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  • 88
    Agilent technologies custom dna microarrays
    Impact of AlpC on CGP3 replication. ( A ) The relative amount of circular phage CGP3 <t>DNA</t> was quantified by qPCR in C. glutamicum wild type (white) and Δ alpC (light gray), and Δ alpA (dark gray) upon treatment with 0.6 μM mitomycin C. Shown are average values with standard deviation of three independent biological replicates. ( B ) Time course of alpC and alpA expression upon prophage induction triggered by the addition of 0.6 μM mitomycin C. Shown is the mRNA ratio of cells treated with mitomycin C versus untreated cells 1 (red), 3 (blue) and 6 h (gray) after mitomycin C addition analyzed by DNA <t>microarrays.</t> ( C ) Time course of the mRNA ratio of the whole CGP3 gene region after addition of mitomycin C (as described in B).
    Custom Dna Microarrays, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 88/100, based on 55 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Agilent technologies custom 11k oligonucleotide microarrays
    Impact of AlpC on CGP3 replication. ( A ) The relative amount of circular phage CGP3 <t>DNA</t> was quantified by qPCR in C. glutamicum wild type (white) and Δ alpC (light gray), and Δ alpA (dark gray) upon treatment with 0.6 μM mitomycin C. Shown are average values with standard deviation of three independent biological replicates. ( B ) Time course of alpC and alpA expression upon prophage induction triggered by the addition of 0.6 μM mitomycin C. Shown is the mRNA ratio of cells treated with mitomycin C versus untreated cells 1 (red), 3 (blue) and 6 h (gray) after mitomycin C addition analyzed by DNA <t>microarrays.</t> ( C ) Time course of the mRNA ratio of the whole CGP3 gene region after addition of mitomycin C (as described in B).
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    86
    Agilent technologies custom 60mer oligonucleotide microarrays
    Impact of AlpC on CGP3 replication. ( A ) The relative amount of circular phage CGP3 <t>DNA</t> was quantified by qPCR in C. glutamicum wild type (white) and Δ alpC (light gray), and Δ alpA (dark gray) upon treatment with 0.6 μM mitomycin C. Shown are average values with standard deviation of three independent biological replicates. ( B ) Time course of alpC and alpA expression upon prophage induction triggered by the addition of 0.6 μM mitomycin C. Shown is the mRNA ratio of cells treated with mitomycin C versus untreated cells 1 (red), 3 (blue) and 6 h (gray) after mitomycin C addition analyzed by DNA <t>microarrays.</t> ( C ) Time course of the mRNA ratio of the whole CGP3 gene region after addition of mitomycin C (as described in B).
    Custom 60mer Oligonucleotide Microarrays, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 86/100, based on 2 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    88
    Agilent technologies custom 180k oligonucleotide microarray
    Impact of AlpC on CGP3 replication. ( A ) The relative amount of circular phage CGP3 <t>DNA</t> was quantified by qPCR in C. glutamicum wild type (white) and Δ alpC (light gray), and Δ alpA (dark gray) upon treatment with 0.6 μM mitomycin C. Shown are average values with standard deviation of three independent biological replicates. ( B ) Time course of alpC and alpA expression upon prophage induction triggered by the addition of 0.6 μM mitomycin C. Shown is the mRNA ratio of cells treated with mitomycin C versus untreated cells 1 (red), 3 (blue) and 6 h (gray) after mitomycin C addition analyzed by DNA <t>microarrays.</t> ( C ) Time course of the mRNA ratio of the whole CGP3 gene region after addition of mitomycin C (as described in B).
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    90
    Agilent technologies custom oligonucleotide microarray platform
    Comparison of RT-qPCR and <t>microarray</t> results. Values represent fold change (Log 2 ) in transcript copy number relative to controls. Red and green highlighted cells represent statistically significant increases and decreases in copy number, respectively.
    Custom Oligonucleotide Microarray Platform, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 90/100, based on 3 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Agilent technologies microarray data custom oligonucleotide microarrays
    Comparison of RT-qPCR and <t>microarray</t> results. Values represent fold change (Log 2 ) in transcript copy number relative to controls. Red and green highlighted cells represent statistically significant increases and decreases in copy number, respectively.
    Microarray Data Custom Oligonucleotide Microarrays, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 85/100, based on 3 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    85
    Agilent technologies custom oligonucleotide microarray chip
    Comparison of RT-qPCR and <t>microarray</t> results. Values represent fold change (Log 2 ) in transcript copy number relative to controls. Red and green highlighted cells represent statistically significant increases and decreases in copy number, respectively.
