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Breast cancer inhibitory factor 1 (IF1)-overexpressing cells have a less migratory and invasive phenotype . (A) The heatmap shows the transcriptome of the 138 differentially expressed genes between control (CRL) and IF1-overexpressing cells that meet the Bonferroni correction. Four different samples of each cell type (CRL and IF1) were included in the <t>Agilent</t> 8x60K Human arrays. (B) Quantitative reverse transcription PCR validation of up and downregulated genes in the <t>microarray</t> analysis in CRL (closed bars) and IF1-overexpressing (gray bars) cells. (C) Protein expression of extracellular matrix and epithelial–mesenchymal transition-related factors detected by immunoblotting. (B,C) The histograms show the quantification of mRNA (B) and protein (C) expression as the means ± SEM. * p ≤ 0.05 when compared to CRL by Student’s t -test.
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1) Product Images from "Overexpression of the ATPase Inhibitory Factor 1 Favors a Non-metastatic Phenotype in Breast Cancer"

Article Title: Overexpression of the ATPase Inhibitory Factor 1 Favors a Non-metastatic Phenotype in Breast Cancer

Journal: Frontiers in Oncology

doi: 10.3389/fonc.2017.00069

Breast cancer inhibitory factor 1 (IF1)-overexpressing cells have a less migratory and invasive phenotype . (A) The heatmap shows the transcriptome of the 138 differentially expressed genes between control (CRL) and IF1-overexpressing cells that meet the Bonferroni correction. Four different samples of each cell type (CRL and IF1) were included in the Agilent 8x60K Human arrays. (B) Quantitative reverse transcription PCR validation of up and downregulated genes in the microarray analysis in CRL (closed bars) and IF1-overexpressing (gray bars) cells. (C) Protein expression of extracellular matrix and epithelial–mesenchymal transition-related factors detected by immunoblotting. (B,C) The histograms show the quantification of mRNA (B) and protein (C) expression as the means ± SEM. * p ≤ 0.05 when compared to CRL by Student’s t -test.
Figure Legend Snippet: Breast cancer inhibitory factor 1 (IF1)-overexpressing cells have a less migratory and invasive phenotype . (A) The heatmap shows the transcriptome of the 138 differentially expressed genes between control (CRL) and IF1-overexpressing cells that meet the Bonferroni correction. Four different samples of each cell type (CRL and IF1) were included in the Agilent 8x60K Human arrays. (B) Quantitative reverse transcription PCR validation of up and downregulated genes in the microarray analysis in CRL (closed bars) and IF1-overexpressing (gray bars) cells. (C) Protein expression of extracellular matrix and epithelial–mesenchymal transition-related factors detected by immunoblotting. (B,C) The histograms show the quantification of mRNA (B) and protein (C) expression as the means ± SEM. * p ≤ 0.05 when compared to CRL by Student’s t -test.

Techniques Used: Polymerase Chain Reaction, Microarray, Expressing

2) Product Images from "A miR-150/TET3 pathway regulates the generation of mouse and human non-classical monocyte subset"

Article Title: A miR-150/TET3 pathway regulates the generation of mouse and human non-classical monocyte subset

Journal: Nature Communications

doi: 10.1038/s41467-018-07801-x

Differentially expressed miRNA from control and CMML patient-sorted CD14 + . a Volcano plot showing the differentially expressed miRNAs in CD14 + cell-sorted monocytes from CMML ( n = 33) and healthy donor ( n = 5 + pool of five samples) peripheral blood samples (learning cohort), as measured using v12.0 Agilent microarray. X -axis, log 2 fold-change value; Y -axis, −log 10 (adjusted P value). b List of the four miRNAs identified as deregulated in the learning cohort. Of note, hsa-miR-923 up-regulation is a known artifact of the v12.0 version of these microarrays. c Box plot showing the relative expression of hsa-miR-150, hsa-miR-451, and hsa-miR-494 analyzed by qRT-PCR in samples of the learning cohort (center line: median; whiskers: min to max). d qRT-PCR analysis of the relative expression levels of hsa-miR-150 (CTL = 24; CMML = 133), hsa-miR-451 (CTL = 24, CMML = 53) and hsa-miR-494 (CTL = 9; CMML = 32) in an independent validation cohort. Red lines, median with interquartile range; Mann–Whitney test: ** P
Figure Legend Snippet: Differentially expressed miRNA from control and CMML patient-sorted CD14 + . a Volcano plot showing the differentially expressed miRNAs in CD14 + cell-sorted monocytes from CMML ( n = 33) and healthy donor ( n = 5 + pool of five samples) peripheral blood samples (learning cohort), as measured using v12.0 Agilent microarray. X -axis, log 2 fold-change value; Y -axis, −log 10 (adjusted P value). b List of the four miRNAs identified as deregulated in the learning cohort. Of note, hsa-miR-923 up-regulation is a known artifact of the v12.0 version of these microarrays. c Box plot showing the relative expression of hsa-miR-150, hsa-miR-451, and hsa-miR-494 analyzed by qRT-PCR in samples of the learning cohort (center line: median; whiskers: min to max). d qRT-PCR analysis of the relative expression levels of hsa-miR-150 (CTL = 24; CMML = 133), hsa-miR-451 (CTL = 24, CMML = 53) and hsa-miR-494 (CTL = 9; CMML = 32) in an independent validation cohort. Red lines, median with interquartile range; Mann–Whitney test: ** P

Techniques Used: Microarray, Expressing, Quantitative RT-PCR, CTL Assay, MANN-WHITNEY

3) Product Images from "The Nuclear-Retained Noncoding RNA MALAT1 Regulates Alternative Splicing by Modulating SR Splicing Factor Phosphorylation"

Article Title: The Nuclear-Retained Noncoding RNA MALAT1 Regulates Alternative Splicing by Modulating SR Splicing Factor Phosphorylation

Journal: Molecular cell

doi: 10.1016/j.molcel.2010.08.011

MALAT1 Regulates AS of Pre-mRNAs (A) Schematic representation of the method used for the global analysis of MALAT1-regulated AS. Black lines designate exon body and exon junction probes used for analyzing AS on a custom 244K Agilent microarray. .
Figure Legend Snippet: MALAT1 Regulates AS of Pre-mRNAs (A) Schematic representation of the method used for the global analysis of MALAT1-regulated AS. Black lines designate exon body and exon junction probes used for analyzing AS on a custom 244K Agilent microarray. .

Techniques Used: Microarray

4) Product Images from "Establishment and characterization of a novel vincristine‐resistant diffuse large B‐cell lymphoma cell line containing the 8q24 homogeneously staining region"

Article Title: Establishment and characterization of a novel vincristine‐resistant diffuse large B‐cell lymphoma cell line containing the 8q24 homogeneously staining region

Journal: FEBS Open Bio

doi: 10.1002/2211-5463.12538

High‐resolution aCGH analysis in AMU ‐ ML 2 cells. Genomewide copy number aberrations in AMU ‐ ML 2 cells were determined using an Agilent SurePrint G3 Human CGH 2× 400K Oligo Microarray (Agilent Technologies). The median probe spacing was approximately 4.6 kb. (A) Summary of the aCGH analysis. The x ‐axis indicates the chromosome number, whereas the y ‐axis indicates the log 2 ratio (copy number aberrations). The red oval indicates a 1462‐kb highly amplified region, containing MYC and PVT 1 at 8q24.21. The blue and green ovals indicate copy number changes at 6p22 to 6p21 and at 17p13, respectively. The other copy number alterations ( CNA s) detected are summarized in Table 1 . (B) The aCGH analysis shows a 7431‐kb deletion at 6p22.1–6p21.31, where the t(6;8) breakpoint was detected by FISH , as indicated in Fig. 4 F. Blue rectangle, copy number changes at 6p22–6p21. (C) A 1462‐kb amplification detected by the aCGH analysis, containing MYC and PVT 1 at 8q24.21, where 8q24.1 HSR was detected by FISH , as indicated in Fig. 4 C. Red rectangle, copy number changes at 8q24. (D) A 7522‐kb deletion at 17p13.3–17p.13.1 detected by the aCGH analysis, where a single copy deletion of TP 53 was detected by FISH , as indicated in Fig. 4 F. Green rectangle, copy number changes at 17p13.
Figure Legend Snippet: High‐resolution aCGH analysis in AMU ‐ ML 2 cells. Genomewide copy number aberrations in AMU ‐ ML 2 cells were determined using an Agilent SurePrint G3 Human CGH 2× 400K Oligo Microarray (Agilent Technologies). The median probe spacing was approximately 4.6 kb. (A) Summary of the aCGH analysis. The x ‐axis indicates the chromosome number, whereas the y ‐axis indicates the log 2 ratio (copy number aberrations). The red oval indicates a 1462‐kb highly amplified region, containing MYC and PVT 1 at 8q24.21. The blue and green ovals indicate copy number changes at 6p22 to 6p21 and at 17p13, respectively. The other copy number alterations ( CNA s) detected are summarized in Table 1 . (B) The aCGH analysis shows a 7431‐kb deletion at 6p22.1–6p21.31, where the t(6;8) breakpoint was detected by FISH , as indicated in Fig. 4 F. Blue rectangle, copy number changes at 6p22–6p21. (C) A 1462‐kb amplification detected by the aCGH analysis, containing MYC and PVT 1 at 8q24.21, where 8q24.1 HSR was detected by FISH , as indicated in Fig. 4 C. Red rectangle, copy number changes at 8q24. (D) A 7522‐kb deletion at 17p13.3–17p.13.1 detected by the aCGH analysis, where a single copy deletion of TP 53 was detected by FISH , as indicated in Fig. 4 F. Green rectangle, copy number changes at 17p13.

Techniques Used: Microarray, Amplification, Fluorescence In Situ Hybridization

5) Product Images from "Benign copy number changes in clinical cytogenetic diagnostics by array CGH"

Article Title: Benign copy number changes in clinical cytogenetic diagnostics by array CGH

Journal: Cytogenetic and Genome Research

doi: 10.1159/000184696

Examples of four of the more commonly observed bCNVs (other than those in Figs. 3 and 4) showing BAC clone locations and copy number variations detected in individual samples by the Agilent CNV microarray set together with the corresponding oligonucleotide
Figure Legend Snippet: Examples of four of the more commonly observed bCNVs (other than those in Figs. 3 and 4) showing BAC clone locations and copy number variations detected in individual samples by the Agilent CNV microarray set together with the corresponding oligonucleotide

Techniques Used: BAC Assay, Microarray

Example of a commonly observed CNV (at 13q21.2) covering approximately the same region as RP11-100C24 with variable size and breakpoints in eight different specimens. Profiles of log2 ratio data from the Agilent CNV microarray set on chromosome 13 from
Figure Legend Snippet: Example of a commonly observed CNV (at 13q21.2) covering approximately the same region as RP11-100C24 with variable size and breakpoints in eight different specimens. Profiles of log2 ratio data from the Agilent CNV microarray set on chromosome 13 from

Techniques Used: Microarray

6) Product Images from "Benign copy number changes in clinical cytogenetic diagnostics by array CGH"

Article Title: Benign copy number changes in clinical cytogenetic diagnostics by array CGH

Journal: Cytogenetic and Genome Research

doi: 10.1159/000184696

Examples of four of the more commonly observed bCNVs (other than those in Figs. 3 and 4) showing BAC clone locations and copy number variations detected in individual samples by the Agilent CNV microarray set together with the corresponding oligonucleotide
Figure Legend Snippet: Examples of four of the more commonly observed bCNVs (other than those in Figs. 3 and 4) showing BAC clone locations and copy number variations detected in individual samples by the Agilent CNV microarray set together with the corresponding oligonucleotide

