replete conditions or comparing fur mutant strain versus wild type strain both in iron-replete condition. The complete set of the genes belonging to each group is listed in Tables 1 , 2 , 3 , 4 and Additional file 1 : Table S1. The upstream region of these genes (−200 to +50 bp relative to the start codon) were searched for sequence motifs using the MEME tool. A 19-pb palindromic motif, corresponding to the Fur binding site, was exclusively found in the group of genes regulated by both iron and Fur.

Techniques Used: Microarray, Construct, Mutagenesis, Sequencing, Binding Assay

20) Product Images from "Microarrays as Model Biosensor Platforms to Investigate the Structure and Affinity of Aptamers"

Article Title: Microarrays as Model Biosensor Platforms to Investigate the Structure and Affinity of Aptamers

Journal: Journal of Nucleic Acids

doi: 10.1155/2016/9718612

Diagram of variables investigated in the current experiment. Linker length: the distance from the microarray surface was varied; linker identity: nucleobase (adenine, cytosine, guanine, or thymine) was used to tether aptamers to the surface; direct labeling method: fluorescent reporter dye conjugated directly to the target molecule is incubated with aptamer microarray; indirect labeling method: biotinylated-target is added to microarray, followed by a short dye-streptavidin incubation with aptamer microarray. Following incubation, all microarrays were washed and imaged and the data was extracted in order to link fluorescence intensity location with aptamer sequence. Nucleobase structures were created using VIDA, part of OpenEye software.
Figure Legend Snippet: Diagram of variables investigated in the current experiment. Linker length: the distance from the microarray surface was varied; linker identity: nucleobase (adenine, cytosine, guanine, or thymine) was used to tether aptamers to the surface; direct labeling method: fluorescent reporter dye conjugated directly to the target molecule is incubated with aptamer microarray; indirect labeling method: biotinylated-target is added to microarray, followed by a short dye-streptavidin incubation with aptamer microarray. Following incubation, all microarrays were washed and imaged and the data was extracted in order to link fluorescence intensity location with aptamer sequence. Nucleobase structures were created using VIDA, part of OpenEye software.

Techniques Used: Microarray, Labeling, Incubation, Fluorescence, Sequencing, Software

21) Product Images from "Targeted inhibition of mammalian target of rapamycin (mTOR) enhances radiosensitivity in pancreatic carcinoma cells"

Article Title: Targeted inhibition of mammalian target of rapamycin (mTOR) enhances radiosensitivity in pancreatic carcinoma cells

Journal: Drug Design, Development and Therapy

doi: 10.2147/DDDT.S42390

( A ) RT-PCR analysis for the DNA-damage repair and transcription genes after the treatment with RPM; ( B ) Difference between the cDNA microarray and RT-PCR in DNA-damage repair and transcription genes. Notes: The genes examined here are: (1) DDB1(NM_001923); (2) RAD51 (NM_002876); (3) XRCC5 (NM_021141); (4) PCNA (NM_002592); and (5) ABCC4 (NM_005845). The values represent the mean ± SD of the data from three independent experiments. Abbreviations: RPM, rapamycin; RT-PCR, reverse transcription polymerase chain reaction; SD, standard deviation.
Figure Legend Snippet: ( A ) RT-PCR analysis for the DNA-damage repair and transcription genes after the treatment with RPM; ( B ) Difference between the cDNA microarray and RT-PCR in DNA-damage repair and transcription genes. Notes: The genes examined here are: (1) DDB1(NM_001923); (2) RAD51 (NM_002876); (3) XRCC5 (NM_021141); (4) PCNA (NM_002592); and (5) ABCC4 (NM_005845). The values represent the mean ± SD of the data from three independent experiments. Abbreviations: RPM, rapamycin; RT-PCR, reverse transcription polymerase chain reaction; SD, standard deviation.

Techniques Used: Reverse Transcription Polymerase Chain Reaction, Microarray, Standard Deviation

Scatter plot of the gene differential expression in PC-2 cells induced by RPM. Notes: The Cy3 (RPM treated group) and Cy5 (untreated control) channel intensities from the two-color DNA microarray experiments were shown in the scatter plot. The variables appear in a linear relationship, and the linear correlation between them is 0.935. The red plots represented upregulated genes, and the green plots represented downregulated genes. Abbreviation: RPM, rapamycin.
Figure Legend Snippet: Scatter plot of the gene differential expression in PC-2 cells induced by RPM. Notes: The Cy3 (RPM treated group) and Cy5 (untreated control) channel intensities from the two-color DNA microarray experiments were shown in the scatter plot. The variables appear in a linear relationship, and the linear correlation between them is 0.935. The red plots represented upregulated genes, and the green plots represented downregulated genes. Abbreviation: RPM, rapamycin.

Techniques Used: Expressing, Microarray

22) Product Images from "Microarrays as Model Biosensor Platforms to Investigate the Structure and Affinity of Aptamers"

Article Title: Microarrays as Model Biosensor Platforms to Investigate the Structure and Affinity of Aptamers

Journal: Journal of Nucleic Acids

doi: 10.1155/2016/9718612

Diagram of variables investigated in the current experiment. Linker length: the distance from the microarray surface was varied; linker identity: nucleobase (adenine, cytosine, guanine, or thymine) was used to tether aptamers to the surface; direct labeling method: fluorescent reporter dye conjugated directly to the target molecule is incubated with aptamer microarray; indirect labeling method: biotinylated-target is added to microarray, followed by a short dye-streptavidin incubation with aptamer microarray. Following incubation, all microarrays were washed and imaged and the data was extracted in order to link fluorescence intensity location with aptamer sequence. Nucleobase structures were created using VIDA, part of OpenEye software.
Figure Legend Snippet: Diagram of variables investigated in the current experiment. Linker length: the distance from the microarray surface was varied; linker identity: nucleobase (adenine, cytosine, guanine, or thymine) was used to tether aptamers to the surface; direct labeling method: fluorescent reporter dye conjugated directly to the target molecule is incubated with aptamer microarray; indirect labeling method: biotinylated-target is added to microarray, followed by a short dye-streptavidin incubation with aptamer microarray. Following incubation, all microarrays were washed and imaged and the data was extracted in order to link fluorescence intensity location with aptamer sequence. Nucleobase structures were created using VIDA, part of OpenEye software.

Techniques Used: Microarray, Labeling, Incubation, Fluorescence, Sequencing, Software

23) Product Images from "Combined Activity of DCL2 and DCL3 Is Crucial in the Defense against Potato Spindle Tuber Viroid"

Article Title: Combined Activity of DCL2 and DCL3 Is Crucial in the Defense against Potato Spindle Tuber Viroid

Journal: PLoS Pathogens

doi: 10.1371/journal.ppat.1005936

DCL levels upon PSTVd infection. (A) Volcano plot from microarray experiment with RNA from leaves of WT and PSTVd N . benthamiana infected plants (3wpi). N . benthamiana genes with no significant alteration of their expression level are indicated with black dots, while red dots represent genes with a significant higher or lower expression (fold change (FC) ≥ 2, Benjamini-Hochberg (BH) FDR-corrected P-value
Figure Legend Snippet: DCL levels upon PSTVd infection. (A) Volcano plot from microarray experiment with RNA from leaves of WT and PSTVd N . benthamiana infected plants (3wpi). N . benthamiana genes with no significant alteration of their expression level are indicated with black dots, while red dots represent genes with a significant higher or lower expression (fold change (FC) ≥ 2, Benjamini-Hochberg (BH) FDR-corrected P-value

Techniques Used: Infection, Microarray, Expressing

24) Product Images from "Hypermethylation of EBF3 and IRX1 Genes in Synovial Fibroblasts of Patients with Rheumatoid Arthritis"