    Custom Oligonucleotide Microarray Chip, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 85/100, based on 4 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Agilent technologies 8x15k custom oligonucleotide microarray platform
    Comparison of RT-qPCR and <t>microarray</t> results. Values represent fold change (Log 2 ) in transcript copy number relative to controls. Red and green highlighted cells represent statistically significant increases and decreases in copy number, respectively.
    8x15k Custom Oligonucleotide Microarray Platform, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 88/100, based on 4 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Agilent technologies custom oligo dna microarray chips
    Clustering analysis of the expression balance between the sense and antisense genes, or the coding and noncoding genes in ES cells, fibroblast cells, brain, heart, and testis. A, B, C was based on the <t>microarray</t> data obtained with the <t>oligo</t> dT priming method, whereas the random priming method was used for the data in D, E , and F . ( A,D ) Clustering with the data of the pairs consisting of the coding genes only. When the sense gene expression is threefold more than the antisense gene expression, the color is shown in red. In the reversed situation, the color is shown in green. ( B,E ) Clustering with the data of the pairs consisting of the noncoding genes only. The coloring is the same as found in A . ( C,F ) Clustering with the data of the pairs consisting of the coding and noncoding genes. When the noncoding gene expression is threefold more than the coding gene expression, the color is shown in red. Note that this figure is intended to show the ratio between sense and antisense, or noncoding and coding expression. The absolute expression values for each gene are found in Supplemental Table 1.
    Custom Oligo Dna Microarray Chips, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 85/100, based on 2 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Agilent technologies oligonucleotides agilent technologies custom microarray
    Clustering analysis of the expression balance between the sense and antisense genes, or the coding and noncoding genes in ES cells, fibroblast cells, brain, heart, and testis. A, B, C was based on the <t>microarray</t> data obtained with the <t>oligo</t> dT priming method, whereas the random priming method was used for the data in D, E , and F . ( A,D ) Clustering with the data of the pairs consisting of the coding genes only. When the sense gene expression is threefold more than the antisense gene expression, the color is shown in red. In the reversed situation, the color is shown in green. ( B,E ) Clustering with the data of the pairs consisting of the noncoding genes only. The coloring is the same as found in A . ( C,F ) Clustering with the data of the pairs consisting of the coding and noncoding genes. When the noncoding gene expression is threefold more than the coding gene expression, the color is shown in red. Note that this figure is intended to show the ratio between sense and antisense, or noncoding and coding expression. The absolute expression values for each gene are found in Supplemental Table 1.
    Oligonucleotides Agilent Technologies Custom Microarray, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 85/100, based on 4 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Agilent technologies custom oligo dna microarray chip
    Clustering analysis of the expression balance between the sense and antisense genes, or the coding and noncoding genes in ES cells, fibroblast cells, brain, heart, and testis. A, B, C was based on the <t>microarray</t> data obtained with the <t>oligo</t> dT priming method, whereas the random priming method was used for the data in D, E , and F . ( A,D ) Clustering with the data of the pairs consisting of the coding genes only. When the sense gene expression is threefold more than the antisense gene expression, the color is shown in red. In the reversed situation, the color is shown in green. ( B,E ) Clustering with the data of the pairs consisting of the noncoding genes only. The coloring is the same as found in A . ( C,F ) Clustering with the data of the pairs consisting of the coding and noncoding genes. When the noncoding gene expression is threefold more than the coding gene expression, the color is shown in red. Note that this figure is intended to show the ratio between sense and antisense, or noncoding and coding expression. The absolute expression values for each gene are found in Supplemental Table 1.
    Custom Oligo Dna Microarray Chip, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 88/100, based on 7 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Agilent technologies custom made 60 mer oligonucleotide microarrays