Techniques Used: BAC Assay, Microarray

Example of a commonly observed CNV (at 13q21.2) covering approximately the same region as RP11-100C24 with variable size and breakpoints in eight different specimens. Profiles of log2 ratio data from the Agilent CNV microarray set on chromosome 13 from
Figure Legend Snippet: Example of a commonly observed CNV (at 13q21.2) covering approximately the same region as RP11-100C24 with variable size and breakpoints in eight different specimens. Profiles of log2 ratio data from the Agilent CNV microarray set on chromosome 13 from

Techniques Used: Microarray

7) Product Images from "Identification of a Selective G1-Phase Benzimidazolone Inhibitor by a Senescence-Targeted Virtual Screen Using Artificial Neural Networks"

Article Title: Identification of a Selective G1-Phase Benzimidazolone Inhibitor by a Senescence-Targeted Virtual Screen Using Artificial Neural Networks

Journal: Neoplasia (New York, N.Y.)

doi: 10.1016/j.neo.2015.08.009

Microarray and structural analysis of CB-20903630. (A) Direct interactions network of differentially expressed genes in HCT116 cells treated with 10 μM CB-20903630. RNA samples from DMSO versus compound-treated cells were profiled on Agilent whole genome expression arrays. Differentially expressed gene lists were analyzed in MetaCore by the direct interactions algorithm to obtain the network model. Green and red arrows indicate known activating or inhibitory interactions between entities, respectively. Red and blue circles indicate upregulation and downregulation of expression relative to vehicle treatment, respectively. (B) Significant differentially affected GeneGo process networks under CB-20903630 treatment in HCT116 cells obtained by enrichment analysis of differentially affected genes. (C) Clustering of process network profiles with cumulative hypergeometric probability of pairwise overlap as the unweighted distance metric. (D) SOM structural clustering of CB-20903630 and known kinase inhibitors (see Materials and Methods section for source of comparator structures) after 200 training cycles. (Upper panel) Compound loadings: CB-20903630 and 15 other compounds loaded on the highlighted neuron in the upper panel. Numbers indicate number of compounds on each neuron. (Lower panel) Visualization of neighbor weights: the CB-20903630 neuron is not strongly clustered with its neighbors (darker bands indicate larger distances).
Figure Legend Snippet: Microarray and structural analysis of CB-20903630. (A) Direct interactions network of differentially expressed genes in HCT116 cells treated with 10 μM CB-20903630. RNA samples from DMSO versus compound-treated cells were profiled on Agilent whole genome expression arrays. Differentially expressed gene lists were analyzed in MetaCore by the direct interactions algorithm to obtain the network model. Green and red arrows indicate known activating or inhibitory interactions between entities, respectively. Red and blue circles indicate upregulation and downregulation of expression relative to vehicle treatment, respectively. (B) Significant differentially affected GeneGo process networks under CB-20903630 treatment in HCT116 cells obtained by enrichment analysis of differentially affected genes. (C) Clustering of process network profiles with cumulative hypergeometric probability of pairwise overlap as the unweighted distance metric. (D) SOM structural clustering of CB-20903630 and known kinase inhibitors (see Materials and Methods section for source of comparator structures) after 200 training cycles. (Upper panel) Compound loadings: CB-20903630 and 15 other compounds loaded on the highlighted neuron in the upper panel. Numbers indicate number of compounds on each neuron. (Lower panel) Visualization of neighbor weights: the CB-20903630 neuron is not strongly clustered with its neighbors (darker bands indicate larger distances).

Techniques Used: Microarray, Expressing

8) Product Images from "Kinetochore assembly and heterochromatin formation occur autonomously in Schizosaccharomyces pombe"

Article Title: Kinetochore assembly and heterochromatin formation occur autonomously in Schizosaccharomyces pombe

Journal: Proceedings of the National Academy of Sciences of the United States of America

doi: 10.1073/pnas.1216934111

Absence of heterochromatin or an increase in Rad21 binding around the centromeres of CBS 2777 chromosomes 2 and 4. ( A ) Comparison of the binding of Swi6 (HP1) to the pericentric DNA held in common by CBS 2777 chromosomes 2 and 4 in strains CBS 2777 and CBS 2776 as measured by ChIP-seq on GFP epitope-tagged Swi6 (HP1). The data from the duplicate experiments of the CBS 2777 are shown in red and blue, and those from CBS 2776 are shown in green and orange. Arrows indicate the increased binding of Swi6 to dps1 and ste4 in CBS 2777. ( B ) Small RNAs derived from the pericentric DNA held in common by CBS 2777 chromosomes 2 and 4 in strains CBS 2777 and CBS 2776. ( C ) Organization of the pericentric DNA held in common by CBS 2777 chromosomes 2 and 4 aligned with respect to the data shown in A and B . ( D ) Absence of gene silencing in the pericentric DNA of CBS 2777 chromosomes 2 and 4. Silencing activity was assayed by testing the growth of URA + cells on 5-FOA. Cells were grown to saturation in YES and inoculated in serial fivefold dilutions starting from an initial concentration of ∼7.5 × 10 3 ), the ura4 gene was placed into the imr1L repeat of 972h − ; this strain served as a positive control for the silencing seen in CBS 2777. ( E ) Absence of repression of gene expression around the acrocentric centromeres of CBS 2777 chromosome 4. Total RNA was extracted from either CBS 2777 or CBS 2776 cells, and cRNA probes were prepared and labeled with CY3 or CY5, respectively, and analyzed by competitive hybridization to a custom 4 × 44K gene expression microarray. The results were processed and analyzed using Agilent Genespring software. Red and green points mark genes with greater or lesser expression, respectively, in CBS 2777 compared with CBS 2776. The region around the centromere of CBS 2777 chromosome 4 is illustrated. The vertical arrow marks the junction with the region duplicated on chromosome 2 defined by breakpoint 7. ( F ) Comparison of the binding of Rad21 to the pericentric DNA held in common by CBS 2777 chromosomes 2 and 4 in strains CBS 2777 and CBS 2776 as measured by ChIP-seq on PK9 epitope-tagged Rad21. The arrow indicates the increase in binding of Rad21 to ste4 in CBS 2777. The traces in F are aligned with those in A and B , and this is indicated by the idiogramatic representation ( C ) of the centromeric region of chromosomes 2 and 4 placed below the three sets of traces.
Figure Legend Snippet: Absence of heterochromatin or an increase in Rad21 binding around the centromeres of CBS 2777 chromosomes 2 and 4. ( A ) Comparison of the binding of Swi6 (HP1) to the pericentric DNA held in common by CBS 2777 chromosomes 2 and 4 in strains CBS 2777 and CBS 2776 as measured by ChIP-seq on GFP epitope-tagged Swi6 (HP1). The data from the duplicate experiments of the CBS 2777 are shown in red and blue, and those from CBS 2776 are shown in green and orange. Arrows indicate the increased binding of Swi6 to dps1 and ste4 in CBS 2777. ( B ) Small RNAs derived from the pericentric DNA held in common by CBS 2777 chromosomes 2 and 4 in strains CBS 2777 and CBS 2776. ( C ) Organization of the pericentric DNA held in common by CBS 2777 chromosomes 2 and 4 aligned with respect to the data shown in A and B . ( D ) Absence of gene silencing in the pericentric DNA of CBS 2777 chromosomes 2 and 4. Silencing activity was assayed by testing the growth of URA + cells on 5-FOA. Cells were grown to saturation in YES and inoculated in serial fivefold dilutions starting from an initial concentration of ∼7.5 × 10 3 ), the ura4 gene was placed into the imr1L repeat of 972h − ; this strain served as a positive control for the silencing seen in CBS 2777. ( E ) Absence of repression of gene expression around the acrocentric centromeres of CBS 2777 chromosome 4. Total RNA was extracted from either CBS 2777 or CBS 2776 cells, and cRNA probes were prepared and labeled with CY3 or CY5, respectively, and analyzed by competitive hybridization to a custom 4 × 44K gene expression microarray. The results were processed and analyzed using Agilent Genespring software. Red and green points mark genes with greater or lesser expression, respectively, in CBS 2777 compared with CBS 2776. The region around the centromere of CBS 2777 chromosome 4 is illustrated. The vertical arrow marks the junction with the region duplicated on chromosome 2 defined by breakpoint 7. ( F ) Comparison of the binding of Rad21 to the pericentric DNA held in common by CBS 2777 chromosomes 2 and 4 in strains CBS 2777 and CBS 2776 as measured by ChIP-seq on PK9 epitope-tagged Rad21. The arrow indicates the increase in binding of Rad21 to ste4 in CBS 2777. The traces in F are aligned with those in A and B , and this is indicated by the idiogramatic representation ( C ) of the centromeric region of chromosomes 2 and 4 placed below the three sets of traces.

Techniques Used: Binding Assay, Chromatin Immunoprecipitation, Derivative Assay, Activity Assay, Concentration Assay, Positive Control, Expressing, Labeling, Hybridization, Microarray, Software

9) Product Images from "Hepatic Transcriptome Responses in Mice (Mus musculus) Exposed to the Nafion Membrane and Its Combustion Products"

Article Title: Hepatic Transcriptome Responses in Mice (Mus musculus) Exposed to the Nafion Membrane and Its Combustion Products

Journal: PLoS ONE

doi: 10.1371/journal.pone.0128591

Functional grouping of differentially expressed genes involved in biological processes. Gene expression profiling using Agilent Whole Mouse Genome Oligo Microarray platform containing 41,174 unique probes was performed in male mice (five-weeks of age) individually exposed to normal diet (Control), 1/100 wt% N117-treated food (Food), 100 mg N117/L treated by combustion lacking oxygen supplementation (CLOS), and 100 mg N117/L treated by oxygen-enriched combustion (OEC) for 24 days. RNA extracted from one mouse liver, which was randomly selected in each group, was one sample, and the obtained raw data were normalized with the Quantile algorithm, Gene Spring Software 11.0. Differentially expressed genes (DEGs) involved in biological processes between the treated groups (A, Food; B, CLOS; C, OEC) and control were identified as the genes with a greater than ± 2.0-fold-change and p -value
Figure Legend Snippet: Functional grouping of differentially expressed genes involved in biological processes. Gene expression profiling using Agilent Whole Mouse Genome Oligo Microarray platform containing 41,174 unique probes was performed in male mice (five-weeks of age) individually exposed to normal diet (Control), 1/100 wt% N117-treated food (Food), 100 mg N117/L treated by combustion lacking oxygen supplementation (CLOS), and 100 mg N117/L treated by oxygen-enriched combustion (OEC) for 24 days. RNA extracted from one mouse liver, which was randomly selected in each group, was one sample, and the obtained raw data were normalized with the Quantile algorithm, Gene Spring Software 11.0. Differentially expressed genes (DEGs) involved in biological processes between the treated groups (A, Food; B, CLOS; C, OEC) and control were identified as the genes with a greater than ± 2.0-fold-change and p -value

Techniques Used: Functional Assay, Expressing, Microarray, Mouse Assay, Software

10) Product Images from "Tissue Specific Diurnal Rhythms of Metabolites and Their Regulation during Herbivore Attack in a Native Tobacco, Nicotiana attenuata"