Article Title: Hypermethylation of EBF3 and IRX1 Genes in Synovial Fibroblasts of Patients with Rheumatoid Arthritis

Journal: Molecules and Cells

doi: 10.1007/s10059-013-2302-0

Scheme of genome-wide screening in RASFs using MeDIA-mediated CpG microarray analysis. (A) Two pooled DNA samples from either two RASFs or two OASFs were amplified, and labeled with Cy5-dUTP and Cy3-dUTP, respectively. The dye-labeled DNA samples were
Figure Legend Snippet: Scheme of genome-wide screening in RASFs using MeDIA-mediated CpG microarray analysis. (A) Two pooled DNA samples from either two RASFs or two OASFs were amplified, and labeled with Cy5-dUTP and Cy3-dUTP, respectively. The dye-labeled DNA samples were

Techniques Used: Genome Wide, Microarray, Amplification, Labeling

Signal intensity of 13 hypermethylated genes in RASFs and OASFs. The signal intensity of the dye-labeled DNA samples at each of three adjacent probes was interpreted using a high resolution microarray scanner. Intensities of DNA of OASFs and RASFs were
Figure Legend Snippet: Signal intensity of 13 hypermethylated genes in RASFs and OASFs. The signal intensity of the dye-labeled DNA samples at each of three adjacent probes was interpreted using a high resolution microarray scanner. Intensities of DNA of OASFs and RASFs were

Techniques Used: Labeling, Microarray

25) Product Images from "Ubiquitin C decrement plays a pivotal role in replicative senescence of bone marrow mesenchymal stromal cells"

Article Title: Ubiquitin C decrement plays a pivotal role in replicative senescence of bone marrow mesenchymal stromal cells

Journal: Cell Death & Disease

doi: 10.1038/s41419-017-0032-5

Biological and genetic characteristics of replicative senescence in hBM-MSCs a Morphologic changes during in vitro culture. Typical homozygous populations of fibroblast-like cells were observed at P2 and P4. Enlarged type II cells with altered morphology were evident at P6 and were more prevalent at P8. Scale bars, 100 μm. b Increment of enlarged type II cells and senescence-associated β-galactosidase (SA-β-gal) positive cells during in vitro culture. Each point corresponds to the mean and SD for at least three independent experiments at each passage. c Representative images of SA-β-gal staining during in vitro culture. SA-β-gal-positive enlarged hBM-MSCs were observed after P5 (indicated with white arrows) and increased in prevalence at P7 and P9. Mean and SD are shown. Scale bars, 100 μm. d Growth kinetics of hBM-MSCs during passaging. Data from three donors are presented and scored as population doubling time (PDT) plotted against passage. e Evaluation of mesodermal differentiation potential of hBM-MSCs at P2, P5 and P8 in terms of adipogenesis (Oil red O), chondrogenesis (Alcian blue) and osteogenesis (silver nitrate). Scale bars, 100 μm. f Changes in metaphase cell count from three donors. The number of available metaphases was decreased after P5. g Single-nucleotide microarray analysis of copy number alterations (CNAs) at P2, P4, P6 and P8 from three donors. Red circle indicates a small CNA at chromosome 7 that was first detected at P6 and was maintained to P8 in MSC3. See also Supplementary Fig. 1S
Figure Legend Snippet: Biological and genetic characteristics of replicative senescence in hBM-MSCs a Morphologic changes during in vitro culture. Typical homozygous populations of fibroblast-like cells were observed at P2 and P4. Enlarged type II cells with altered morphology were evident at P6 and were more prevalent at P8. Scale bars, 100 μm. b Increment of enlarged type II cells and senescence-associated β-galactosidase (SA-β-gal) positive cells during in vitro culture. Each point corresponds to the mean and SD for at least three independent experiments at each passage. c Representative images of SA-β-gal staining during in vitro culture. SA-β-gal-positive enlarged hBM-MSCs were observed after P5 (indicated with white arrows) and increased in prevalence at P7 and P9. Mean and SD are shown. Scale bars, 100 μm. d Growth kinetics of hBM-MSCs during passaging. Data from three donors are presented and scored as population doubling time (PDT) plotted against passage. e Evaluation of mesodermal differentiation potential of hBM-MSCs at P2, P5 and P8 in terms of adipogenesis (Oil red O), chondrogenesis (Alcian blue) and osteogenesis (silver nitrate). Scale bars, 100 μm. f Changes in metaphase cell count from three donors. The number of available metaphases was decreased after P5. g Single-nucleotide microarray analysis of copy number alterations (CNAs) at P2, P4, P6 and P8 from three donors. Red circle indicates a small CNA at chromosome 7 that was first detected at P6 and was maintained to P8 in MSC3. See also Supplementary Fig. 1S

Techniques Used: In Vitro, Staining, Passaging, Cell Counting, Microarray

26) Product Images from "Suppression of cell division-associated genes by Helicobacter pylori attenuates proliferation of RAW264.7 monocytic macrophage cells"

Article Title: Suppression of cell division-associated genes by Helicobacter pylori attenuates proliferation of RAW264.7 monocytic macrophage cells

Journal: Scientific Reports

doi: 10.1038/srep11046

Microarray analysis of H. pylori -infected RAW264.7 cells. ( a and b ) Scatter plots show the expressions of total probes ( a ) and significant probes ( b ), in the non-infected control versus H. pylori (MOI 10, 24 h)-infected cells. Significant probes were selected based on FC
Figure Legend Snippet: Microarray analysis of H. pylori -infected RAW264.7 cells. ( a and b ) Scatter plots show the expressions of total probes ( a ) and significant probes ( b ), in the non-infected control versus H. pylori (MOI 10, 24 h)-infected cells. Significant probes were selected based on FC

Techniques Used: Microarray, Infection

27) Product Images from "Transcriptome profiling of the rice blast fungus during invasive plant infection and in vitro stresses"

Article Title: Transcriptome profiling of the rice blast fungus during invasive plant infection and in vitro stresses

Journal: BMC Genomics

doi: 10.1186/1471-2164-12-49

Gene profiling during a barley infection time-course . Eight genes were chosen from the microarray validation experiments with increased gene expression among all seven conditions (MAS3: MGG_09875.6; SOD: MGG_07697.6; xylanase: MGG_07868.6) and decreased gene expression among all seven conditions (cutinase: MGG_02393.6; endothiapepsin: MGG_02201.6; HSP30 : MGG_05719.6; urea active transporter: MGG_09063.6; glutamine synthetase: MGG_06888.6), compared to the reference sample. Real-time qRT-PCR was performed on all eight genes, with glyceraldehyde 3-phosphate dehydrogenase (GAPDH) used as the endogenous control (housekeeping gene). Five time-points were examined, 24, 48, 72, 96 and 120 hours post-inoculation (hpi), and all samples were performed in triplicate.
Figure Legend Snippet: Gene profiling during a barley infection time-course . Eight genes were chosen from the microarray validation experiments with increased gene expression among all seven conditions (MAS3: MGG_09875.6; SOD: MGG_07697.6; xylanase: MGG_07868.6) and decreased gene expression among all seven conditions (cutinase: MGG_02393.6; endothiapepsin: MGG_02201.6; HSP30 : MGG_05719.6; urea active transporter: MGG_09063.6; glutamine synthetase: MGG_06888.6), compared to the reference sample. Real-time qRT-PCR was performed on all eight genes, with glyceraldehyde 3-phosphate dehydrogenase (GAPDH) used as the endogenous control (housekeeping gene). Five time-points were examined, 24, 48, 72, 96 and 120 hours post-inoculation (hpi), and all samples were performed in triplicate.