    Clustering analysis of the expression balance between the sense and antisense genes, or the coding and noncoding genes in ES cells, fibroblast cells, brain, heart, and testis. A, B, C was based on the <t>microarray</t> data obtained with the <t>oligo</t> dT priming method, whereas the random priming method was used for the data in D, E , and F . ( A,D ) Clustering with the data of the pairs consisting of the coding genes only. When the sense gene expression is threefold more than the antisense gene expression, the color is shown in red. In the reversed situation, the color is shown in green. ( B,E ) Clustering with the data of the pairs consisting of the noncoding genes only. The coloring is the same as found in A . ( C,F ) Clustering with the data of the pairs consisting of the coding and noncoding genes. When the noncoding gene expression is threefold more than the coding gene expression, the color is shown in red. Note that this figure is intended to show the ratio between sense and antisense, or noncoding and coding expression. The absolute expression values for each gene are found in Supplemental Table 1.
    Custom Made 60 Mer Oligonucleotide Microarrays, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 85/100, based on 5 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Agilent technologies 15k format custom synthesized oligonucleotide microarrays
    Clustering analysis of the expression balance between the sense and antisense genes, or the coding and noncoding genes in ES cells, fibroblast cells, brain, heart, and testis. A, B, C was based on the <t>microarray</t> data obtained with the <t>oligo</t> dT priming method, whereas the random priming method was used for the data in D, E , and F . ( A,D ) Clustering with the data of the pairs consisting of the coding genes only. When the sense gene expression is threefold more than the antisense gene expression, the color is shown in red. In the reversed situation, the color is shown in green. ( B,E ) Clustering with the data of the pairs consisting of the noncoding genes only. The coloring is the same as found in A . ( C,F ) Clustering with the data of the pairs consisting of the coding and noncoding genes. When the noncoding gene expression is threefold more than the coding gene expression, the color is shown in red. Note that this figure is intended to show the ratio between sense and antisense, or noncoding and coding expression. The absolute expression values for each gene are found in Supplemental Table 1.
    15k Format Custom Synthesized Oligonucleotide Microarrays, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 85/100, based on 4 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Agilent technologies custom built oligonucleotide agilent technologies 4x44k microarrays
    Clustering analysis of the expression balance between the sense and antisense genes, or the coding and noncoding genes in ES cells, fibroblast cells, brain, heart, and testis. A, B, C was based on the <t>microarray</t> data obtained with the <t>oligo</t> dT priming method, whereas the random priming method was used for the data in D, E , and F . ( A,D ) Clustering with the data of the pairs consisting of the coding genes only. When the sense gene expression is threefold more than the antisense gene expression, the color is shown in red. In the reversed situation, the color is shown in green. ( B,E ) Clustering with the data of the pairs consisting of the noncoding genes only. The coloring is the same as found in A . ( C,F ) Clustering with the data of the pairs consisting of the coding and noncoding genes. When the noncoding gene expression is threefold more than the coding gene expression, the color is shown in red. Note that this figure is intended to show the ratio between sense and antisense, or noncoding and coding expression. The absolute expression values for each gene are found in Supplemental Table 1.
    Custom Built Oligonucleotide Agilent Technologies 4x44k Microarrays, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 85/100, based on 4 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Agilent technologies custom designed isothermal agilent microarray dna chip
    Clustering analysis of the expression balance between the sense and antisense genes, or the coding and noncoding genes in ES cells, fibroblast cells, brain, heart, and testis. A, B, C was based on the <t>microarray</t> data obtained with the <t>oligo</t> dT priming method, whereas the random priming method was used for the data in D, E , and F . ( A,D ) Clustering with the data of the pairs consisting of the coding genes only. When the sense gene expression is threefold more than the antisense gene expression, the color is shown in red. In the reversed situation, the color is shown in green. ( B,E ) Clustering with the data of the pairs consisting of the noncoding genes only. The coloring is the same as found in A . ( C,F ) Clustering with the data of the pairs consisting of the coding and noncoding genes. When the noncoding gene expression is threefold more than the coding gene expression, the color is shown in red. Note that this figure is intended to show the ratio between sense and antisense, or noncoding and coding expression. The absolute expression values for each gene are found in Supplemental Table 1.
    Custom Designed Isothermal Agilent Microarray Dna Chip, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 90/100, based on 6 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    85
    Agilent technologies 44k custom oligonucleotide microarray