Article Title: Tissue Specific Diurnal Rhythms of Metabolites and Their Regulation during Herbivore Attack in a Native Tobacco, Nicotiana attenuata

Journal: PLoS ONE

doi: 10.1371/journal.pone.0026214

Experimental procedures used to identify oscillating and herbivore-induced metabolites and their associated genes in different tissues of Nicotiana attenuata . (A) Wild type (WT) N. attenuata plants were harvested every 4 h for two days during the initiation of stem elongation. To mimic herbivory, oral secretions (OS) of the larvae of the specialist herbivore, M. sexta , were immediately applied to puncture wounds made in leaves at 1 pm. Water treatment of puncture wounds on separate plants was used to distinguish OS-specific from wound-induced changes in metabolites and transcripts. (B) Metabolites from three different tissues, source leaves, sink leaves, and roots of N. attenuata were isolated. The leaf at node 0 had completed the sink to source transition and the leaf at node +1 was older by one leaf position than the leaf at node 0 and so forth. Source leaves (at nodes +2, +1, 0) were wounded with a fabric pattern wheel and treated with 20 µl of M. sexta OS, which was diluted 1∶5 with water. Untreated leaves (at nodes −1, −2) and roots were harvested to monitor systemic responses. (C) After sample preparation from six biological replicates, a 40% methanol extraction method optimized for the defense metabolites of N. attenuata was used and the metabolites separated with a rapid separation liquid chromatography (RSLC) on a C 18 column and detected by ESI-TOF-MS (electrospray ionization time-of-flight mass spectrometer) for parents and their daughter ions. Peak picking and alignments were performed with the XCMS package [19] . Diurnal oscillating metabolites were extracted by the pattern matching algorithms of HAYSTACK tool [20] . In-house and public databases were used to identify oscillating metabolites and a 44K Agilent microarray designed for N. attenuata was used to examine the expression of metabolite-related genes.
Figure Legend Snippet: Experimental procedures used to identify oscillating and herbivore-induced metabolites and their associated genes in different tissues of Nicotiana attenuata . (A) Wild type (WT) N. attenuata plants were harvested every 4 h for two days during the initiation of stem elongation. To mimic herbivory, oral secretions (OS) of the larvae of the specialist herbivore, M. sexta , were immediately applied to puncture wounds made in leaves at 1 pm. Water treatment of puncture wounds on separate plants was used to distinguish OS-specific from wound-induced changes in metabolites and transcripts. (B) Metabolites from three different tissues, source leaves, sink leaves, and roots of N. attenuata were isolated. The leaf at node 0 had completed the sink to source transition and the leaf at node +1 was older by one leaf position than the leaf at node 0 and so forth. Source leaves (at nodes +2, +1, 0) were wounded with a fabric pattern wheel and treated with 20 µl of M. sexta OS, which was diluted 1∶5 with water. Untreated leaves (at nodes −1, −2) and roots were harvested to monitor systemic responses. (C) After sample preparation from six biological replicates, a 40% methanol extraction method optimized for the defense metabolites of N. attenuata was used and the metabolites separated with a rapid separation liquid chromatography (RSLC) on a C 18 column and detected by ESI-TOF-MS (electrospray ionization time-of-flight mass spectrometer) for parents and their daughter ions. Peak picking and alignments were performed with the XCMS package [19] . Diurnal oscillating metabolites were extracted by the pattern matching algorithms of HAYSTACK tool [20] . In-house and public databases were used to identify oscillating metabolites and a 44K Agilent microarray designed for N. attenuata was used to examine the expression of metabolite-related genes.

Techniques Used: Isolation, Sample Prep, Liquid Chromatography, Mass Spectrometry, Microarray, Expressing

11) Product Images from "Antiproliferative Effect of Ascorbic Acid Is Associated with the Inhibition of Genes Necessary to Cell Cycle Progression"

Article Title: Antiproliferative Effect of Ascorbic Acid Is Associated with the Inhibition of Genes Necessary to Cell Cycle Progression

Journal: PLoS ONE

doi: 10.1371/journal.pone.0004409

Human pangenomic microarrays and qPCR analysis. (a) Primary cultures of human skin fibroblasts were incubated in medium containing 0, 0.3, 0.6, and 0.8 mM AA. After 24 h, RNA was extracted; reverse transcribed, and hybridized on AGILENT human pangenomic microarrays. Dye swap experiments were also conducted. Data were analyzed using the Rosetta Luminator software package. And only those genes that were up- or downregulated in AA-treated cells were analyzed further. Among the downregulated genes, 40% belong to two classes (tRNA synthetases and translation initiation factor subunits) involved in protein synthesis. (b) Validation of microarray results using qPCR and Roche UPL-specific probes.
Figure Legend Snippet: Human pangenomic microarrays and qPCR analysis. (a) Primary cultures of human skin fibroblasts were incubated in medium containing 0, 0.3, 0.6, and 0.8 mM AA. After 24 h, RNA was extracted; reverse transcribed, and hybridized on AGILENT human pangenomic microarrays. Dye swap experiments were also conducted. Data were analyzed using the Rosetta Luminator software package. And only those genes that were up- or downregulated in AA-treated cells were analyzed further. Among the downregulated genes, 40% belong to two classes (tRNA synthetases and translation initiation factor subunits) involved in protein synthesis. (b) Validation of microarray results using qPCR and Roche UPL-specific probes.

Techniques Used: Real-time Polymerase Chain Reaction, Incubation, Software, Microarray

12) Product Images from "The impact of disparate isolation methods for extracellular vesicles on downstream RNA profiling"

Article Title: The impact of disparate isolation methods for extracellular vesicles on downstream RNA profiling

Journal: Journal of Extracellular Vesicles

doi: 10.3402/jev.v3.24858

Agilent microarray-based RNA profiling of exosome samples. (a) Heatmap showing unsupervised hierarchical clustering of samples. Code from blue (−2 log2 normalized expression) to red (+2 log2 normalized expression) indicates RNA expression levels. NB: Replicates 1 and 2 are technical, 3 is biological. (b) Plot showing mean expression difference and corresponding density of probes for the 3 different methods. (c) Venn diagram of unique and shared mRNAs in UC, ODG and EQ samples.
Figure Legend Snippet: Agilent microarray-based RNA profiling of exosome samples. (a) Heatmap showing unsupervised hierarchical clustering of samples. Code from blue (−2 log2 normalized expression) to red (+2 log2 normalized expression) indicates RNA expression levels. NB: Replicates 1 and 2 are technical, 3 is biological. (b) Plot showing mean expression difference and corresponding density of probes for the 3 different methods. (c) Venn diagram of unique and shared mRNAs in UC, ODG and EQ samples.

Techniques Used: Microarray, Expressing, RNA Expression

13) Product Images from "Global Mapping of Transposon Location"

Article Title: Global Mapping of Transposon Location

Journal: PLoS Genetics

doi: 10.1371/journal.pgen.0020212

Validation of Whole Genome Transposon Analysis Using Two Sequenced Strains of S. cerevisiae (A) Whole genome comparison of full-length Ty1 and Ty2 elements from yeast strains RM11 and S288c after hybridization to the same Agilent yeast whole genome microarray. Black circles indicate the position of Ty1 or Ty2 full-length elements annotated for S288c in SGD. Triangles indicate full-length Ty2 elements identified in the sequence of RM11. Red peaks correspond to potential Ty1 or Ty2 elements present in S288c, while green peaks correspond to potential Ty1 or Ty2 peaks present in RM11. (B) Comparison of location of Ty1 full-length elements (green) and Ty2 full-length elements present in S288c. Symbols are as above. Numbers above various peaks refer to the following: 1, false-negative S288c elements obscured by overlapping elements in RM11; 2, false-negative S288c elements located in regions that are poorly represented by features on the array; 3, false-negative S288c elements that missed the criteria for calling a peak; 4, unannotated Ty1 full-length elements in S288c confirmed in this study; 5, false-positive peaks due to borderline elevated differential hybridization; 6, false-positive peaks corresponding to non-Ty repetitive elements in the genome. Grey horizontal lines above and below the central line for each chromosome correspond to a 3-fold difference in normalized ratio of Cy5 and Cy3 signal intensity.
Figure Legend Snippet: Validation of Whole Genome Transposon Analysis Using Two Sequenced Strains of S. cerevisiae (A) Whole genome comparison of full-length Ty1 and Ty2 elements from yeast strains RM11 and S288c after hybridization to the same Agilent yeast whole genome microarray. Black circles indicate the position of Ty1 or Ty2 full-length elements annotated for S288c in SGD. Triangles indicate full-length Ty2 elements identified in the sequence of RM11. Red peaks correspond to potential Ty1 or Ty2 elements present in S288c, while green peaks correspond to potential Ty1 or Ty2 peaks present in RM11. (B) Comparison of location of Ty1 full-length elements (green) and Ty2 full-length elements present in S288c. Symbols are as above. Numbers above various peaks refer to the following: 1, false-negative S288c elements obscured by overlapping elements in RM11; 2, false-negative S288c elements located in regions that are poorly represented by features on the array; 3, false-negative S288c elements that missed the criteria for calling a peak; 4, unannotated Ty1 full-length elements in S288c confirmed in this study; 5, false-positive peaks due to borderline elevated differential hybridization; 6, false-positive peaks corresponding to non-Ty repetitive elements in the genome. Grey horizontal lines above and below the central line for each chromosome correspond to a 3-fold difference in normalized ratio of Cy5 and Cy3 signal intensity.

Techniques Used: Hybridization, Microarray, Sequencing

Identifying a Unique Ty1 Element in Otherwise Isogenic Strains (A) Two isogenic yeast strains (FY5 and FY2) differ only by the presence of a Ty1 insertion in Chromosome V within the URA3 gene in FY2. After labeling transposon extracted DNA from FY2 with Cy3 (green) and transposon extracted DNA from FY5 with Cy5 (red), the labeled DNA was hybridized to an Agilent yeast whole genome microarray with > 40,000 unique features (yeast repetitive DNA was avoided during array construction). Log 2 ratio of hybridization for each feature along each chromosome is shown plotted in genome order using the TreeView Karyoscope function. The one region of significant differential hybridization is marked with an arrow. The grey horizontal lines above and below each chromosome correspond to 3-fold differential hybridization intensity. (B) Zoom view of a portion of Chromosome V and the peak of differential hybridization corresponding to the ∼8 kb surrounding URA3 (red box). The positions of nearby restriction sites for the enzymes used initially to digest genomic DNA are shown based on a GBrowse view of the region from SGD.
Figure Legend Snippet: Identifying a Unique Ty1 Element in Otherwise Isogenic Strains (A) Two isogenic yeast strains (FY5 and FY2) differ only by the presence of a Ty1 insertion in Chromosome V within the URA3 gene in FY2. After labeling transposon extracted DNA from FY2 with Cy3 (green) and transposon extracted DNA from FY5 with Cy5 (red), the labeled DNA was hybridized to an Agilent yeast whole genome microarray with > 40,000 unique features (yeast repetitive DNA was avoided during array construction). Log 2 ratio of hybridization for each feature along each chromosome is shown plotted in genome order using the TreeView Karyoscope function. The one region of significant differential hybridization is marked with an arrow. The grey horizontal lines above and below each chromosome correspond to 3-fold differential hybridization intensity. (B) Zoom view of a portion of Chromosome V and the peak of differential hybridization corresponding to the ∼8 kb surrounding URA3 (red box). The positions of nearby restriction sites for the enzymes used initially to digest genomic DNA are shown based on a GBrowse view of the region from SGD.