Techniques Used: Infection, Microarray, Expressing, Quantitative RT-PCR

28) Product Images from "The RNA-Binding Protein hnRNP K Mediates the Effect of BDNF on Dendritic mRNA Metabolism and Regulates Synaptic NMDA Receptors in Hippocampal Neurons"

Article Title: The RNA-Binding Protein hnRNP K Mediates the Effect of BDNF on Dendritic mRNA Metabolism and Regulates Synaptic NMDA Receptors in Hippocampal Neurons

Journal: eNeuro

doi: 10.1523/ENEURO.0268-17.2017

BDNF induces the dissociation of mRNA from hnRNP K at the synapse. A , B , Effect of BDNF stimulation (50 ng/ml; 10 min) on transcript coimmunoprecipitation with hnRNP K in cultured hippocampal neurons as assessed by microarray and qPCR. The specificity of transcripts associated with hnRNP K was assessed by subtracting the levels of correspondent mRNAs pulled down together with mouse IgG antibodies. hnRNP K-associated mRNAs were then compared between control and BDNF treated neurons. A , Genes coding for synaptic proteins: GluA1, AMPA receptor subunit 1; GluA2, AMPA receptor subunit 2; GluN1, NMDAR subunit 1. B , Other genes: TrkB, tropomyosin-related kinase B receptor; NPAS4, neuronal PAS domain protein 4. The results represent quantitation of four different experiments performed in independent preparations, and are expressed as percentage [mean ± SEM (qPCR) or SD (microarray)] of control; * p
Figure Legend Snippet: BDNF induces the dissociation of mRNA from hnRNP K at the synapse. A , B , Effect of BDNF stimulation (50 ng/ml; 10 min) on transcript coimmunoprecipitation with hnRNP K in cultured hippocampal neurons as assessed by microarray and qPCR. The specificity of transcripts associated with hnRNP K was assessed by subtracting the levels of correspondent mRNAs pulled down together with mouse IgG antibodies. hnRNP K-associated mRNAs were then compared between control and BDNF treated neurons. A , Genes coding for synaptic proteins: GluA1, AMPA receptor subunit 1; GluA2, AMPA receptor subunit 2; GluN1, NMDAR subunit 1. B , Other genes: TrkB, tropomyosin-related kinase B receptor; NPAS4, neuronal PAS domain protein 4. The results represent quantitation of four different experiments performed in independent preparations, and are expressed as percentage [mean ± SEM (qPCR) or SD (microarray)] of control; * p

Techniques Used: Cell Culture, Microarray, Real-time Polymerase Chain Reaction, Quantitation Assay

Stimulation of hippocampal neurons with BDNF decreases the interaction of hnRNP K with a large number of transcripts. A , B , List of the 10 most significantly enriched biological processes associated with mRNAs bound to hnRNP K ( A ) and those that were regulated by BDNF (50 ng/ml for 10 min) ( B ), identified with the PANTHER classification system. Only categories showing at least a 2-fold enrichment (considering the size of our lists) were analyzed and the 10 categories displaying the highest –log 10 ( p value) are shown. The number of transcripts belonging to each category and the fold change (designated in parenthesis) are indicated within graph bars. reg., regulation; pres., presynaptic; chem, chemical; syn., synaptic; pos., positive; proj., projection; diff., differentiation; neg., negative; sys., system; devel., development. C , Cultured hippocampal neurons were stimulated or not with BDNF (50 ng/ml) for 10 min before preparation of cellular extracts. hnRNP K was immunoprecipitated from control and BDNF-treated hippocampal neuron homogenates, and the associated transcripts were identified by microarray analysis. The specificity of transcripts associated with hnRNP K was assessed by subtracting the levels of correspondent mRNAs pulled down together with mouse IgG antibodies. hnRNP K-associated mRNAs were then compared between control and BDNF treated neurons. The results were obtained from the quantification of four different experiments performed in independent preparations, and are expressed as -log ( p value) and log fold change (BDNF vs control). A total of 9509 transcripts showed a decrease in the interaction with hnRNP K in cells stimulated with BDNF; p
Figure Legend Snippet: Stimulation of hippocampal neurons with BDNF decreases the interaction of hnRNP K with a large number of transcripts. A , B , List of the 10 most significantly enriched biological processes associated with mRNAs bound to hnRNP K ( A ) and those that were regulated by BDNF (50 ng/ml for 10 min) ( B ), identified with the PANTHER classification system. Only categories showing at least a 2-fold enrichment (considering the size of our lists) were analyzed and the 10 categories displaying the highest –log 10 ( p value) are shown. The number of transcripts belonging to each category and the fold change (designated in parenthesis) are indicated within graph bars. reg., regulation; pres., presynaptic; chem, chemical; syn., synaptic; pos., positive; proj., projection; diff., differentiation; neg., negative; sys., system; devel., development. C , Cultured hippocampal neurons were stimulated or not with BDNF (50 ng/ml) for 10 min before preparation of cellular extracts. hnRNP K was immunoprecipitated from control and BDNF-treated hippocampal neuron homogenates, and the associated transcripts were identified by microarray analysis. The specificity of transcripts associated with hnRNP K was assessed by subtracting the levels of correspondent mRNAs pulled down together with mouse IgG antibodies. hnRNP K-associated mRNAs were then compared between control and BDNF treated neurons. The results were obtained from the quantification of four different experiments performed in independent preparations, and are expressed as -log ( p value) and log fold change (BDNF vs control). A total of 9509 transcripts showed a decrease in the interaction with hnRNP K in cells stimulated with BDNF; p

Techniques Used: Cell Culture, Immunoprecipitation, Microarray

29) Product Images from "The concentrations of EGFR, LRG1, ITIH4, and F5 in serum correlate with the number of colonic adenomas in ApcPirc/+ rats"

Article Title: The concentrations of EGFR, LRG1, ITIH4, and F5 in serum correlate with the number of colonic adenomas in ApcPirc/+ rats

Journal: Cancer prevention research (Philadelphia, Pa.)

doi: 10.1158/1940-6207.CAPR-14-0056

Gene transcripts upregulated in tumor compared to normal tissue using Agilent Whole Genome Microarray discovery and RT-PCR validation. Microarray candidates (bar graph) represent genes which: 1) show a 5-fold or greater upregulation in mRNA expression
Figure Legend Snippet: Gene transcripts upregulated in tumor compared to normal tissue using Agilent Whole Genome Microarray discovery and RT-PCR validation. Microarray candidates (bar graph) represent genes which: 1) show a 5-fold or greater upregulation in mRNA expression

Techniques Used: Microarray, Reverse Transcription Polymerase Chain Reaction, Expressing

30) Product Images from "Susceptibility of juvenile and adult blood-brain barrier to endothelin-1: regulation of P-glycoprotein and breast cancer resistance protein expression and transport activity"

Article Title: Susceptibility of juvenile and adult blood-brain barrier to endothelin-1: regulation of P-glycoprotein and breast cancer resistance protein expression and transport activity

Journal: Journal of Neuroinflammation

doi: 10.1186/1742-2094-9-273

Cytokines and chemokines levels for 24 hours in juveniles (P21) and adult (P84) rat brains after a single intracerebral injection of endothelin-1. All cytokines, IL-1α, IL-1β, IL-6, IL-10, MCP-1/ccl2, fractalkine and TIMP-1 were simultaneously measured in brain and serum samples using the Agilent technology cytokine microarray (Tebu-bio). All brain values were corrected for individual serum measurements as described previously [ 6 ]. Comparisons between groups were performed using one-way analysis of variance (ANOVA) with the Student-Bonferroni post test. Data are presented as mean ± S.E.M. Statistical significance was set at P
Figure Legend Snippet: Cytokines and chemokines levels for 24 hours in juveniles (P21) and adult (P84) rat brains after a single intracerebral injection of endothelin-1. All cytokines, IL-1α, IL-1β, IL-6, IL-10, MCP-1/ccl2, fractalkine and TIMP-1 were simultaneously measured in brain and serum samples using the Agilent technology cytokine microarray (Tebu-bio). All brain values were corrected for individual serum measurements as described previously [ 6 ]. Comparisons between groups were performed using one-way analysis of variance (ANOVA) with the Student-Bonferroni post test. Data are presented as mean ± S.E.M. Statistical significance was set at P

