Journal: Journal of Virology

Article Title: Role of Nuclear Factor Y in Stress-Induced Activation of the Herpes Simplex Virus Type 1 ICP0 Promoter ▿ †

doi: 10.1128/JVI.01377-09

Figure Lengend Snippet: Response of selected HSV-1 promoters to heat shock. (A) Viral promoter- and control-luciferase constructs used in these studies. Vero cells were transfected with the indicated HSV-1 promoter-firefly luciferase constructs in duplicate. At 24 h posttransfection, cells were heat shocked for 3 h at 43°C or maintained at 37°C (mock heat shocked). After a 4-h recovery period at 37°C, cells were harvested and subjected to the luciferase reporter assay (Promega). (B) Basal promoter activity (mock heat shocked) presented as relative light units (RLU). (C) Fold induction following heat shock. The data are presented as the fold change versus non-heat-shocked control (43°C/37°C) ± the standard error of the mean (SEM). IE genes are represented by hatched bars, E genes are represented by cross-hatched bars, DE genes are represented by small cross-hatched bars, and L genes are represented by a striped bar (n ≥ 3). The luciferase activity of all samples was at least threefold higher than the background level (mock-transfected cells).

Article Snippet: To extend the luciferase assay findings, we utilized custom-designed oligonucleotide-based microarrays (SABiosciences) specific for all HSV-1 open reading frame sequences to assay changes in viral gene expression after heat shock during viral infection.

Techniques: Luciferase, Construct, Transfection, Reporter Assay, Activity Assay

Journal: Journal of Virology

Article Title: Role of Nuclear Factor Y in Stress-Induced Activation of the Herpes Simplex Virus Type 1 ICP0 Promoter ▿ †

doi: 10.1128/JVI.01377-09

Figure Lengend Snippet: Effect of heat shock on global HSV-1 transcription during lytic infection. Vero cells were infected with HSV-1 KOS at an MOI of 10 PFU/cell for 30 min, heat shocked for 1 h at 43°C or maintained at 37°C (mock heat shocked), and allowed to recover at 37°C for 1 h. Total RNA was then harvested, labeled, and hybridized to HSV-1 microarrays. Arrays were visualized by chemiluminescence, and images were captured with a charge-coupled device camera and processed with GEArray Expression Analysis Suite 2.0 (SABiosciences). The microarrays were standardized by using the interquartile method. The upper line represents a 1.5-fold increase, the middle line represents no change in expression, and the lower line represents a 1.5-fold decrease relative to the mock-treated control. Red stars indicate data points upregulated by >1.5-fold with treatment, black stars indicate data points not significantly affected by treatment, and green stars indicate data points downregulated by >1.5-fold compared to control. Upregulated genes of interest are indicated by circles and arrows. The figure represents three independent experiments.

Article Snippet: To extend the luciferase assay findings, we utilized custom-designed oligonucleotide-based microarrays (SABiosciences) specific for all HSV-1 open reading frame sequences to assay changes in viral gene expression after heat shock during viral infection.

Techniques: Infection, Labeling, Expressing

Journal: Journal of Virology

Article Title: Role of Nuclear Factor Y in Stress-Induced Activation of the Herpes Simplex Virus Type 1 ICP0 Promoter ▿ †

doi: 10.1128/JVI.01377-09

Figure Lengend Snippet: NF-Y activity is necessary for induction of the ICP0 promoter after heat shock during lytic infection. Vero cells were infected with wild-type, DN NF-YA, or GFP adenoviruses at an MOI of 25 PFU/cell and superinfected with HSV-1 KOS at an MOI of 1 PFU/cell for 30 min, heat shocked for 1 h at 43°C, and allowed to recover for 1 h at 37°C, and the RNA was harvested for RT-PCR. PCRs were performed in triplicate with primers specific for ICP0, ICP22, and β-actin. Reactions were standardized to β-actin. ICP0 (A) and ICP22 (B) transcript levels. The results are presented as the fold induction of transcription in response to heat shock (43 or 37°C) ± the SEM (n = 3).

Article Snippet: To extend the luciferase assay findings, we utilized custom-designed oligonucleotide-based microarrays (SABiosciences) specific for all HSV-1 open reading frame sequences to assay changes in viral gene expression after heat shock during viral infection.