Techniques Used: Labeling, Microarray, Hybridization

Transposon Map of SK1 The positions of Ty1 and Ty2 full-length elements and Ty3 LTR elements in strain SK1 are shown, based on Agilent yeast whole genome microarray (Ty1 and Ty2) and Agilent ORF array (Ty3 LTR) analysis of this uncharacterized genome.
Figure Legend Snippet: Transposon Map of SK1 The positions of Ty1 and Ty2 full-length elements and Ty3 LTR elements in strain SK1 are shown, based on Agilent yeast whole genome microarray (Ty1 and Ty2) and Agilent ORF array (Ty3 LTR) analysis of this uncharacterized genome.

Techniques Used: Microarray

Analysis of Modified Bacterial (“Artificial”) Transposon Insertions in the S. cerevisiae Genome (A) Positions of five independent pooled artificial transposons from a yeast insertion library were determined after extracting StuI-digested yeast genomic DNA with probes designed to correspond to either strand at the 5′ or 3′ end of URA3, labeling with Cy3 and Cy5, respectively, and hybridizing to an Agilent yeast whole genome microarray. Arrows signify locations of significant differential hybridization. “URA3” indicates the actual URA3 locus on Chromosome V. The asterisk indicates an insertion on Chromosome XVI in which only the flanking region 3′ to the transposon is detected. Vertical lines above and below the horizontal for each chromosome represent the log 2 ratio of hybridization intensity for Cy5 versus Cy3 at each feature along the Agilent yeast whole genome microarray. For each insertion, the actual insertion site, determined by sequencing, and the position of the first significant flanking features are as follows: Chromosome IV, 368020, and 367656–367715 and 368589–368648; Chromosome IX, 55576, and 55291–55350 and 55808–55867; Chromosome XI, 613654, and 612706–612765 and 614005–614064; Chromosome XII, 387226, and 386346–386405 and 387248–387307; and Chromosome XVI, 296609, and 296350–296409 to 297592–297651. (B) An enlargement of the region detected on Chromosome XI, showing the structure of the artificial transposon, its unique StuI site, the bases covered by the oligonucleotides in the features on either side of the transition from significant differential Cy5 labeling to Cy3 labeling, and the position of the actual insertion. The map of the region from GBrowse of SGD shows the position of StuI restriction sites in the region. Grey horizontal lines above and below the central line for each chromosome correspond to a 3-fold ratio of signal intensity. Note that the transposon inserted in opposite orientation relative to the chromosome numbering, and is therefore flipped in the figure.
Figure Legend Snippet: Analysis of Modified Bacterial (“Artificial”) Transposon Insertions in the S. cerevisiae Genome (A) Positions of five independent pooled artificial transposons from a yeast insertion library were determined after extracting StuI-digested yeast genomic DNA with probes designed to correspond to either strand at the 5′ or 3′ end of URA3, labeling with Cy3 and Cy5, respectively, and hybridizing to an Agilent yeast whole genome microarray. Arrows signify locations of significant differential hybridization. “URA3” indicates the actual URA3 locus on Chromosome V. The asterisk indicates an insertion on Chromosome XVI in which only the flanking region 3′ to the transposon is detected. Vertical lines above and below the horizontal for each chromosome represent the log 2 ratio of hybridization intensity for Cy5 versus Cy3 at each feature along the Agilent yeast whole genome microarray. For each insertion, the actual insertion site, determined by sequencing, and the position of the first significant flanking features are as follows: Chromosome IV, 368020, and 367656–367715 and 368589–368648; Chromosome IX, 55576, and 55291–55350 and 55808–55867; Chromosome XI, 613654, and 612706–612765 and 614005–614064; Chromosome XII, 387226, and 386346–386405 and 387248–387307; and Chromosome XVI, 296609, and 296350–296409 to 297592–297651. (B) An enlargement of the region detected on Chromosome XI, showing the structure of the artificial transposon, its unique StuI site, the bases covered by the oligonucleotides in the features on either side of the transition from significant differential Cy5 labeling to Cy3 labeling, and the position of the actual insertion. The map of the region from GBrowse of SGD shows the position of StuI restriction sites in the region. Grey horizontal lines above and below the central line for each chromosome correspond to a 3-fold ratio of signal intensity. Note that the transposon inserted in opposite orientation relative to the chromosome numbering, and is therefore flipped in the figure.

Techniques Used: Modification, Labeling, Microarray, Hybridization, Sequencing

14) Product Images from "A Discovery Resource of Rare Copy Number Variations in Individuals with Autism Spectrum Disorder"

Article Title: A Discovery Resource of Rare Copy Number Variations in Individuals with Autism Spectrum Disorder

Journal: G3: Genes|Genomes|Genetics

doi: 10.1534/g3.112.004689

A Venn diagram showing comparison of Agilent 1M CNV calls with those detected by other SNP microarray platforms including Illumina 1M single/duo array, Affymetrix500K, Affymetrix6.0, and Illumina Omni 2.5M array for a total of 615 samples. Agilent 1M CGH data yielded 21,346 stringent CNVs and the SNP (other) microarray platforms yielded 21,782 stringent CNVs. A total of 7774 CNVs (36%) detected by the Agilent 1M array (AGLT1M) were detected by other platforms, whereas 8107 CNVs (37%) detected by other microarrays were detected by the Agilent 1M array. A total of 6213 (29%) Agilent 1M CNVs have less than 5 probe coverage in other SNP microarray platforms and 10,173 (47%) CNVs from the other SNP microarray platforms have less than 5 probe coverage in Agilent 1M array and are shown as smaller circles in this figure.
Figure Legend Snippet: A Venn diagram showing comparison of Agilent 1M CNV calls with those detected by other SNP microarray platforms including Illumina 1M single/duo array, Affymetrix500K, Affymetrix6.0, and Illumina Omni 2.5M array for a total of 615 samples. Agilent 1M CGH data yielded 21,346 stringent CNVs and the SNP (other) microarray platforms yielded 21,782 stringent CNVs. A total of 7774 CNVs (36%) detected by the Agilent 1M array (AGLT1M) were detected by other platforms, whereas 8107 CNVs (37%) detected by other microarrays were detected by the Agilent 1M array. A total of 6213 (29%) Agilent 1M CNVs have less than 5 probe coverage in other SNP microarray platforms and 10,173 (47%) CNVs from the other SNP microarray platforms have less than 5 probe coverage in Agilent 1M array and are shown as smaller circles in this figure.

Techniques Used: Microarray

Genome browser views of a subset of novel rare CNVs occurring in two or more ASD cases or are de novo (from Table 4 ). The genome coordinates are from genome build 36 (hg18) and, in each panel, ASD case ID numbers are listed next to blue bars (denoting a duplication/gain) or red bar (denoting a deletion/loss). Each panel also shows, in separate tracks, the RefSeq genes, UCSC segmental duplications, and probe distributions for the different microarray platforms used for CNV detection (Affy500K, Affy6.0, Illumina 1M, and Agilent 1M). (A) Maternally inherited duplications at the 15q25.1 locus encompassing an exon of the CIB2 gene in three unrelated ASD cases. (B) Paternally inherited duplications at the 4q23 locus encompassing several exons of the DAPP1 gene in two unrelated ASD cases. (C) Maternally inherited duplications at the 17p13.3 locus encompassing exons of the YWHAE gene in two unrelated ASD cases. (D) Duplications at the 19q13.32 locus encompassing exons of SAE1 gene in four unrelated ASD cases, three of which are novel and the fourth (ASD case 90278) was previously detected using an Affymetrix 6.0 array. (E) A paternally inherited deletion and a maternally inherited duplication at the 7q32.3 locus encompassing exons of the PLXNA4 gene (F). A de novo deletion at the 14q23.3 locus encompassing an intronic region of the GPHN gene in one ASD case.
Figure Legend Snippet: Genome browser views of a subset of novel rare CNVs occurring in two or more ASD cases or are de novo (from Table 4 ). The genome coordinates are from genome build 36 (hg18) and, in each panel, ASD case ID numbers are listed next to blue bars (denoting a duplication/gain) or red bar (denoting a deletion/loss). Each panel also shows, in separate tracks, the RefSeq genes, UCSC segmental duplications, and probe distributions for the different microarray platforms used for CNV detection (Affy500K, Affy6.0, Illumina 1M, and Agilent 1M). (A) Maternally inherited duplications at the 15q25.1 locus encompassing an exon of the CIB2 gene in three unrelated ASD cases. (B) Paternally inherited duplications at the 4q23 locus encompassing several exons of the DAPP1 gene in two unrelated ASD cases. (C) Maternally inherited duplications at the 17p13.3 locus encompassing exons of the YWHAE gene in two unrelated ASD cases. (D) Duplications at the 19q13.32 locus encompassing exons of SAE1 gene in four unrelated ASD cases, three of which are novel and the fourth (ASD case 90278) was previously detected using an Affymetrix 6.0 array. (E) A paternally inherited deletion and a maternally inherited duplication at the 7q32.3 locus encompassing exons of the PLXNA4 gene (F). A de novo deletion at the 14q23.3 locus encompassing an intronic region of the GPHN gene in one ASD case.

Techniques Used: Microarray

CNV analysis workflow. The ASD cases and controls were typed using the Agilent 1M CGH array, and CNVs were identified using two algorithms, DNA Analytics and DNAcopy. CNVs detected by both algorithms were defined as the stringent dataset and were used for novel rare variant discovery. Rare variants were defined as described in the Materials and Methods . The 1884 rare ASD CNVs (as reported in Table S2) were compared with the CNVs obtained from SNP microarray studies and this resulted in identification of 946 rare CNVs that were novel to the Agilent 1M CGH platform. The rare CNVs from only European ASD cases (505 cases) were then used for global rare CNV burden analysis and gene-set association tests by comparison to 1000 PDx controls.
Figure Legend Snippet: CNV analysis workflow. The ASD cases and controls were typed using the Agilent 1M CGH array, and CNVs were identified using two algorithms, DNA Analytics and DNAcopy. CNVs detected by both algorithms were defined as the stringent dataset and were used for novel rare variant discovery. Rare variants were defined as described in the Materials and Methods . The 1884 rare ASD CNVs (as reported in Table S2) were compared with the CNVs obtained from SNP microarray studies and this resulted in identification of 946 rare CNVs that were novel to the Agilent 1M CGH platform. The rare CNVs from only European ASD cases (505 cases) were then used for global rare CNV burden analysis and gene-set association tests by comparison to 1000 PDx controls.