Techniques Used: Injection, Microarray

31) Product Images from "Multiple environmental stressors induce complex transcriptomic responses indicative of phenotypic outcomes in Western fence lizard"

Article Title: Multiple environmental stressors induce complex transcriptomic responses indicative of phenotypic outcomes in Western fence lizard

Journal: BMC Genomics

doi: 10.1186/s12864-018-5270-0

Summary results for microarray analyses. Venn diagrams in panel ( a ) display the differentially expressed transcripts found in common among treatments based on matching RefSeq Accession IDs. Hierarchical clustering analyses ( b ) identifed relationships based on significant differential transcript expression among treatment combinations for each exposure. Transcripts differentially expressed in common among repeated experimental exposures ( c ) and correlations in expression among these transcripts ( d ) provided opportunities for assessing reproducibility of experimental results. Note that no correlation was calculated for Diet given that only two targets were found in common. Key for Venn Diagrams: Exp = Exposures 1–3, Diet = food level, and Mal = malaria treatment. For hierarchical clustering analysis: infected = malaria infection, restricted = restricted diet and the values 0, 5, 10 and 20 = TNT dosing levels in mg/kg-d
Figure Legend Snippet: Summary results for microarray analyses. Venn diagrams in panel ( a ) display the differentially expressed transcripts found in common among treatments based on matching RefSeq Accession IDs. Hierarchical clustering analyses ( b ) identifed relationships based on significant differential transcript expression among treatment combinations for each exposure. Transcripts differentially expressed in common among repeated experimental exposures ( c ) and correlations in expression among these transcripts ( d ) provided opportunities for assessing reproducibility of experimental results. Note that no correlation was calculated for Diet given that only two targets were found in common. Key for Venn Diagrams: Exp = Exposures 1–3, Diet = food level, and Mal = malaria treatment. For hierarchical clustering analysis: infected = malaria infection, restricted = restricted diet and the values 0, 5, 10 and 20 = TNT dosing levels in mg/kg-d

Techniques Used: Microarray, Expressing, Infection

Experimental designs for microarray experiments across the three single/combined-stressor exposures in the Western fence lizard ( Sceloporus occidentalis ). Numbers within each cell represent the number of biological replicate microarray hybridizations contributing to the overall microarray analysis in the exposure matrix. Cells highlighted in gray represent microarrays hybridized using the same biological replicates for corresponding treatments across Exposure 2 and Exposure 3. Exp1, Exp2 and Exp3 represent Exposure 1, Exposure 2 and Exposure 3, respectively
Figure Legend Snippet: Experimental designs for microarray experiments across the three single/combined-stressor exposures in the Western fence lizard ( Sceloporus occidentalis ). Numbers within each cell represent the number of biological replicate microarray hybridizations contributing to the overall microarray analysis in the exposure matrix. Cells highlighted in gray represent microarrays hybridized using the same biological replicates for corresponding treatments across Exposure 2 and Exposure 3. Exp1, Exp2 and Exp3 represent Exposure 1, Exposure 2 and Exposure 3, respectively

Techniques Used: Microarray, Western Blot

32) Product Images from "Hypermethylation of EBF3 and IRX1 Genes in Synovial Fibroblasts of Patients with Rheumatoid Arthritis"

Article Title: Hypermethylation of EBF3 and IRX1 Genes in Synovial Fibroblasts of Patients with Rheumatoid Arthritis

Journal: Molecules and Cells

doi: 10.1007/s10059-013-2302-0

Scheme of genome-wide screening in RASFs using MeDIA-mediated CpG microarray analysis. (A) Two pooled DNA samples from either two RASFs or two OASFs were amplified, and labeled with Cy5-dUTP and Cy3-dUTP, respectively. The dye-labeled DNA samples were
Figure Legend Snippet: Scheme of genome-wide screening in RASFs using MeDIA-mediated CpG microarray analysis. (A) Two pooled DNA samples from either two RASFs or two OASFs were amplified, and labeled with Cy5-dUTP and Cy3-dUTP, respectively. The dye-labeled DNA samples were

Techniques Used: Genome Wide, Microarray, Amplification, Labeling

Signal intensity of 13 hypermethylated genes in RASFs and OASFs. The signal intensity of the dye-labeled DNA samples at each of three adjacent probes was interpreted using a high resolution microarray scanner. Intensities of DNA of OASFs and RASFs were
Figure Legend Snippet: Signal intensity of 13 hypermethylated genes in RASFs and OASFs. The signal intensity of the dye-labeled DNA samples at each of three adjacent probes was interpreted using a high resolution microarray scanner. Intensities of DNA of OASFs and RASFs were

Techniques Used: Labeling, Microarray

33) Product Images from "High multiple carriage and emergence of Streptococcus pneumoniae vaccine serotype variants in Malawian children"

Article Title: High multiple carriage and emergence of Streptococcus pneumoniae vaccine serotype variants in Malawian children

Journal: BMC Infectious Diseases

doi: 10.1186/s12879-015-0980-2

A comparison of the CPS locus sequence between serotype 6B variant and wild type. These variants were initially detected by microarray as having atypical CPS genes and were further analysed by whole-genome sequencing. A comparative analysis of the CPS locus sequences between variants of serotype 6B and reference sequence CR931639 was performed using Artemis. The divergent gene(s) for the variant are highlighted in red. The 6B variant [ERS096169] harboured an intact allele of the licD- phosphotransferase gene, while a 297 bp deletion was observed in the reference
Figure Legend Snippet: A comparison of the CPS locus sequence between serotype 6B variant and wild type. These variants were initially detected by microarray as having atypical CPS genes and were further analysed by whole-genome sequencing. A comparative analysis of the CPS locus sequences between variants of serotype 6B and reference sequence CR931639 was performed using Artemis. The divergent gene(s) for the variant are highlighted in red. The 6B variant [ERS096169] harboured an intact allele of the licD- phosphotransferase gene, while a 297 bp deletion was observed in the reference

Techniques Used: Sequencing, Variant Assay, Microarray

A comparison of the CPS locus sequence between serotype 19A variant and wild type. These variants were initially detected by microarray as having unusual CPS genes and were further analysed by whole-genome sequencing. The CPS locus sequences were compared between variants of serotype 19A and reference sequences CR931675. The divergent gene(s) for the variant are highlighted in red. The CPS loci of serotype 19A variant [ERS096157] showed an inversion in rmlD gene
Figure Legend Snippet: A comparison of the CPS locus sequence between serotype 19A variant and wild type. These variants were initially detected by microarray as having unusual CPS genes and were further analysed by whole-genome sequencing. The CPS locus sequences were compared between variants of serotype 19A and reference sequences CR931675. The divergent gene(s) for the variant are highlighted in red. The CPS loci of serotype 19A variant [ERS096157] showed an inversion in rmlD gene

Techniques Used: Sequencing, Variant Assay, Microarray

A comparison of the CPS locus sequence between serotype 20 variant and wild type. These variants were initially detected by microarray as having unusual CPS genes and were further analysed by whole-genome sequencing. A comparative analysis of the CPS locus sequences between variants of serotype 20 and reference sequences CR931679 was performed using EasyFig [ 47 ]. The divergent gene(s) for the variant are highlighted in red. The serotype 20 variant [ERS096158] contained a 717 base pair gene deletion within the whaF gene compared to the reference (CR931679)
Figure Legend Snippet: A comparison of the CPS locus sequence between serotype 20 variant and wild type. These variants were initially detected by microarray as having unusual CPS genes and were further analysed by whole-genome sequencing. A comparative analysis of the CPS locus sequences between variants of serotype 20 and reference sequences CR931679 was performed using EasyFig [ 47 ]. The divergent gene(s) for the variant are highlighted in red. The serotype 20 variant [ERS096158] contained a 717 base pair gene deletion within the whaF gene compared to the reference (CR931679)