Techniques: Activity Assay, Infection, Reverse Transcription Polymerase Chain Reaction

Journal: PLoS ONE

Article Title: Molecular Analysis of Endocrine Disruption in Hornyhead Turbot at Wastewater Outfalls in Southern California Using a Second Generation Multi-Species Microarray

doi: 10.1371/journal.pone.0075553

Figure Lengend Snippet: Comparison of the performance characteristics of on both prototype (spotted oligonucleotide) and second generation (Agilent ink jet oligonucleotide) endocrine multi-species microarray platforms; Panels A and B: scatter plots of log 2 signal intensities of an individual fish from the Los Angeles Sanitation District versus the control fish pool. Panels A and B depict prototype and second generation platforms respectively. Panel C; direct comparison of platform sensitivity defined as log 2 ratio between treatment and ABC control. Panel D: Analysis of signal concordance. Panel E: Analysis of variance with both platforms. To measure internal consistency (variance of internal replicates), log 2 transformed expression value was plotted on the x-axis. Standard deviation is plotted on the y-axis, with a range of plus or minus one standard deviation from the mean expression value. The y-axis is a measure of the deviation of individual replicate probes stray from the mean value. The second generation platform has smaller variance of the internal replicates. Probe variance on both platforms is independent of the signal. Panel F: Comparison of the probe signal intensity distribution (plotted as log 2 transformed) for 149 probes that were present on both platforms.

Article Snippet: We designed in silico a 60-mer oligonucleotide-based multi-species microarray using the eArray – Custom Microarray Design Application from Agilent (Santa Clara, CA).

Techniques: Microarray, Transformation Assay, Expressing, Standard Deviation

Journal: PLoS ONE

Article Title: Molecular Analysis of Endocrine Disruption in Hornyhead Turbot at Wastewater Outfalls in Southern California Using a Second Generation Multi-Species Microarray

doi: 10.1371/journal.pone.0075553

Figure Lengend Snippet: The mRNA level fold changes observed between exposed and control fish are depicted as a diagnostic heat map representative of all the genes present on the multi-species array. The log 2 ratio for each gene is defined as the mean of all representations of that gene on the microarray; these include probes from different regions of the gene, as well as from different species of fish (individual log 2 ratios for each unique probe are calculated as the median of 46 replicates present on the array). The range of colors is between -8-fold and +8-fold and preserves qualitative relationships among individual values. All fold changes outside of this range have been truncated to ± 8.

Article Snippet: We designed in silico a 60-mer oligonucleotide-based multi-species microarray using the eArray – Custom Microarray Design Application from Agilent (Santa Clara, CA).

Techniques: Diagnostic Assay, Microarray

Journal: PLoS ONE

Article Title: Molecular Analysis of Endocrine Disruption in Hornyhead Turbot at Wastewater Outfalls in Southern California Using a Second Generation Multi-Species Microarray

doi: 10.1371/journal.pone.0075553

Figure Lengend Snippet: Multi-species SYBR green Q-PCR validation of multi-species microarray for (A) CYP3A (B) Vit1 (C) Vit2 (D) ESR1/ ERα (E) ESR2/ ERβ specific transcripts. GAPDH -normalized fold changes (based on triplicate measurements) of gene expression in turbot liver from selected impacted sites with respect to reference fish are presented. Each fold change was derived from the mean log 2 ratio between each fish and a reference derived from two control fish. Vit1 and Vit2 transcripts were strongly up-regulated in all fish. ERα was down-regulated in one fish and up-regulated in two others relative to control fish. ERβ was down-regulated in all fish examined relative to control fish. CYP3A was up-regulated in eight and down-regulated in two fish.

Article Snippet: We designed in silico a 60-mer oligonucleotide-based multi-species microarray using the eArray – Custom Microarray Design Application from Agilent (Santa Clara, CA).

Techniques: SYBR Green Assay, Microarray, Expressing, Derivative Assay

Journal: Molecular Cytogenetics

Article Title: Comparative analysis of copy number detection by whole-genome BAC and oligonucleotide array CGH

doi: 10.1186/1755-8166-3-11

Figure Lengend Snippet: Identification by oligonucleotide microarray of additional complexity missed by BAC microarray . (A) BAC microarray results showing a single-copy loss of 34 BAC clones from the terminus of 5p, approximately 6.8 Mb in size (chr5: 387,034-7,150,950, based on UCSC 2006 hg 18 assembly). Probes are ordered on the x axis according to physical mapping positions, with the p-arm probes to the left and q-arm probes to the right. (B) shows oligonucleotide microarray results of the terminal deletion shown in (A) in addition to single-copy gain of 29 probes from 5p, approximately 1.38 Mb in size (chr5: 8,511,592-9,888,817, based on UCSC 2006 hg 18 assembly). Probes are ordered as in the BAC array. Regions shaded in blue represent deletions detected by microarray, whereas duplications are shaded in pink.