Techniques Used: Variant Assay, Microarray

Genome browser view of a subset of the novel rare CNVs found in one ASD case that impact one or more exons ( Table 5 ). The genome coordinates are from genome build 36 (hg18) and, in each panel, the ASD case ID number is listed next to a red bar (denoting a deletion/loss). Each panel also shows, in separate tracks, the RefSeq genes and probe distributions for the different microarray platforms used for CNV detection (Affy500K, Affy6.0, Illumina 1M and Agilent 1M). (A) Paternally inherited deletion at the 9p22.1 locus impacting the 5′-end of the SLC24A2 gene. (B) Deletion at the 22q11.21 locus resulting in loss of an exon of the CECR2 gene. (C) Paternally inherited deletion at the 11q12.2 impacting the 3′-end of the DAGLA gene. (D) Maternally inherited deletion at the 22q11.23 impacting exons near the 5′-end of the UPB1 gene. (E) Pedigrees of ASD families for the CNVs in novel loci occurring in one ASD case that correspond to panels A-D. The open symbols represent unaffected individuals, filled symbols represent individuals with ASD diagnosis and arrows indicate the probands. Individuals from which DNA was not available (N/A) for testing are denoted inside the symbols.
Figure Legend Snippet: Genome browser view of a subset of the novel rare CNVs found in one ASD case that impact one or more exons ( Table 5 ). The genome coordinates are from genome build 36 (hg18) and, in each panel, the ASD case ID number is listed next to a red bar (denoting a deletion/loss). Each panel also shows, in separate tracks, the RefSeq genes and probe distributions for the different microarray platforms used for CNV detection (Affy500K, Affy6.0, Illumina 1M and Agilent 1M). (A) Paternally inherited deletion at the 9p22.1 locus impacting the 5′-end of the SLC24A2 gene. (B) Deletion at the 22q11.21 locus resulting in loss of an exon of the CECR2 gene. (C) Paternally inherited deletion at the 11q12.2 impacting the 3′-end of the DAGLA gene. (D) Maternally inherited deletion at the 22q11.23 impacting exons near the 5′-end of the UPB1 gene. (E) Pedigrees of ASD families for the CNVs in novel loci occurring in one ASD case that correspond to panels A-D. The open symbols represent unaffected individuals, filled symbols represent individuals with ASD diagnosis and arrows indicate the probands. Individuals from which DNA was not available (N/A) for testing are denoted inside the symbols.

Techniques Used: Microarray

15) Product Images from "Identification of Novel Low-Dose Bisphenol A Targets in Human Foreskin Fibroblast Cells Derived from Hypospadias Patients"

Article Title: Identification of Novel Low-Dose Bisphenol A Targets in Human Foreskin Fibroblast Cells Derived from Hypospadias Patients

Journal: PLoS ONE

doi: 10.1371/journal.pone.0036711

Network associated genes differentially expressed in response to BPA. ( A ) “Endocrine System Disorders, Gastrointestinal Disease, Genetic Disorder” network and ( B ) “Cell Death, Cellular Growth and Proliferation, Cancer” network. The images were created using the IPA platform by overlaying the differentially expressed genes in response to BPA detected by Agilent microarray analysis onto a global molecular network from the Ingenuity knowledgebase. Red indicates upregulated genes, green indicates downregulated genes, and white indicates genes that were not annotated in this array but that form part of this network. The bottom numbers indicate the fold changes induced by BPA, and the top numbers are the P -values between the DMSO control group and the BPA treated group. Direct relationships are exhibited with solid arrows and indirect relationships with dashed arrows.
Figure Legend Snippet: Network associated genes differentially expressed in response to BPA. ( A ) “Endocrine System Disorders, Gastrointestinal Disease, Genetic Disorder” network and ( B ) “Cell Death, Cellular Growth and Proliferation, Cancer” network. The images were created using the IPA platform by overlaying the differentially expressed genes in response to BPA detected by Agilent microarray analysis onto a global molecular network from the Ingenuity knowledgebase. Red indicates upregulated genes, green indicates downregulated genes, and white indicates genes that were not annotated in this array but that form part of this network. The bottom numbers indicate the fold changes induced by BPA, and the top numbers are the P -values between the DMSO control group and the BPA treated group. Direct relationships are exhibited with solid arrows and indirect relationships with dashed arrows.

Techniques Used: Indirect Immunoperoxidase Assay, Microarray

16) Product Images from "Human chromosome 21 orthologous region on mouse chromosome 17 is a major determinant of Down syndrome-related developmental cognitive deficits"

Article Title: Human chromosome 21 orthologous region on mouse chromosome 17 is a major determinant of Down syndrome-related developmental cognitive deficits

Journal: Human Molecular Genetics

doi: 10.1093/hmg/ddt446

The mouse models of DS carrying three copies in the different Hsa21 orthologous regions on Mmu10, Mmu16 and Mmu17. ( A ) Schematic representation of Hsa21 and the triplicated Hsa21 syntenic regions in the mouse models. ( B ) Agilent microarray CGH profiles
Figure Legend Snippet: The mouse models of DS carrying three copies in the different Hsa21 orthologous regions on Mmu10, Mmu16 and Mmu17. ( A ) Schematic representation of Hsa21 and the triplicated Hsa21 syntenic regions in the mouse models. ( B ) Agilent microarray CGH profiles

Techniques Used: Microarray

The mouse models of DS carrying three copies in the different Hsa21 orthologous regions on Mmu16. ( A ) Schematic representation of Hsa21 and the triplicated Hsa21 syntenic regions in the mouse models. ( B ) Agilent microarray CGH profiles show the duplication
Figure Legend Snippet: The mouse models of DS carrying three copies in the different Hsa21 orthologous regions on Mmu16. ( A ) Schematic representation of Hsa21 and the triplicated Hsa21 syntenic regions in the mouse models. ( B ) Agilent microarray CGH profiles show the duplication

Techniques Used: Microarray

17) Product Images from "A miR-150/TET3 pathway regulates the generation of mouse and human non-classical monocyte subset"

Article Title: A miR-150/TET3 pathway regulates the generation of mouse and human non-classical monocyte subset

Journal: Nature Communications

doi: 10.1038/s41467-018-07801-x

Differentially expressed miRNA from control and CMML patient-sorted CD14 + . a Volcano plot showing the differentially expressed miRNAs in CD14 + cell-sorted monocytes from CMML ( n = 33) and healthy donor ( n = 5 + pool of five samples) peripheral blood samples (learning cohort), as measured using v12.0 Agilent microarray. X -axis, log 2 fold-change value; Y -axis, −log 10 (adjusted P value). b List of the four miRNAs identified as deregulated in the learning cohort. Of note, hsa-miR-923 up-regulation is a known artifact of the v12.0 version of these microarrays. c Box plot showing the relative expression of hsa-miR-150, hsa-miR-451, and hsa-miR-494 analyzed by qRT-PCR in samples of the learning cohort (center line: median; whiskers: min to max). d qRT-PCR analysis of the relative expression levels of hsa-miR-150 (CTL = 24; CMML = 133), hsa-miR-451 (CTL = 24, CMML = 53) and hsa-miR-494 (CTL = 9; CMML = 32) in an independent validation cohort. Red lines, median with interquartile range; Mann–Whitney test: ** P
Figure Legend Snippet: Differentially expressed miRNA from control and CMML patient-sorted CD14 + . a Volcano plot showing the differentially expressed miRNAs in CD14 + cell-sorted monocytes from CMML ( n = 33) and healthy donor ( n = 5 + pool of five samples) peripheral blood samples (learning cohort), as measured using v12.0 Agilent microarray. X -axis, log 2 fold-change value; Y -axis, −log 10 (adjusted P value). b List of the four miRNAs identified as deregulated in the learning cohort. Of note, hsa-miR-923 up-regulation is a known artifact of the v12.0 version of these microarrays. c Box plot showing the relative expression of hsa-miR-150, hsa-miR-451, and hsa-miR-494 analyzed by qRT-PCR in samples of the learning cohort (center line: median; whiskers: min to max). d qRT-PCR analysis of the relative expression levels of hsa-miR-150 (CTL = 24; CMML = 133), hsa-miR-451 (CTL = 24, CMML = 53) and hsa-miR-494 (CTL = 9; CMML = 32) in an independent validation cohort. Red lines, median with interquartile range; Mann–Whitney test: ** P

Techniques Used: Microarray, Expressing, Quantitative RT-PCR, CTL Assay, MANN-WHITNEY

18) Product Images from "DNA repair in higher plants; photoreactivation is the major DNA repair pathway in non-proliferating cells while excision repair (nucleotide excision repair and base excision repair) is active in proliferating cells"

Article Title: DNA repair in higher plants; photoreactivation is the major DNA repair pathway in non-proliferating cells while excision repair (nucleotide excision repair and base excision repair) is active in proliferating cells

Journal: Nucleic Acids Research

doi: 10.1093/nar/gkh591

Scatter plots comparing gene expression levels in SAM and mature leaves. An Agilent rice 22K custom oligo DNA microarray was used. Each spot on the array is represented by a dot in the scatter plot. The results of color-swap experiments (left, mature leaf-Cy 3/SAM-Cy 5; right, SAM-Cy 3/mature leaf-Cy 5) are shown. The red line represents the diagonal (equal expression in the two tissues). The yellow line above represents a Cy-3/Cy-5 ratio of 5:1, while that below represents a Cy-3/Cy-5 ratio of 1:5.
Figure Legend Snippet: Scatter plots comparing gene expression levels in SAM and mature leaves. An Agilent rice 22K custom oligo DNA microarray was used. Each spot on the array is represented by a dot in the scatter plot. The results of color-swap experiments (left, mature leaf-Cy 3/SAM-Cy 5; right, SAM-Cy 3/mature leaf-Cy 5) are shown. The red line represents the diagonal (equal expression in the two tissues). The yellow line above represents a Cy-3/Cy-5 ratio of 5:1, while that below represents a Cy-3/Cy-5 ratio of 1:5.

Techniques Used: Expressing, Microarray

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Article Snippet: Microarray Processing RNA was labeled and amplified using the one-color microarray gene expression analysis protocol (Agilent Technologies, Santa Clara, CA), hybridized to Agilent whole human genome 4 × 44k Agilent whole human genome microarrays, and incubated for 17 hours at 60°C in a hybridization oven. .. Slides were scanned on an Agilent microarray scanner at 5-μm resolution, photomultiplier tube (PMT) gain at 100% and 10%.

Article Title: Overexpression of the ATPase Inhibitory Factor 1 Favors a Non-metastatic Phenotype in Breast Cancer
Article Snippet: Briefly, for each hybridization, 600 ng of Cy3 probes were mixed and added to 5 μl of 10× blocking agent, 1 μl of 25× fragmentation buffer, and nuclease-free water in a 25-μl reaction, incubated at 60°C for 30 min to fragment RNA, and stopped with 25 μl of 2× hybridization buffer. .. Images were captured with an Agilent Microarray Scanner and spots quantified using Feature Extraction Software (Agilent Technologies).

Article Title: Antiproliferative Effect of Ascorbic Acid Is Associated with the Inhibition of Genes Necessary to Cell Cycle Progression
Article Snippet: The reaction was carried out in a solution containing 500 μM dNTP and 400 U MMLV reverse transcriptase at 40°C for 2 h, and then terminated by incubation at 65°C for 15 min. .. Hybridization was carried out in 440 μl of mixture containing 750 ng of Cy3- and Cy5-labeled cDNA probes, control targets, and the fragmented DNA supplied by the manufacturer at 60°C for 17 h. The microarrays were then washed according to the manufacturer’s protocol, dried, and scanned using an Agilent microarray scanner with 532 nm laser for Cy3 measurement and a 635 nm laser for Cy5 measurement.

Expressing:

Article Title: The impact of disparate isolation methods for extracellular vesicles on downstream RNA profiling
Article Snippet: Whole genome mRNA expression profiling was performed using a custom gene expression microarray (Agilent Technologies, Amstelveen, The Netherlands). .. Cy-3-labelled cRNA was hybridized and probe intensities were analysed using an Agilent microarray scanner and Feature Extraction software.