Techniques Used: Sequencing, Variant Assay, Microarray

Serotype-specific pneumococcal carriage in Malawian children, determined by microarray. A total of 179 pneumococcal strains were detected from 116 nasopharyngeal swabs, comprising 43 distinct pneumococcal serotypes and non-typeable strains (NT). The blue and red bar graphs represent serotypes detected in HIV positive and HIV negative children respectively. The serotypes were classified as Vaccine Type and Non-Vaccine Type. The non-vaccine serotypes were subdivided into high (Non-Vaccine Type (*)) and low (Non-Vaccine Type (**)) invasive potential based on the global frequency of isolation from invasive disease [ 24 ]. Individuals carrying multiple serotypes are represented more than once. The line graph represents cumulative frequency of serotypes isolated and was used to estimate the proportion of Vaccine Type (60 %) and Non-Vaccine Type (40 %)
Figure Legend Snippet: Serotype-specific pneumococcal carriage in Malawian children, determined by microarray. A total of 179 pneumococcal strains were detected from 116 nasopharyngeal swabs, comprising 43 distinct pneumococcal serotypes and non-typeable strains (NT). The blue and red bar graphs represent serotypes detected in HIV positive and HIV negative children respectively. The serotypes were classified as Vaccine Type and Non-Vaccine Type. The non-vaccine serotypes were subdivided into high (Non-Vaccine Type (*)) and low (Non-Vaccine Type (**)) invasive potential based on the global frequency of isolation from invasive disease [ 24 ]. Individuals carrying multiple serotypes are represented more than once. The line graph represents cumulative frequency of serotypes isolated and was used to estimate the proportion of Vaccine Type (60 %) and Non-Vaccine Type (40 %)

Techniques Used: Microarray, Isolation

Multiple carriage of S. pneumoniae serotypes in Malawian children. Microarray was used to determine carriage of multiple pneumococcal serotypes in the nasopharynx of Malawian children. The overall frequency of multiple serotype carriage was 40 % (46/116), with co-colonising samples expressing two (27 %, 31/116)), three (11 %, 13/116) or four (2 %, 2/116) capsular types
Figure Legend Snippet: Multiple carriage of S. pneumoniae serotypes in Malawian children. Microarray was used to determine carriage of multiple pneumococcal serotypes in the nasopharynx of Malawian children. The overall frequency of multiple serotype carriage was 40 % (46/116), with co-colonising samples expressing two (27 %, 31/116)), three (11 %, 13/116) or four (2 %, 2/116) capsular types

Techniques Used: Microarray, Expressing

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Hybridization:

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RNA Extraction:

Article Title: New miRNA Profiles Accurately Distinguish Renal Cell Carcinomas and Upper Tract Urothelial Carcinomas from the Normal Kidney
Article Snippet: Paragraph title: RNA extraction and microRNA microarray analysis ... After hybridization, the microarray slides were scanned at 10 μm using the High-Resolution Microarray Scanner (Agilent Technologies) and stored in an ozone free environment.

Amplification:

Article Title: Lassa and Marburg viruses elicit distinct host transcriptional responses early after infection
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Sample Prep:

Article Title: Lassa and Marburg viruses elicit distinct host transcriptional responses early after infection
Article Snippet: Paragraph title: Sample preparation ... Images were scanned using the Agilent High-Resolution Microarray Scanner and raw microarray images were processed using Agilent’s Feature Extraction software.

Microarray:

Article Title: New miRNA Profiles Accurately Distinguish Renal Cell Carcinomas and Upper Tract Urothelial Carcinomas from the Normal Kidney
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Article Title: Single-Round Patterned DNA Library Microarray Aptamer Lead Identification
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Article Title: Insights into the prevalence and underlying causes of clonal variation through transcriptomic analysis in Pichia pastoris
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Isolation:

Article Title: New miRNA Profiles Accurately Distinguish Renal Cell Carcinomas and Upper Tract Urothelial Carcinomas from the Normal Kidney
Article Snippet: Tissue sections were deparaffinized with xylene and ethanol washes, treated with protease and total RNA containing small RNAs was isolated using the High Pure FFPE RNA Micro Kit (Roche Applied Science). .. After hybridization, the microarray slides were scanned at 10 μm using the High-Resolution Microarray Scanner (Agilent Technologies) and stored in an ozone free environment.

Article Title: Insights into the prevalence and underlying causes of clonal variation through transcriptomic analysis in Pichia pastoris
Article Snippet: After hybridization, slides were washed for 1 min at room temperature in GE wash buffer 1 and 1 min at 37 °C in GE wash buffer 2 (Agilent Technologies UK Ltd., Wokingham, UK), placed beneath an Ozone Barrier Slide cover (Agilent Technologies UK Ltd., Wokingham, UK) and scanned immediately, using an Agilent High-Resolution Microarray Scanner, at 2 μm resolution. .. Furthermore, the linking of regulation patterns through pathway analysis provides greater robustness than when looking at single genes in isolation.

Incubation:

Article Title: The Distribution of Mobile Genetic Elements (MGEs) in MRSA CC398 Is Associated with Both Host and Country
Article Snippet: Eighteen microliters of Cy3- and Cy5-labeled genomic DNA mixture was prepared for microarray hybridization using the Agilent Hybridization Kit (Agilent Technologies) in a total volume of 45 μl and incubated at 95 °C for 3 min then 37 °C for 30 min; 40 μl of the hybridization sample mixture was loaded onto an 8 × 60k microarray and hybridized for 18 h at 65 °C and 20 revolutions per minute in a hybridization oven (Agilent Technologies). .. Slides were then scanned using an Agilent High Resolution Microarray Scanner (Agilent Technologies).

Article Title: Deciphering the response of Mycobacterium smegmatis to nitrogen stress using bipartite active modules
Article Snippet: Labelled cDNA was purified by Qiagen MinElute column, combined with 10× CGH blocking agent and 2× Hi-RPM hybridisation buffer (Agilent) and heated at 95°C for 5 minutes prior to loading onto microarray slides which were incubated overnight in an Agilent rotating oven at 65°C, 20 rpm. .. After hybridization, slides were washed for 5 minutes at room temperature with CGH Wash Buffer 1 (Agilent) and 1 minute at 37°C with CGH Wash buffer 2 (Agilent) and scanned immediately, using an Agilent High Resolution Microarray Scanner, at 2 μm resolution, 100% PMT.

Article Title: Insights into the prevalence and underlying causes of clonal variation through transcriptomic analysis in Pichia pastoris
Article Snippet: Purified samples were hybridised to an Agilent 8 × 60,000 format Sureprint G3 gene expression custom array and incubated overnight in a rotating oven (Agilent Technologies UK Ltd., Wokingham, UK) at 65 °C, 20 rpm. .. After hybridization, slides were washed for 1 min at room temperature in GE wash buffer 1 and 1 min at 37 °C in GE wash buffer 2 (Agilent Technologies UK Ltd., Wokingham, UK), placed beneath an Ozone Barrier Slide cover (Agilent Technologies UK Ltd., Wokingham, UK) and scanned immediately, using an Agilent High-Resolution Microarray Scanner, at 2 μm resolution.