    Clustering analysis of the expression balance between the sense and antisense genes, or the coding and noncoding genes in ES cells, fibroblast cells, brain, heart, and testis. A, B, C was based on the <t>microarray</t> data obtained with the <t>oligo</t> dT priming method, whereas the random priming method was used for the data in D, E , and F . ( A,D ) Clustering with the data of the pairs consisting of the coding genes only. When the sense gene expression is threefold more than the antisense gene expression, the color is shown in red. In the reversed situation, the color is shown in green. ( B,E ) Clustering with the data of the pairs consisting of the noncoding genes only. The coloring is the same as found in A . ( C,F ) Clustering with the data of the pairs consisting of the coding and noncoding genes. When the noncoding gene expression is threefold more than the coding gene expression, the color is shown in red. Note that this figure is intended to show the ratio between sense and antisense, or noncoding and coding expression. The absolute expression values for each gene are found in Supplemental Table 1.
    44k Custom Oligonucleotide Microarray, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 85/100, based on 3 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    89
    Agilent technologies hs dna chip
    FES expression is regulated by promoter methylation in human melanomas. ( A ) Analysis of FES expression in 474 melanoma clinical samples from the TCGA cohort. The left panel shows FES mRNA levels ordered from the highest (red) to the lowest (green). The middle panel shows <t>DNA</t> methylation profile obtained from 19 array probes located in the CpG sites of FES . The schematic above shows a representation of the FES locus, with UTR regions in white and exons in black. CpG positions are shown as red stripes. The right panel depicts the copy number status of the FES locus split into cases that show loss (in blue) and gain (in red) and samples in which the CNA status of FES was not assessed (in gray). ( B ) FES expression in short-term melanoma cultures (MM) and 3 normal melanocyte cultures (NM). Upper graph shows expression of FES mRNA levels as determined by RT-qPCR. Values are normalized to the mean <t>RNA</t> level of normal melanocytes, which was set to 1. Error bars show mean ± SD ( n = 2). The middle panel shows Western blot analysis of FES. Actin served as a loading control. The bottom panel shows methylation profile of short-term melanoma cultures and normal melanocytes as determined by bisulfite sequencing of 20 CpG sites located at positions ranging from –72 to +115 from the FES ′ TSS. BRAF V600E (B) and NRAS Q61K,L,R (N) mutational status is indicated on top of the sample name. ( C ) Expression of FES in MM031 cell culture after treatment with demethylating agent decitabine or its vehicle. The upper panel shows FES mRNA levels assessed by qRT-PCR. Western blot analysis in the 2 lower panels shows FES protein levels. GAPDH served as a loading control.
    Hs Dna Chip, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 89/100, based on 231 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    85
    Agilent technologies 244k custom oligonucleotide microarrays
    FES expression is regulated by promoter methylation in human melanomas. ( A ) Analysis of FES expression in 474 melanoma clinical samples from the TCGA cohort. The left panel shows FES mRNA levels ordered from the highest (red) to the lowest (green). The middle panel shows <t>DNA</t> methylation profile obtained from 19 array probes located in the CpG sites of FES . The schematic above shows a representation of the FES locus, with UTR regions in white and exons in black. CpG positions are shown as red stripes. The right panel depicts the copy number status of the FES locus split into cases that show loss (in blue) and gain (in red) and samples in which the CNA status of FES was not assessed (in gray). ( B ) FES expression in short-term melanoma cultures (MM) and 3 normal melanocyte cultures (NM). Upper graph shows expression of FES mRNA levels as determined by RT-qPCR. Values are normalized to the mean <t>RNA</t> level of normal melanocytes, which was set to 1. Error bars show mean ± SD ( n = 2). The middle panel shows Western blot analysis of FES. Actin served as a loading control. The bottom panel shows methylation profile of short-term melanoma cultures and normal melanocytes as determined by bisulfite sequencing of 20 CpG sites located at positions ranging from –72 to +115 from the FES ′ TSS. BRAF V600E (B) and NRAS Q61K,L,R (N) mutational status is indicated on top of the sample name. ( C ) Expression of FES in MM031 cell culture after treatment with demethylating agent decitabine or its vehicle. The upper panel shows FES mRNA levels assessed by qRT-PCR. Western blot analysis in the 2 lower panels shows FES protein levels. GAPDH served as a loading control.
    244k Custom Oligonucleotide Microarrays, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 85/100, based on 5 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Image Search Results