Article Title: The Nuclear-Retained Noncoding RNA MALAT1 Regulates Alternative Splicing by Modulating SR Splicing Factor Phosphorylation
Article Snippet: Microarray slides were scanned with an Agilent microarray scanner at 5 μm resolution, and TIFF images were processed using Feature Extraction Software (Agilent). .. The AS microarray data have been deposited in NCBI’s Gene Expression Omnibus ( ) and are accessible through GEO series accession number (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc= ).

Article Title: Hepatic Transcriptome Responses in Mice (Mus musculus) Exposed to the Nafion Membrane and Its Combustion Products
Article Snippet: RNA samples with a 2100 RIN value ≥ 7 and 28S/18S ≥ 0.7 were used for the gene expression analysis. .. After the hybridization, the microarray slides were scanned with an Agilent Microarray Scanner (Agilent Technologies, Santa Clara, CA, USA) at a 5 μ m resolution for each slide with a photomultiplier tube setting of 100% and 10%.

Article Title: Identification of a Selective G1-Phase Benzimidazolone Inhibitor by a Senescence-Targeted Virtual Screen Using Artificial Neural Networks
Article Snippet: Microarray Processing RNA was labeled and amplified using the one-color microarray gene expression analysis protocol (Agilent Technologies, Santa Clara, CA), hybridized to Agilent whole human genome 4 × 44k Agilent whole human genome microarrays, and incubated for 17 hours at 60°C in a hybridization oven. .. Slides were scanned on an Agilent microarray scanner at 5-μm resolution, photomultiplier tube (PMT) gain at 100% and 10%.

Article Title: Kinetochore assembly and heterochromatin formation occur autonomously in Schizosaccharomyces pombe
Article Snippet: Paragraph title: Microarray Expression Analysis. ... The results were scanned with an Agilent microarray scanner, processed, and analyzed using Agilent Genespring software.

Article Title: Tissue Specific Diurnal Rhythms of Metabolites and Their Regulation during Herbivore Attack in a Native Tobacco, Nicotiana attenuata
Article Snippet: Agilent microarray scanner (G2565BA) and Scan Control software were used to obtain intensity of the spots. .. The resulting gene expression profiles were analyzed using GeneSpring GX software (Silicon Genetics, Redwood City, CA).

Hybridization:

Article Title: The Nuclear-Retained Noncoding RNA MALAT1 Regulates Alternative Splicing by Modulating SR Splicing Factor Phosphorylation
Article Snippet: Hybridization of Cy3- and Cy5-labeled cDNA synthesized from polyA+ RNA from MALAT1-antisense oligo treated or GFP-antisense oligo-treated HeLa cells was performed using a HS4800 Pro Hybridization Station (Tecan) at 42°C for 22 hr. .. Microarray slides were scanned with an Agilent microarray scanner at 5 μm resolution, and TIFF images were processed using Feature Extraction Software (Agilent).

Article Title: Hepatic Transcriptome Responses in Mice (Mus musculus) Exposed to the Nafion Membrane and Its Combustion Products
Article Snippet: .. After the hybridization, the microarray slides were scanned with an Agilent Microarray Scanner (Agilent Technologies, Santa Clara, CA, USA) at a 5 μ m resolution for each slide with a photomultiplier tube setting of 100% and 10%. .. The data were extracted with the Feature Extraction software 10.7 (Agilent Technologies, Santa Clara, CA, USA).

Article Title: Benign copy number changes in clinical cytogenetic diagnostics by array CGH
Article Snippet: .. Following manufacturer‘s recommended hybridization and washes, the arrays were scanned at 5 μm resolution using the Agilent microarray scanner and analyzed using Feature Extraction v9.5.3.1, DNA Analytics v4.0 (Agilent Technologies), and prototype software tools using similar statistical methods. ..

Article Title: Identification of a Selective G1-Phase Benzimidazolone Inhibitor by a Senescence-Targeted Virtual Screen Using Artificial Neural Networks
Article Snippet: Microarray Processing RNA was labeled and amplified using the one-color microarray gene expression analysis protocol (Agilent Technologies, Santa Clara, CA), hybridized to Agilent whole human genome 4 × 44k Agilent whole human genome microarrays, and incubated for 17 hours at 60°C in a hybridization oven. .. Slides were scanned on an Agilent microarray scanner at 5-μm resolution, photomultiplier tube (PMT) gain at 100% and 10%.

Article Title: Overexpression of the ATPase Inhibitory Factor 1 Favors a Non-metastatic Phenotype in Breast Cancer
Article Snippet: Paragraph title: Gene Array Hybridization ... Images were captured with an Agilent Microarray Scanner and spots quantified using Feature Extraction Software (Agilent Technologies).

Article Title: Kinetochore assembly and heterochromatin formation occur autonomously in Schizosaccharomyces pombe
Article Snippet: The probes were purified, fragmented, and analyzed by competitive hybridization to a custom 4 × 44K gene expression microarray (design ID 033946; courtesy of Jurg Bähler and colleagues, University College, London). .. The results were scanned with an Agilent microarray scanner, processed, and analyzed using Agilent Genespring software.

Article Title: A miR-150/TET3 pathway regulates the generation of mouse and human non-classical monocyte subset
Article Snippet: Paragraph title: MiRNA preparation and hybridization ... After washes, microarrays were scanned with an Agilent microarray scanner using high dynamic range settings before extracting data using the Agilent Feature Extraction Software (10.7.3.1).

Article Title: Antiproliferative Effect of Ascorbic Acid Is Associated with the Inhibition of Genes Necessary to Cell Cycle Progression
Article Snippet: .. Hybridization was carried out in 440 μl of mixture containing 750 ng of Cy3- and Cy5-labeled cDNA probes, control targets, and the fragmented DNA supplied by the manufacturer at 60°C for 17 h. The microarrays were then washed according to the manufacturer’s protocol, dried, and scanned using an Agilent microarray scanner with 532 nm laser for Cy3 measurement and a 635 nm laser for Cy5 measurement. .. The results were analyzed using the Luminator Bioinformatics platform (Rosetta Biosoftware).

DNA Labeling:

Article Title: Benign copy number changes in clinical cytogenetic diagnostics by array CGH
Article Snippet: Sample and control DNAs were labeled with Cy5 or Cy3, respectively, using the Agilent DNA labeling kit. .. Following manufacturer‘s recommended hybridization and washes, the arrays were scanned at 5 μm resolution using the Agilent microarray scanner and analyzed using Feature Extraction v9.5.3.1, DNA Analytics v4.0 (Agilent Technologies), and prototype software tools using similar statistical methods.

Sequencing:

Article Title: Benign copy number changes in clinical cytogenetic diagnostics by array CGH
Article Snippet: Following manufacturer‘s recommended hybridization and washes, the arrays were scanned at 5 μm resolution using the Agilent microarray scanner and analyzed using Feature Extraction v9.5.3.1, DNA Analytics v4.0 (Agilent Technologies), and prototype software tools using similar statistical methods. .. Log2 ratios of fluorescent signals for each measured probe sequence were assigned to all perfect genomic matches of this sequence in the NCBI 36.1 build of the reference genome resulting in probes being assigned to a total of 500,974 genomic locations.

Isolation:

Article Title: The impact of disparate isolation methods for extracellular vesicles on downstream RNA profiling
Article Snippet: RNA analysis Total RNA was isolated from exosome samples using the miRNeasy Micro kit according to manufacturer's instructions (Qiagen, Valencia, CA, USA). .. Cy-3-labelled cRNA was hybridized and probe intensities were analysed using an Agilent microarray scanner and Feature Extraction software.

Article Title: Tissue Specific Diurnal Rhythms of Metabolites and Their Regulation during Herbivore Attack in a Native Tobacco, Nicotiana attenuata
Article Snippet: Total RNA was isolated with TRIZOL reagent and labeled cRNA with the Quick Amp labeling kit (Agilent). .. Agilent microarray scanner (G2565BA) and Scan Control software were used to obtain intensity of the spots.

Negative Control:

Article Title: The impact of disparate isolation methods for extracellular vesicles on downstream RNA profiling
Article Snippet: Cy-3-labelled cRNA was hybridized and probe intensities were analysed using an Agilent microarray scanner and Feature Extraction software. .. For downstream data analysis, only probes with a normalized signal at least 2-fold above that of the negative control probe (DarkCorner) were labelled as expressed.

Labeling:

Article Title: Benign copy number changes in clinical cytogenetic diagnostics by array CGH
Article Snippet: Sample and control DNAs were labeled with Cy5 or Cy3, respectively, using the Agilent DNA labeling kit. .. Following manufacturer‘s recommended hybridization and washes, the arrays were scanned at 5 μm resolution using the Agilent microarray scanner and analyzed using Feature Extraction v9.5.3.1, DNA Analytics v4.0 (Agilent Technologies), and prototype software tools using similar statistical methods.

Article Title: Identification of a Selective G1-Phase Benzimidazolone Inhibitor by a Senescence-Targeted Virtual Screen Using Artificial Neural Networks
Article Snippet: Microarray Processing RNA was labeled and amplified using the one-color microarray gene expression analysis protocol (Agilent Technologies, Santa Clara, CA), hybridized to Agilent whole human genome 4 × 44k Agilent whole human genome microarrays, and incubated for 17 hours at 60°C in a hybridization oven. .. Slides were scanned on an Agilent microarray scanner at 5-μm resolution, photomultiplier tube (PMT) gain at 100% and 10%.

Article Title: Overexpression of the ATPase Inhibitory Factor 1 Favors a Non-metastatic Phenotype in Breast Cancer
Article Snippet: Total RNA (200 ng) was amplified using One-Color Low Input Quick Amp Labeling Kit (Agilent Technologies) and purified with RNeasy Mini Kit (Qiagen). .. Images were captured with an Agilent Microarray Scanner and spots quantified using Feature Extraction Software (Agilent Technologies).

Article Title: Kinetochore assembly and heterochromatin formation occur autonomously in Schizosaccharomyces pombe
Article Snippet: The size and integrity were checked by agarose gel electrophoresis. cRNA probes were prepared and labeled with CY3 or CY5 using the Agilent Low-Input Quick Amp Labeling Kit. .. The results were scanned with an Agilent microarray scanner, processed, and analyzed using Agilent Genespring software.

Article Title: Tissue Specific Diurnal Rhythms of Metabolites and Their Regulation during Herbivore Attack in a Native Tobacco, Nicotiana attenuata
Article Snippet: Total RNA was isolated with TRIZOL reagent and labeled cRNA with the Quick Amp labeling kit (Agilent). .. Agilent microarray scanner (G2565BA) and Scan Control software were used to obtain intensity of the spots.

Article Title: A miR-150/TET3 pathway regulates the generation of mouse and human non-classical monocyte subset
Article Snippet: MiRNA preparation and hybridization RNA samples were dephosphorylated with calf intestine alkaline phosphatase (GE Healthcare Europe GmbH, Velizy Villacoublay, France), denatured with dimethyl sulfoxide, and labeled with pCp-Cy3 using T4 RNA ligase before RNA hybridization to Agilent human miRNA microarrays v3.0 (Agilent, Les Ulis, France) for 20 h at 55 °C under rotation. .. After washes, microarrays were scanned with an Agilent microarray scanner using high dynamic range settings before extracting data using the Agilent Feature Extraction Software (10.7.3.1).

Purification:

Article Title: Overexpression of the ATPase Inhibitory Factor 1 Favors a Non-metastatic Phenotype in Breast Cancer
Article Snippet: Total RNA (200 ng) was amplified using One-Color Low Input Quick Amp Labeling Kit (Agilent Technologies) and purified with RNeasy Mini Kit (Qiagen). .. Images were captured with an Agilent Microarray Scanner and spots quantified using Feature Extraction Software (Agilent Technologies).