Labeling:

Article Title: New miRNA Profiles Accurately Distinguish Renal Cell Carcinomas and Upper Tract Urothelial Carcinomas from the Normal Kidney
Article Snippet: Total RNA (0.5 μg) from each sample and reference was labeled with Hy3 fluorescent label, using the miRCURY LNA microRNA Hi-Power Labeling Kit (Exiqon, Vedbaek, Denmark), according to the manufacturer protocol. .. After hybridization, the microarray slides were scanned at 10 μm using the High-Resolution Microarray Scanner (Agilent Technologies) and stored in an ozone free environment.

Article Title: Lassa and Marburg viruses elicit distinct host transcriptional responses early after infection
Article Snippet: Briefly, total RNA was extracted from the TRI Reagent LS samples, then amplified using the Low-Input Quick Amp Labeling kit (Agilent Technologies, Santa Clara, CA) and hybridized to Whole Human Genome Oligo Microarrays (Agilent Technologies, Santa Clara, CA) in a 2-color comparative format along with a reference pool of messenger RNA. .. Images were scanned using the Agilent High-Resolution Microarray Scanner and raw microarray images were processed using Agilent’s Feature Extraction software.

Article Title: The Distribution of Mobile Genetic Elements (MGEs) in MRSA CC398 Is Associated with Both Host and Country
Article Snippet: Paragraph title: Microarray Labeling, Hybridizations, and Scanning ... Slides were then scanned using an Agilent High Resolution Microarray Scanner (Agilent Technologies).

Article Title: Highly expressed placental miRNAs control key biological processes in human cancer cell lines
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Article Title: Design and validation of an oligonucleotide microarray for the detection of genomic rearrangements associated with common hereditary cancer syndromes
Article Snippet: Microarray analysis Genomic DNA was labeled with Cy3 & Cy5 dyes using an Enzymatic Labeling Kit (Agilent Technologies, Santa Clara, CA) according to manufacturer’s instructions. .. Array hybridization and washing were performed on custom Agilent 8×15k arrays (Agilent Technologies), and arrays were scanned using a High Resolution Microarray Scanner (Agilent Technologies).

Article Title: The lysine‐specific methyltransferase KMT2C/ MLL3 regulates DNA repair components in cancer
Article Snippet: .. Following purification, the combined labeled DNA samples were applied to the microarray (hybridization for 40 h at 67°C), washed, and scanned at 3 micron resolution on the Agilent High‐Resolution Microarray Scanner (G2505C, Agilent Technologies). .. The images were extracted and analyzed using the Agilent Feature Extraction software and the CytoGenomics v.3.0 software suite.

Purification:

Article Title: The Distribution of Mobile Genetic Elements (MGEs) in MRSA CC398 Is Associated with Both Host and Country
Article Snippet: Labeled DNA samples were pooled and purified using Amicon Ultra Millipore 30-kDa filters (Millipore) and eluted in Tris–ethylenediaminetetraacetic acid in a 20-μl volume. .. Slides were then scanned using an Agilent High Resolution Microarray Scanner (Agilent Technologies).

Article Title: Deciphering the response of Mycobacterium smegmatis to nitrogen stress using bipartite active modules
Article Snippet: Labelled cDNA was purified by Qiagen MinElute column, combined with 10× CGH blocking agent and 2× Hi-RPM hybridisation buffer (Agilent) and heated at 95°C for 5 minutes prior to loading onto microarray slides which were incubated overnight in an Agilent rotating oven at 65°C, 20 rpm. .. After hybridization, slides were washed for 5 minutes at room temperature with CGH Wash Buffer 1 (Agilent) and 1 minute at 37°C with CGH Wash buffer 2 (Agilent) and scanned immediately, using an Agilent High Resolution Microarray Scanner, at 2 μm resolution, 100% PMT.

Article Title: The lysine‐specific methyltransferase KMT2C/ MLL3 regulates DNA repair components in cancer
Article Snippet: .. Following purification, the combined labeled DNA samples were applied to the microarray (hybridization for 40 h at 67°C), washed, and scanned at 3 micron resolution on the Agilent High‐Resolution Microarray Scanner (G2505C, Agilent Technologies). .. The images were extracted and analyzed using the Agilent Feature Extraction software and the CytoGenomics v.3.0 software suite.

Article Title: Insights into the prevalence and underlying causes of clonal variation through transcriptomic analysis in Pichia pastoris
Article Snippet: Purified samples were hybridised to an Agilent 8 × 60,000 format Sureprint G3 gene expression custom array and incubated overnight in a rotating oven (Agilent Technologies UK Ltd., Wokingham, UK) at 65 °C, 20 rpm. .. After hybridization, slides were washed for 1 min at room temperature in GE wash buffer 1 and 1 min at 37 °C in GE wash buffer 2 (Agilent Technologies UK Ltd., Wokingham, UK), placed beneath an Ozone Barrier Slide cover (Agilent Technologies UK Ltd., Wokingham, UK) and scanned immediately, using an Agilent High-Resolution Microarray Scanner, at 2 μm resolution.

Concentration Assay:

Article Title: New miRNA Profiles Accurately Distinguish Renal Cell Carcinomas and Upper Tract Urothelial Carcinomas from the Normal Kidney
Article Snippet: The quality of the total RNA was verified by an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA) and the concentration was measured spectrophotometrically (Nanodrop technologies, Montchanin, DE). .. After hybridization, the microarray slides were scanned at 10 μm using the High-Resolution Microarray Scanner (Agilent Technologies) and stored in an ozone free environment.

Random Hexamer Labeling:

Article Title: Deciphering the response of Mycobacterium smegmatis to nitrogen stress using bipartite active modules
Article Snippet: Preparation of labelled cDNA from total RNA Labelled cDNA was prepared from 1.5 μg total RNA using Cy3-dCTP (GE Healthcare) and SuperScript II reverse transcriptase with random hexamer primers (Life Technologies – Invitrogen ). .. After hybridization, slides were washed for 5 minutes at room temperature with CGH Wash Buffer 1 (Agilent) and 1 minute at 37°C with CGH Wash buffer 2 (Agilent) and scanned immediately, using an Agilent High Resolution Microarray Scanner, at 2 μm resolution, 100% PMT.

Formalin-fixed Paraffin-Embedded:

Article Title: New miRNA Profiles Accurately Distinguish Renal Cell Carcinomas and Upper Tract Urothelial Carcinomas from the Normal Kidney
Article Snippet: Tissue sections were deparaffinized with xylene and ethanol washes, treated with protease and total RNA containing small RNAs was isolated using the High Pure FFPE RNA Micro Kit (Roche Applied Science). .. After hybridization, the microarray slides were scanned at 10 μm using the High-Resolution Microarray Scanner (Agilent Technologies) and stored in an ozone free environment.

Blocking Assay:

Article Title: Deciphering the response of Mycobacterium smegmatis to nitrogen stress using bipartite active modules
Article Snippet: Labelled cDNA was purified by Qiagen MinElute column, combined with 10× CGH blocking agent and 2× Hi-RPM hybridisation buffer (Agilent) and heated at 95°C for 5 minutes prior to loading onto microarray slides which were incubated overnight in an Agilent rotating oven at 65°C, 20 rpm. .. After hybridization, slides were washed for 5 minutes at room temperature with CGH Wash Buffer 1 (Agilent) and 1 minute at 37°C with CGH Wash buffer 2 (Agilent) and scanned immediately, using an Agilent High Resolution Microarray Scanner, at 2 μm resolution, 100% PMT.

Expressing:

Article Title: Expressed miRNAs target feather related mRNAs involved in cell signaling, cell adhesion and structure during chicken epidermal development
Article Snippet: After hybridization and washing, the processed slides were scanned with the Agilent High-Resolution Microarray Scanner (Agilent Technologies; Palo Alto, CA). .. All 8 samples were analyzed with 4 biological replicates, except for the scutate scale day 8 sample which was in triplicate thereby resulting in a total of 31 individual microarray expression samples.