Article Snippet: Oligonucleotide-based microarray analysis was performed using a custom-designed, 105K-feature whole-genome microarray manufactured by Agilent Technologies (Santa Clara, CA) with one probe every 10 kb in regions of interest--microdeletion/microduplication syndromes, the pericentromeric regions, subtelomeres and genes involved in important developmental pathways--for an average of 50 oligos per clinical locus.

Techniques: Microarray, Clone Assay

Journal: Molecular Cytogenetics

Article Title: Comparative analysis of copy number detection by whole-genome BAC and oligonucleotide array CGH

doi: 10.1186/1755-8166-3-11

Figure Lengend Snippet: Oligonucleotide microarray analysis of a mosaic 16q12.1 deletion (shaded blue region) . The zoomed-in microarray plot shows a single-copy loss of 289 probes from 16q12.1, approximately 2.77 Mb in size (chr16: 46,837,260-49,605,054, based on UCSC 2006 hg 18 assembly). Probes are ordered on the x axis according to physical mapping positions, with the most proximal 16q11.2 probes to the left and the most distal 16q12.2 probes to the right.

Article Snippet: Oligonucleotide-based microarray analysis was performed using a custom-designed, 105K-feature whole-genome microarray manufactured by Agilent Technologies (Santa Clara, CA) with one probe every 10 kb in regions of interest--microdeletion/microduplication syndromes, the pericentromeric regions, subtelomeres and genes involved in important developmental pathways--for an average of 50 oligos per clinical locus.

Techniques: Microarray

Journal: Molecular Cytogenetics

Article Title: Comparative analysis of copy number detection by whole-genome BAC and oligonucleotide array CGH

doi: 10.1186/1755-8166-3-11

Figure Lengend Snippet: Oligonucleotide microarray analysis of artificially derived mosaic trisomy 21 samples . (A) 10% trisomy 21 showing a very subtle copy-number gain for all clones on chromosome 21. The profile was generated using DNA extracted from a mixture of blood which contained 10% WBCs from a trisomy 21 subject and 90% WBCs from a normal male individual. (B) 15% trisomy 21, generated as in (A), showing a very subtle copy-number gain for all clones on chromosome 21. (C) 20% trisomy 21, generated as in (A) showing a subtle copy-number gain for all clones on chromosome 21. (D) 30% trisomy 21, generated as in (A), showing a clear copy-number gain for all clones on chromosome 21. The inset images to the right of each array plot show the average log 2 ratio of all probes mapping to chromosome 21, with the horizontal dotted line representing a log 2 ratio of zero and the vertical dotted line representing the centromere. A pink bar plotted above the horizontal line represents a copy-number gain of all probes on chromosome 21. To the left of each inset image is the average log 2 ratio at the specified proportion of trisomic cells.

Article Snippet: Oligonucleotide-based microarray analysis was performed using a custom-designed, 105K-feature whole-genome microarray manufactured by Agilent Technologies (Santa Clara, CA) with one probe every 10 kb in regions of interest--microdeletion/microduplication syndromes, the pericentromeric regions, subtelomeres and genes involved in important developmental pathways--for an average of 50 oligos per clinical locus.

Techniques: Microarray, Derivative Assay, Clone Assay, Generated

Journal: Molecular Cytogenetics

Article Title: Comparative analysis of copy number detection by whole-genome BAC and oligonucleotide array CGH

doi: 10.1186/1755-8166-3-11

Figure Lengend Snippet: Oligonucleotide microarray characterization of an interstitial deletion at 17p13.3 . The zoomed-in microarray plot shows a single-copy loss of six probes from the short arm of chromosome 17 at 17p13.3, approximately 44.0 kb in size (chr17: 2,415,074-2,459,051, based on UCSC 2006 hg 18 assembly). Probes are ordered on the x axis according to physical mapping positions, with the most distal 17p13.3 probes to the left and the most proximal 17p13.3 probes to the right. Below is a schematic of the deletion region. The deletion disrupts the PAFAH1B1/LIS1 gene.