Article Title: Kinetochore assembly and heterochromatin formation occur autonomously in Schizosaccharomyces pombe
Article Snippet: The probes were purified, fragmented, and analyzed by competitive hybridization to a custom 4 × 44K gene expression microarray (design ID 033946; courtesy of Jurg Bähler and colleagues, University College, London). .. The results were scanned with an Agilent microarray scanner, processed, and analyzed using Agilent Genespring software.

Software:

Article Title: The impact of disparate isolation methods for extracellular vesicles on downstream RNA profiling
Article Snippet: .. Cy-3-labelled cRNA was hybridized and probe intensities were analysed using an Agilent microarray scanner and Feature Extraction software. ..

Article Title: The Nuclear-Retained Noncoding RNA MALAT1 Regulates Alternative Splicing by Modulating SR Splicing Factor Phosphorylation
Article Snippet: .. Microarray slides were scanned with an Agilent microarray scanner at 5 μm resolution, and TIFF images were processed using Feature Extraction Software (Agilent). ..

Article Title: Hepatic Transcriptome Responses in Mice (Mus musculus) Exposed to the Nafion Membrane and Its Combustion Products
Article Snippet: After the hybridization, the microarray slides were scanned with an Agilent Microarray Scanner (Agilent Technologies, Santa Clara, CA, USA) at a 5 μ m resolution for each slide with a photomultiplier tube setting of 100% and 10%. .. The data were extracted with the Feature Extraction software 10.7 (Agilent Technologies, Santa Clara, CA, USA).

Article Title: Benign copy number changes in clinical cytogenetic diagnostics by array CGH
Article Snippet: .. Following manufacturer‘s recommended hybridization and washes, the arrays were scanned at 5 μm resolution using the Agilent microarray scanner and analyzed using Feature Extraction v9.5.3.1, DNA Analytics v4.0 (Agilent Technologies), and prototype software tools using similar statistical methods. ..

Article Title: Overexpression of the ATPase Inhibitory Factor 1 Favors a Non-metastatic Phenotype in Breast Cancer
Article Snippet: .. Images were captured with an Agilent Microarray Scanner and spots quantified using Feature Extraction Software (Agilent Technologies). .. Background correction and normalization of expression data were performed using LIMMA ( , ).

Article Title: Kinetochore assembly and heterochromatin formation occur autonomously in Schizosaccharomyces pombe
Article Snippet: .. The results were scanned with an Agilent microarray scanner, processed, and analyzed using Agilent Genespring software. .. We thank Christian Rudolph for discussion, Robin Allshire for strains; Jun-ichi Nakayama for the Swi6 GFP tagging plasmid EGFP-pAL2U; Frank Uhlmann and Wolfgang Zachariae for the details of the tagging of Rad21 with PK-9; Jian-qui Wu and Valerie Coffman for details of their Cnp1 mGFP tag, plasmids, and advice; Jurg Bähler for microarray design; and Danielle Fletcher and Darren Marjenberg (both of Agilent) for help with microarray data analysis.

Article Title: Establishment and characterization of a novel vincristine‐resistant diffuse large B‐cell lymphoma cell line containing the 8q24 homogeneously staining region
Article Snippet: Scanning analyses were performed using the Agilent Microarray Scanner (Agilent Technologies). .. The array data were analyzed to determine chromosomal copy numbers using the feature extractions version 11.0 software program (Agilent Technologies) and the analytical software program dna analytics , version 4.0 (Agilent Technologies).

Article Title: Tissue Specific Diurnal Rhythms of Metabolites and Their Regulation during Herbivore Attack in a Native Tobacco, Nicotiana attenuata
Article Snippet: .. Agilent microarray scanner (G2565BA) and Scan Control software were used to obtain intensity of the spots. .. All microarray data with each probe name were deposited in the NCBI GEO database (accession number GSE30287).

Article Title: A miR-150/TET3 pathway regulates the generation of mouse and human non-classical monocyte subset
Article Snippet: .. After washes, microarrays were scanned with an Agilent microarray scanner using high dynamic range settings before extracting data using the Agilent Feature Extraction Software (10.7.3.1). ..

Article Title: Benign copy number changes in clinical cytogenetic diagnostics by array CGH
Article Snippet: .. Chips were scanned using either the Gene Pix 4000B or the Agilent Microarray scanner and the Gene Pix Pro 6.0 software package (Axon Instruments, Union City, CA). .. The data were analyzed using the SpectralWare software program (SGI/PE).

RNA Extraction:

Article Title: Hepatic Transcriptome Responses in Mice (Mus musculus) Exposed to the Nafion Membrane and Its Combustion Products
Article Snippet: Paragraph title: RNA extraction and microarray analysis ... After the hybridization, the microarray slides were scanned with an Agilent Microarray Scanner (Agilent Technologies, Santa Clara, CA, USA) at a 5 μ m resolution for each slide with a photomultiplier tube setting of 100% and 10%.

Variant Assay:

Article Title: Benign copy number changes in clinical cytogenetic diagnostics by array CGH
Article Snippet: A copy number variant was called only if confirmed on both hybridizations. .. Chips were scanned using either the Gene Pix 4000B or the Agilent Microarray scanner and the Gene Pix Pro 6.0 software package (Axon Instruments, Union City, CA).

Agarose Gel Electrophoresis:

Article Title: Kinetochore assembly and heterochromatin formation occur autonomously in Schizosaccharomyces pombe
Article Snippet: The size and integrity were checked by agarose gel electrophoresis. cRNA probes were prepared and labeled with CY3 or CY5 using the Agilent Low-Input Quick Amp Labeling Kit. .. The results were scanned with an Agilent microarray scanner, processed, and analyzed using Agilent Genespring software.

Spectrophotometry:

Article Title: The impact of disparate isolation methods for extracellular vesicles on downstream RNA profiling
Article Snippet: RNA concentration was measured using a UV-Vis spectrophotometer (Nanodrop Technologies, Wilmington, DE, USA). .. Cy-3-labelled cRNA was hybridized and probe intensities were analysed using an Agilent microarray scanner and Feature Extraction software.

Article Title: Benign copy number changes in clinical cytogenetic diagnostics by array CGH
Article Snippet: DNA concentration was measured using a NanoDrop Spectrophotometer (NanoDrop Technologies, Inc, Wilmington, DE). .. Chips were scanned using either the Gene Pix 4000B or the Agilent Microarray scanner and the Gene Pix Pro 6.0 software package (Axon Instruments, Union City, CA).

Concentration Assay:

Article Title: The impact of disparate isolation methods for extracellular vesicles on downstream RNA profiling
Article Snippet: RNA concentration was measured using a UV-Vis spectrophotometer (Nanodrop Technologies, Wilmington, DE, USA). .. Cy-3-labelled cRNA was hybridized and probe intensities were analysed using an Agilent microarray scanner and Feature Extraction software.

Article Title: Benign copy number changes in clinical cytogenetic diagnostics by array CGH
Article Snippet: DNA concentration was measured using a NanoDrop Spectrophotometer (NanoDrop Technologies, Inc, Wilmington, DE). .. Chips were scanned using either the Gene Pix 4000B or the Agilent Microarray scanner and the Gene Pix Pro 6.0 software package (Axon Instruments, Union City, CA).

BAC Assay:

Article Title: Benign copy number changes in clinical cytogenetic diagnostics by array CGH
Article Snippet: A set of ten samples which showed common bCNVs based on the BAC array data set was chosen for analysis on the Agilent Human Genome CNV microarray. .. Following manufacturer‘s recommended hybridization and washes, the arrays were scanned at 5 μm resolution using the Agilent microarray scanner and analyzed using Feature Extraction v9.5.3.1, DNA Analytics v4.0 (Agilent Technologies), and prototype software tools using similar statistical methods.

Article Title: Benign copy number changes in clinical cytogenetic diagnostics by array CGH
Article Snippet: The BAC microarrays were run in duplicate using a dye-reversal strategy. .. Chips were scanned using either the Gene Pix 4000B or the Agilent Microarray scanner and the Gene Pix Pro 6.0 software package (Axon Instruments, Union City, CA).

T-Test:

Article Title: Hepatic Transcriptome Responses in Mice (Mus musculus) Exposed to the Nafion Membrane and Its Combustion Products
Article Snippet: After the hybridization, the microarray slides were scanned with an Agilent Microarray Scanner (Agilent Technologies, Santa Clara, CA, USA) at a 5 μ m resolution for each slide with a photomultiplier tube setting of 100% and 10%. .. Differentially expressed genes (DEGs) between the treated groups and control were identified as the genes with a greater than ± 2.0-fold-change and p -value < 0.05 (t -test).

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  • 98
    Agilent technologies microarray scanner system
    Hierarchical cluster plot generated from miRNA expression profiling of a repertoire of a variety of CNS cell lineages (neuronal, microglia, astrocytes). A microglia specific cluster of miRNAs is indicated. Red indicates high levels of miRNA expression, green low levels and gray indicates expression that was undetected by the <t>microarray</t> used.
    Microarray Scanner System, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 98/100, based on 118 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/microarray scanner system/product/Agilent technologies
    Average 98 stars, based on 118 article reviews
    Price from $9.99 to $1999.99
    microarray scanner system - by Bioz Stars, 2020-04
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    91
    Agilent technologies alternative microarray scanner
    Custom DNA and RNA pool generation from <t>microarray.</t> A) Agilent microarrays contain ssDNA probes that have variable designed sequences (multicoloured) and a T7 promoter sequence (orange lines). A Cy3 (green circle) labeled T7 promoter primer (orange line) is annealed to ssDNA microarray probes which are subsequently double-stranded by enzymatic primer extension using T4 DNA polymerase (blue dotted line). A dsDNA linker (purple lines), labeled with Cy5 (red circle), is ligated to the dsDNA microarray probes using T4 DNA ligase. Cy3 and Cy5 signals are detected on microarrays by scanning at 532 and 635 nm, respectively, to verify efficient T7 primer annealing and linker ligation. Scanned Cy3 and Cy5 microarray images are shown (enclosed by dotted blue circles). B) PCR amplification of the dsDNA pool using ssDNA pool purified from the microarray as template. ssDNA pool (PCR template) dilutions as well as bands corresponding to an 80 bp DNA ladder and a 80–91 bp dsDNA pool are indicated on the ethidium bromide stained agarose gel image. C) Linker cleavage is mediated by a Type IIS restriction enzymes, BspQI. Representative bands corresponding to undigested PCR amplified dsDNA pool (enclosed by yellow box), BspQI digested dsDNA template (enclosed by pink box), and cleaved dsDNA linker (enclosed by blue box) are indicated. D) The non-random RNA pool (multicoloured lines and high intensity band in the agarose gel image) is generated via T7 RNA polymerase mediated transcription reactions, using gel purified dsDNA templates (shown in panel 2C ).
    Alternative Microarray Scanner, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 91/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/alternative microarray scanner/product/Agilent technologies
    Average 91 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    alternative microarray scanner - by Bioz Stars, 2020-04
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      Buy from Supplier

    Image Search Results


    Hierarchical cluster plot generated from miRNA expression profiling of a repertoire of a variety of CNS cell lineages (neuronal, microglia, astrocytes). A microglia specific cluster of miRNAs is indicated. Red indicates high levels of miRNA expression, green low levels and gray indicates expression that was undetected by the microarray used.