Article Title: Highly expressed placental miRNAs control key biological processes in human cancer cell lines
Article Snippet: Paragraph title: miRNA expression in normal placenta samples ... Microarray slides were scanned using the High-Resolution Microarray Scanner (Agilent Technologies, Santa Clara, CA, USA).

Article Title: Insights into the prevalence and underlying causes of clonal variation through transcriptomic analysis in Pichia pastoris
Article Snippet: Purified samples were hybridised to an Agilent 8 × 60,000 format Sureprint G3 gene expression custom array and incubated overnight in a rotating oven (Agilent Technologies UK Ltd., Wokingham, UK) at 65 °C, 20 rpm. .. After hybridization, slides were washed for 1 min at room temperature in GE wash buffer 1 and 1 min at 37 °C in GE wash buffer 2 (Agilent Technologies UK Ltd., Wokingham, UK), placed beneath an Ozone Barrier Slide cover (Agilent Technologies UK Ltd., Wokingham, UK) and scanned immediately, using an Agilent High-Resolution Microarray Scanner, at 2 μm resolution.

Standard Deviation:

Article Title: Linking Microbial Community and Catabolic Gene Structures during the Adaptation of Three Contaminated Soils under Continuous Long-Term Pollutant Stress
Article Snippet: After scanning with a high-resolution microarray scanner (Agilent Technologies, Life Sciences and Chemical Analysis Group, Santa Clara, CA), spots corresponding to the internal control 50-mers A to D were used to generate a standard curve , and those samples where a linear curve could not be observed were discarded. .. Signal intensities were normalized against the background using the formula NI = [(probe intensity − background intensity)/background intensity], where NI is the normalized signal intensity, and the average intensity and standard deviation of three experimental replicas were determined.

Binding Assay:

Article Title: Single-Round Patterned DNA Library Microarray Aptamer Lead Identification
Article Snippet: Microarray equipment consisted of the following: custom 8 × 15 k DNA microarrays, 8 × 15 k gasket slides, ozone barrier slides, hybridization chambers, scanner cassettes, hybridization oven, and High-resolution Microarray Scanner (all Agilent) and slide rack and wash dishes (Shandon) and Kimtech polypropylene wipes (Kimberly-Clark). .. Buffers: Binding [PBSMTB]-1x PBS (8.1 mM Na2 HPO4 , 1.1 mM KH2 PO4 , 2.7 mM KCl, 137 mM NaCl, pH 7.4) + 1 mM MgCl2 + 0.1% Tween-20 and 1% BSA; Washing [PBSM]-1x PBS (8.1 mM Na2 HPO4 , 1.1 mM KH2 PO4 , 2.7 mM KCl, 137 mM NaCl, pH 7.4) + 1 mM MgCl2 ; Rinse [R]-1/4 dilution of PBSM and nuclease free water.

Chromatin Immunoprecipitation:

Article Title: Expressed miRNAs target feather related mRNAs involved in cell signaling, cell adhesion and structure during chicken epidermal development
Article Snippet: Total RNA was reversed transcribed into cDNA and then the cDNA was fragmented, labelled and hybridized to the single color custom Agilent microarray gene chip at the South Carolina College of Pharmacy Microarray Core Facility (University of South Carolina, Columbia, SC). .. After hybridization and washing, the processed slides were scanned with the Agilent High-Resolution Microarray Scanner (Agilent Technologies; Palo Alto, CA).

Software:

Article Title: New miRNA Profiles Accurately Distinguish Renal Cell Carcinomas and Upper Tract Urothelial Carcinomas from the Normal Kidney
Article Snippet: After hybridization, the microarray slides were scanned at 10 μm using the High-Resolution Microarray Scanner (Agilent Technologies) and stored in an ozone free environment. .. The image analysis was carried out using the ImaGene 8.0 software (BioDiscovery, Inc., USA).

Article Title: Lassa and Marburg viruses elicit distinct host transcriptional responses early after infection
Article Snippet: .. Images were scanned using the Agilent High-Resolution Microarray Scanner and raw microarray images were processed using Agilent’s Feature Extraction software. .. Fold-change analysis Agilent two-color human gene expression microarrays were processed using limma [ ].

Article Title: Expressed miRNAs target feather related mRNAs involved in cell signaling, cell adhesion and structure during chicken epidermal development
Article Snippet: After hybridization and washing, the processed slides were scanned with the Agilent High-Resolution Microarray Scanner (Agilent Technologies; Palo Alto, CA). .. Raw gene expression level files were imported into Agilent GeneSpring software 12.5 (Agilent Technologies; Palo Alto, CA) and normalized by the quantile method, enabling 14 sample comparisons with the 8 samples.

Article Title: Highly expressed placental miRNAs control key biological processes in human cancer cell lines
Article Snippet: Microarray slides were scanned using the High-Resolution Microarray Scanner (Agilent Technologies, Santa Clara, CA, USA). .. Captured images were processed, and raw data were extracted by the Agilent Feature Extraction Software v.8.5 (Agilent Technologies, Santa Clara, CA, USA).

Article Title: Deciphering the response of Mycobacterium smegmatis to nitrogen stress using bipartite active modules
Article Snippet: After hybridization, slides were washed for 5 minutes at room temperature with CGH Wash Buffer 1 (Agilent) and 1 minute at 37°C with CGH Wash buffer 2 (Agilent) and scanned immediately, using an Agilent High Resolution Microarray Scanner, at 2 μm resolution, 100% PMT. .. Scanned images were quantified using Feature Extraction software v 10.7.3.1.

Article Title: Design and validation of an oligonucleotide microarray for the detection of genomic rearrangements associated with common hereditary cancer syndromes
Article Snippet: Array hybridization and washing were performed on custom Agilent 8×15k arrays (Agilent Technologies), and arrays were scanned using a High Resolution Microarray Scanner (Agilent Technologies). .. First, a proprietary software prediction program predicted the likelihood of a particular result for a given sample.

Article Title: The lysine‐specific methyltransferase KMT2C/ MLL3 regulates DNA repair components in cancer
Article Snippet: Following purification, the combined labeled DNA samples were applied to the microarray (hybridization for 40 h at 67°C), washed, and scanned at 3 micron resolution on the Agilent High‐Resolution Microarray Scanner (G2505C, Agilent Technologies). .. The images were extracted and analyzed using the Agilent Feature Extraction software and the CytoGenomics v.3.0 software suite.

Article Title: Insights into the prevalence and underlying causes of clonal variation through transcriptomic analysis in Pichia pastoris
Article Snippet: After hybridization, slides were washed for 1 min at room temperature in GE wash buffer 1 and 1 min at 37 °C in GE wash buffer 2 (Agilent Technologies UK Ltd., Wokingham, UK), placed beneath an Ozone Barrier Slide cover (Agilent Technologies UK Ltd., Wokingham, UK) and scanned immediately, using an Agilent High-Resolution Microarray Scanner, at 2 μm resolution. .. Scanned images were quantified using Feature Extraction software v 10.7.3.1 (Agilent Technologies UK Ltd., Wokingham, UK).