Article Snippet: Oligonucleotide-based microarray analysis was performed using a custom-designed, 105K-feature whole-genome microarray manufactured by Agilent Technologies (Santa Clara, CA) with one probe every 10 kb in regions of interest--microdeletion/microduplication syndromes, the pericentromeric regions, subtelomeres and genes involved in important developmental pathways--for an average of 50 oligos per clinical locus.

Techniques: Microarray

Journal: Molecular Cytogenetics

Article Title: Comparative analysis of copy number detection by whole-genome BAC and oligonucleotide array CGH

doi: 10.1186/1755-8166-3-11

Figure Lengend Snippet: Oligonucleotide microarray characterization of an interstitial deletion at 6q14.1 . The zoomed-in microarray plot shows a single-copy loss of 43 oligonucleotide probes from the long arm of chromosome 6 at 6q14.1, approximately 2.9 Mb in size (chr6: 79,838,518-82,730,466, based on UCSC 2006 hg 18 assembly). Probes are ordered on the x axis according to physical mapping positions, with the most proximal 6q14.1 probes to the left and the most distal 6q14.1 probes to the right. Below is a schematic of the deletion region. Blue and gray boxes represent genes in the deletion region.

Article Snippet: Oligonucleotide-based microarray analysis was performed using a custom-designed, 105K-feature whole-genome microarray manufactured by Agilent Technologies (Santa Clara, CA) with one probe every 10 kb in regions of interest--microdeletion/microduplication syndromes, the pericentromeric regions, subtelomeres and genes involved in important developmental pathways--for an average of 50 oligos per clinical locus.

Techniques: Microarray

Journal: Molecular Cytogenetics

Article Title: Comparative analysis of copy number detection by whole-genome BAC and oligonucleotide array CGH

doi: 10.1186/1755-8166-3-11

Figure Lengend Snippet: BAC microarray characterization of a 9q33.1 deletion . The zoomed-in microarray plot shows a single-copy loss of three BAC clones from the long arm of chromosome 9 at 9q33.1, approximately 262 kb in size (chr9: 119,452,279-119,714,054 based on UCSC 2006 hg 18 assembly). The nearest distal clone on chromosome 9 that is not deleted is RP11-977E8 and is approximately 4.0 Mb away from the deleted region. The nearest proximal clone on chromosome 9 that is not deleted is RP11-999I23 and is approximately 4.4 Mb away from the deleted region. Probes are ordered on the x axis according to physical mapping positions, with proximal 9q32 clones to the left and distal 9q33.2 clones to the right. Below is a schematic of the deletion region. Vertical blue lines represent the minimum size of this alteration, which encompasses one gene, TLR4 .

Article Snippet: Oligonucleotide-based microarray analysis was performed using a custom-designed, 105K-feature whole-genome microarray manufactured by Agilent Technologies (Santa Clara, CA) with one probe every 10 kb in regions of interest--microdeletion/microduplication syndromes, the pericentromeric regions, subtelomeres and genes involved in important developmental pathways--for an average of 50 oligos per clinical locus.

Techniques: Microarray, Clone Assay

Journal: Molecular Cytogenetics

Article Title: Comparative analysis of copy number detection by whole-genome BAC and oligonucleotide array CGH

doi: 10.1186/1755-8166-3-11

Figure Lengend Snippet: Oligonucleotide microarray characterization of an interstitial deletion at 4q25 . The zoomed-in microarray plots shows a single-copy loss of 15 oligonucleotide probes from the long arm of chromosome 4 at 4q25, approximately 159.6 kb in size (chr4: 108,834,399-108,994,048, based on UCSC 2006 hg 18 assembly). Probes are ordered on the x axis according to physical mapping positions, with proximal 4q25 clones to the left and distal 4q25 clones to the right. Below is a schematic of the deletion region. The deletion disrupts the PAPSS1 and SGMS2 genes, represented by blue boxes.

Article Snippet: Oligonucleotide-based microarray analysis was performed using a custom-designed, 105K-feature whole-genome microarray manufactured by Agilent Technologies (Santa Clara, CA) with one probe every 10 kb in regions of interest--microdeletion/microduplication syndromes, the pericentromeric regions, subtelomeres and genes involved in important developmental pathways--for an average of 50 oligos per clinical locus.

Techniques: Microarray, Clone Assay