    Journal: PLoS ONE

    Article Title: MicroRNA 146a (miR-146a) Is Over-Expressed during Prion Disease and Modulates the Innate Immune Response and the Microglial Activation State

    doi: 10.1371/journal.pone.0030832

    Figure Lengend Snippet: Hierarchical cluster plot generated from miRNA expression profiling of a repertoire of a variety of CNS cell lineages (neuronal, microglia, astrocytes). A microglia specific cluster of miRNAs is indicated. Red indicates high levels of miRNA expression, green low levels and gray indicates expression that was undetected by the microarray used.

    Article Snippet: Microarray slide washing and scanning The slides were washed according to Agilent's manufacturer's protocol for 4×44K arrays and scanned with the Agilent Microarray Scanner system with surescan technology (v.6.3) using the scanner settings for the 4×44K array format according to Agilent technologies manufacturer's instructions.

    Techniques: Generated, Expressing, Microarray

    EOC 13.31 cells were stimulated with 100 ng/ml semi-pure LPS and temporal changes in cytokine gene expression relative to mock-treated control were measured by microarray analysis. MiR-146a expression relative to mock-treated control was measured by TaqMan® qRT-PCR and expression is shown as grey bars.

    Journal: PLoS ONE

    Article Title: MicroRNA 146a (miR-146a) Is Over-Expressed during Prion Disease and Modulates the Innate Immune Response and the Microglial Activation State

    doi: 10.1371/journal.pone.0030832

    Figure Lengend Snippet: EOC 13.31 cells were stimulated with 100 ng/ml semi-pure LPS and temporal changes in cytokine gene expression relative to mock-treated control were measured by microarray analysis. MiR-146a expression relative to mock-treated control was measured by TaqMan® qRT-PCR and expression is shown as grey bars.

    Article Snippet: Microarray slide washing and scanning The slides were washed according to Agilent's manufacturer's protocol for 4×44K arrays and scanned with the Agilent Microarray Scanner system with surescan technology (v.6.3) using the scanner settings for the 4×44K array format according to Agilent technologies manufacturer's instructions.

    Techniques: Expressing, Microarray, Quantitative RT-PCR

    Expression microarray analysis identifies novel putative targets of HOXD10. ( A ) Heat map from the microarray data showing the top 48 differentially expressed genes on manipulation of HOXD10 expression (one-1way ANOVA, Benjamini–Hochberg corrected P -value

    Journal: British Journal of Cancer

    Article Title: The roles of HOXD10 in the development and progression of head and neck squamous cell carcinoma (HNSCC)

    doi: 10.1038/bjc.2014.372

    Figure Lengend Snippet: Expression microarray analysis identifies novel putative targets of HOXD10. ( A ) Heat map from the microarray data showing the top 48 differentially expressed genes on manipulation of HOXD10 expression (one-1way ANOVA, Benjamini–Hochberg corrected P -value

    Article Snippet: After 17 h, hybridised slides scanned at 3-μ m resolution using Agilent C Microarray Scanner.

    Techniques: Expressing, Microarray

    Validation of the microarray data for AMOT-p80 and miR-146a and confirmation of direct effect of HOXD10 on expression. ( A ) Expression of AMOT-p80 assessed by qPCR and WB, confirming raised expression in the HOXD10-transfected cells, compared with empty vector-transfected controls. β -actin is used as a loading control. ( B ) Expression of AMOT-p80 assessed using qPCR, confirming reduced expression in the HOXD10 siRNA-transfected cells, compared with scrambled siRNA controls. ( D ) Expression of miR-146a assessed using qPCR, confirming increased expression in the HOXD10 siRNA-transfected cells, compared with scrambled siRNA controls. ( E ) pGL3 luciferase reporter vectors containing either WT AMOT promoter, AMOT promoter with either mutated HOXD10 binding sites or AMOT promoter with both mutated binding sites were transfected into D19 cells stably transfected with either pcDNA3.1-HOXD10 or pcDNA3.1 control plasmids. DLR analysis shows that HOXD10 increases luciferase expression when pGL3 vector contains WT promoter. However, luciferase expression decreases when either of HOXD10-binding sites in AMOT promoter were mutated. No significant reduction in luciferase expression was detected when both mutated sites existed in the same pGL3 vector compared with pGL3 vector containing only one mutated binding site. ** P

    Journal: British Journal of Cancer

    Article Title: The roles of HOXD10 in the development and progression of head and neck squamous cell carcinoma (HNSCC)

    doi: 10.1038/bjc.2014.372

    Figure Lengend Snippet: Validation of the microarray data for AMOT-p80 and miR-146a and confirmation of direct effect of HOXD10 on expression. ( A ) Expression of AMOT-p80 assessed by qPCR and WB, confirming raised expression in the HOXD10-transfected cells, compared with empty vector-transfected controls. β -actin is used as a loading control. ( B ) Expression of AMOT-p80 assessed using qPCR, confirming reduced expression in the HOXD10 siRNA-transfected cells, compared with scrambled siRNA controls. ( D ) Expression of miR-146a assessed using qPCR, confirming increased expression in the HOXD10 siRNA-transfected cells, compared with scrambled siRNA controls. ( E ) pGL3 luciferase reporter vectors containing either WT AMOT promoter, AMOT promoter with either mutated HOXD10 binding sites or AMOT promoter with both mutated binding sites were transfected into D19 cells stably transfected with either pcDNA3.1-HOXD10 or pcDNA3.1 control plasmids. DLR analysis shows that HOXD10 increases luciferase expression when pGL3 vector contains WT promoter. However, luciferase expression decreases when either of HOXD10-binding sites in AMOT promoter were mutated. No significant reduction in luciferase expression was detected when both mutated sites existed in the same pGL3 vector compared with pGL3 vector containing only one mutated binding site. ** P

    Article Snippet: After 17 h, hybridised slides scanned at 3-μ m resolution using Agilent C Microarray Scanner.

    Techniques: Microarray, Expressing, Real-time Polymerase Chain Reaction, Western Blot, Transfection, Plasmid Preparation, Luciferase, Binding Assay, Stable Transfection

    Custom DNA and RNA pool generation from microarray. A) Agilent microarrays contain ssDNA probes that have variable designed sequences (multicoloured) and a T7 promoter sequence (orange lines). A Cy3 (green circle) labeled T7 promoter primer (orange line) is annealed to ssDNA microarray probes which are subsequently double-stranded by enzymatic primer extension using T4 DNA polymerase (blue dotted line). A dsDNA linker (purple lines), labeled with Cy5 (red circle), is ligated to the dsDNA microarray probes using T4 DNA ligase. Cy3 and Cy5 signals are detected on microarrays by scanning at 532 and 635 nm, respectively, to verify efficient T7 primer annealing and linker ligation. Scanned Cy3 and Cy5 microarray images are shown (enclosed by dotted blue circles). B) PCR amplification of the dsDNA pool using ssDNA pool purified from the microarray as template. ssDNA pool (PCR template) dilutions as well as bands corresponding to an 80 bp DNA ladder and a 80–91 bp dsDNA pool are indicated on the ethidium bromide stained agarose gel image. C) Linker cleavage is mediated by a Type IIS restriction enzymes, BspQI. Representative bands corresponding to undigested PCR amplified dsDNA pool (enclosed by yellow box), BspQI digested dsDNA template (enclosed by pink box), and cleaved dsDNA linker (enclosed by blue box) are indicated. D) The non-random RNA pool (multicoloured lines and high intensity band in the agarose gel image) is generated via T7 RNA polymerase mediated transcription reactions, using gel purified dsDNA templates (shown in panel 2C ).

    Journal: Methods (San Diego, Calif.)

    Article Title: RNAcompete methodology and application to determine sequence preferences of unconventional RNA-binding proteins

    doi: 10.1016/j.ymeth.2016.12.003

    Figure Lengend Snippet: Custom DNA and RNA pool generation from microarray. A) Agilent microarrays contain ssDNA probes that have variable designed sequences (multicoloured) and a T7 promoter sequence (orange lines). A Cy3 (green circle) labeled T7 promoter primer (orange line) is annealed to ssDNA microarray probes which are subsequently double-stranded by enzymatic primer extension using T4 DNA polymerase (blue dotted line). A dsDNA linker (purple lines), labeled with Cy5 (red circle), is ligated to the dsDNA microarray probes using T4 DNA ligase. Cy3 and Cy5 signals are detected on microarrays by scanning at 532 and 635 nm, respectively, to verify efficient T7 primer annealing and linker ligation. Scanned Cy3 and Cy5 microarray images are shown (enclosed by dotted blue circles). B) PCR amplification of the dsDNA pool using ssDNA pool purified from the microarray as template. ssDNA pool (PCR template) dilutions as well as bands corresponding to an 80 bp DNA ladder and a 80–91 bp dsDNA pool are indicated on the ethidium bromide stained agarose gel image. C) Linker cleavage is mediated by a Type IIS restriction enzymes, BspQI. Representative bands corresponding to undigested PCR amplified dsDNA pool (enclosed by yellow box), BspQI digested dsDNA template (enclosed by pink box), and cleaved dsDNA linker (enclosed by blue box) are indicated. D) The non-random RNA pool (multicoloured lines and high intensity band in the agarose gel image) is generated via T7 RNA polymerase mediated transcription reactions, using gel purified dsDNA templates (shown in panel 2C ).

    Article Snippet: Scan microarray for Cy5 signal using Axon Genepix 4000B Microarray Scanner, or an alternative microarray scanner, (600 PMT at a wavelength of 635 nm) to confirm that all spots excluding empty Agilent controls have a high intensity Cy5 signal.

    Techniques: Microarray, Sequencing, Labeling, Ligation, Polymerase Chain Reaction, Amplification, Purification, Staining, Agarose Gel Electrophoresis, Generated

    Schematic of the RNAcompete assay. A GST-tagged RBP (RBP is orange oval, GST-tag is blue crescent), is incubated with a 75-fold excess of a non-random, custom designed RNA pool (multicoloured lines). RNA selectively bound (purple line) to an RBP during a GST-pulldown assay (GST bead is represented as a beige oval) is eluted, directly labeled with either Cy3 or Cy5 (green circles), and hybridized to a custom Agilent 244K microarray. Microarray data is analyzed computationally to generate RNA-binding motifs represented as logos.

    Journal: Methods (San Diego, Calif.)

    Article Title: RNAcompete methodology and application to determine sequence preferences of unconventional RNA-binding proteins

    doi: 10.1016/j.ymeth.2016.12.003

    Figure Lengend Snippet: Schematic of the RNAcompete assay. A GST-tagged RBP (RBP is orange oval, GST-tag is blue crescent), is incubated with a 75-fold excess of a non-random, custom designed RNA pool (multicoloured lines). RNA selectively bound (purple line) to an RBP during a GST-pulldown assay (GST bead is represented as a beige oval) is eluted, directly labeled with either Cy3 or Cy5 (green circles), and hybridized to a custom Agilent 244K microarray. Microarray data is analyzed computationally to generate RNA-binding motifs represented as logos.

    Article Snippet: Scan microarray for Cy5 signal using Axon Genepix 4000B Microarray Scanner, or an alternative microarray scanner, (600 PMT at a wavelength of 635 nm) to confirm that all spots excluding empty Agilent controls have a high intensity Cy5 signal.

    Techniques: Incubation, GST Pulldown Assay, Labeling, Microarray, RNA Binding Assay