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    Agilent technologies high resolution microarray scanner
    High expressed miRNAs in normal human placenta ( A ) HeatMap representing the top 30 high expressed miRNAs in normal human placenta. ( B ) Boxplot presenting normalized level of expression of the 866 miRNAs evaluated in normal human placenta using <t>microarray</t> miRNA expression profile. The bold line indicates de median of signal intensity of all miRNAs; the top edge represents the 75th percentile and the bottom edge the 25th percentile. Vertical bars indicate the upper and inferior limits and circles represent outlier points/samples (points 1.5 IQR above the 3rd quartile of the boxplot).
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    High expressed miRNAs in normal human placenta ( A ) HeatMap representing the top 30 high expressed miRNAs in normal human placenta. ( B ) Boxplot presenting normalized level of expression of the 866 miRNAs evaluated in normal human placenta using microarray miRNA expression profile. The bold line indicates de median of signal intensity of all miRNAs; the top edge represents the 75th percentile and the bottom edge the 25th percentile. Vertical bars indicate the upper and inferior limits and circles represent outlier points/samples (points 1.5 IQR above the 3rd quartile of the boxplot).

    Journal: Oncotarget

    Article Title: Highly expressed placental miRNAs control key biological processes in human cancer cell lines

    doi: 10.18632/oncotarget.25264

    Figure Lengend Snippet: High expressed miRNAs in normal human placenta ( A ) HeatMap representing the top 30 high expressed miRNAs in normal human placenta. ( B ) Boxplot presenting normalized level of expression of the 866 miRNAs evaluated in normal human placenta using microarray miRNA expression profile. The bold line indicates de median of signal intensity of all miRNAs; the top edge represents the 75th percentile and the bottom edge the 25th percentile. Vertical bars indicate the upper and inferior limits and circles represent outlier points/samples (points 1.5 IQR above the 3rd quartile of the boxplot).

    Article Snippet: Microarray slides were scanned using the High-Resolution Microarray Scanner (Agilent Technologies, Santa Clara, CA, USA).

    Techniques: Expressing, Microarray

    Validation of the 62-strain Staphylococcus aureus microarray. ( A ) Clustering of triplicate microarray data generated from eight sequenced strains. Note: 1) replicate isolates cluster together and 2) isolates belonging to the same S. aureus lineage cluster more closely together than isolates from different S. aureus lineages. ( B ) Microarray heatmap showing the distribution of 60-mer oligos representing the hsdS genes. The distribution of gene variants of highly variable S. aureus genes can be investigated. An example is the hsdS genes that encode the specificity factor of the RM system and distinguish CC lineages. Staphylococcus aureus carry one or two hsdS genes, and each hsdS gene has two variable regions, TRD1 and TRD2. Horizontal lines represent 90 different 60-mer oligo probes specific to 14 TRD1 variants and 20 TRD2 variants. Isolates are represented by vertical lines and information about the lineage of each isolate is shown at the bottom of the figure. The colour in the middle depicts whether the gene variant is present in the respective isolate; red/yellow = present, black/blue = absent. The intensity of all the colors is an indicator of the total signal intensity, whereas the color is an indicator of test signal over reference signal ratio.

    Journal: Genome Biology and Evolution

    Article Title: The Distribution of Mobile Genetic Elements (MGEs) in MRSA CC398 Is Associated with Both Host and Country

    doi: 10.1093/gbe/evr092

    Figure Lengend Snippet: Validation of the 62-strain Staphylococcus aureus microarray. ( A ) Clustering of triplicate microarray data generated from eight sequenced strains. Note: 1) replicate isolates cluster together and 2) isolates belonging to the same S. aureus lineage cluster more closely together than isolates from different S. aureus lineages. ( B ) Microarray heatmap showing the distribution of 60-mer oligos representing the hsdS genes. The distribution of gene variants of highly variable S. aureus genes can be investigated. An example is the hsdS genes that encode the specificity factor of the RM system and distinguish CC lineages. Staphylococcus aureus carry one or two hsdS genes, and each hsdS gene has two variable regions, TRD1 and TRD2. Horizontal lines represent 90 different 60-mer oligo probes specific to 14 TRD1 variants and 20 TRD2 variants. Isolates are represented by vertical lines and information about the lineage of each isolate is shown at the bottom of the figure. The colour in the middle depicts whether the gene variant is present in the respective isolate; red/yellow = present, black/blue = absent. The intensity of all the colors is an indicator of the total signal intensity, whereas the color is an indicator of test signal over reference signal ratio.

    Article Snippet: Slides were then scanned using an Agilent High Resolution Microarray Scanner (Agilent Technologies).

    Techniques: Microarray, Generated, Variant Assay

    ROC analysis using microarray data. ROC curves of the top 30 up-regulated miRNAs in each tissue type using the microarray expression data. Of them, the miRNAs with a p

    Journal: PLoS ONE

    Article Title: New miRNA Profiles Accurately Distinguish Renal Cell Carcinomas and Upper Tract Urothelial Carcinomas from the Normal Kidney

    doi: 10.1371/journal.pone.0091646

    Figure Lengend Snippet: ROC analysis using microarray data. ROC curves of the top 30 up-regulated miRNAs in each tissue type using the microarray expression data. Of them, the miRNAs with a p

    Article Snippet: After hybridization, the microarray slides were scanned at 10 μm using the High-Resolution Microarray Scanner (Agilent Technologies) and stored in an ozone free environment.

    Techniques: Microarray, Expressing

    Correlation between microarrays and qRT-PCR. Median log 2 fold change expression levels of the 14 most up-regulated and 11 most down-regulated miRNAs between ccRCC, papRCC, chRCC and UT-UC and the normal kidney tissue, as determined by both qRT-PCR and microarray analysis. As shown in the figure, qRT-PCR and microarray results were highly compatible. The most identical results between the two techniques were those for ccRCC, which was expected due to the high sample number (Pearson’s CC = 0.778, p

    Journal: PLoS ONE

    Article Title: New miRNA Profiles Accurately Distinguish Renal Cell Carcinomas and Upper Tract Urothelial Carcinomas from the Normal Kidney

    doi: 10.1371/journal.pone.0091646

    Figure Lengend Snippet: Correlation between microarrays and qRT-PCR. Median log 2 fold change expression levels of the 14 most up-regulated and 11 most down-regulated miRNAs between ccRCC, papRCC, chRCC and UT-UC and the normal kidney tissue, as determined by both qRT-PCR and microarray analysis. As shown in the figure, qRT-PCR and microarray results were highly compatible. The most identical results between the two techniques were those for ccRCC, which was expected due to the high sample number (Pearson’s CC = 0.778, p

    Article Snippet: After hybridization, the microarray slides were scanned at 10 μm using the High-Resolution Microarray Scanner (Agilent Technologies) and stored in an ozone free environment.

    Techniques: Quantitative RT-PCR, Expressing, Microarray

    High expressed miRNAs in normal human placenta ( A ) HeatMap representing the top 30 high expressed miRNAs in normal human placenta. ( B ) Boxplot presenting normalized level of expression of the 866 miRNAs evaluated in normal human placenta using microarray miRNA expression profile. The bold line indicates de median of signal intensity of all miRNAs; the top edge represents the 75th percentile and the bottom edge the 25th percentile. Vertical bars indicate the upper and inferior limits and circles represent outlier points/samples (points 1.5 IQR above the 3rd quartile of the boxplot).

    Journal: Oncotarget

    Article Title: Highly expressed placental miRNAs control key biological processes in human cancer cell lines

    doi: 10.18632/oncotarget.25264

    Figure Lengend Snippet: High expressed miRNAs in normal human placenta ( A ) HeatMap representing the top 30 high expressed miRNAs in normal human placenta. ( B ) Boxplot presenting normalized level of expression of the 866 miRNAs evaluated in normal human placenta using microarray miRNA expression profile. The bold line indicates de median of signal intensity of all miRNAs; the top edge represents the 75th percentile and the bottom edge the 25th percentile. Vertical bars indicate the upper and inferior limits and circles represent outlier points/samples (points 1.5 IQR above the 3rd quartile of the boxplot).

    Article Snippet: Microarray slides were scanned using the High-Resolution Microarray Scanner (Agilent Technologies, Santa Clara, CA, USA).

    Techniques: Expressing, Microarray