    Impact of AlpC on CGP3 replication. ( A ) The relative amount of circular phage CGP3 DNA was quantified by qPCR in C. glutamicum wild type (white) and Δ alpC (light gray), and Δ alpA (dark gray) upon treatment with 0.6 μM mitomycin C. Shown are average values with standard deviation of three independent biological replicates. ( B ) Time course of alpC and alpA expression upon prophage induction triggered by the addition of 0.6 μM mitomycin C. Shown is the mRNA ratio of cells treated with mitomycin C versus untreated cells 1 (red), 3 (blue) and 6 h (gray) after mitomycin C addition analyzed by DNA microarrays. ( C ) Time course of the mRNA ratio of the whole CGP3 gene region after addition of mitomycin C (as described in B).

    Journal: Nucleic Acids Research

    Article Title: A prophage-encoded actin-like protein required for efficient viral DNA replication in bacteria

    doi: 10.1093/nar/gkv374

    Figure Lengend Snippet: Impact of AlpC on CGP3 replication. ( A ) The relative amount of circular phage CGP3 DNA was quantified by qPCR in C. glutamicum wild type (white) and Δ alpC (light gray), and Δ alpA (dark gray) upon treatment with 0.6 μM mitomycin C. Shown are average values with standard deviation of three independent biological replicates. ( B ) Time course of alpC and alpA expression upon prophage induction triggered by the addition of 0.6 μM mitomycin C. Shown is the mRNA ratio of cells treated with mitomycin C versus untreated cells 1 (red), 3 (blue) and 6 h (gray) after mitomycin C addition analyzed by DNA microarrays. ( C ) Time course of the mRNA ratio of the whole CGP3 gene region after addition of mitomycin C (as described in B).

    Article Snippet: Transcriptomes of C. glutamicum ATCC 13032 were comparisons of cells treated with or without 0.6 mM mitomycin C after 1, 3, 6 and 9 h after addition of mitomycin C. The custom DNA microarrays were obtained from Agilent Technologies (Waldbronn, Germany).

    Techniques: Real-time Polymerase Chain Reaction, Standard Deviation, Expressing

    The EmrR regulon includes mainly EmrR-repressed genes. (A) Data from DNA microarray analysis for selected EmrR-repressed genes are shown as average ratios with standard deviations from three biological replicates comparing transcriptome from C. violaceum ATCC 12472 with Δ emrR mutant. For a complete list of the genes with altered expression levels, see Supplementary Table S4 . (B) Northern blot assays validated several genes as members of the EmrR regulon. Total RNA extracted from C. violaceum ATCC 12472 and Δ emrR mutant were probed for the indicated genes. Levels of rRNA indicated equal RNA loading (bottom panels).

    Journal: Frontiers in Microbiology

    Article Title: EmrR-Dependent Upregulation of the Efflux Pump EmrCAB Contributes to Antibiotic Resistance in Chromobacterium violaceum

    doi: 10.3389/fmicb.2018.02756

    Figure Lengend Snippet: The EmrR regulon includes mainly EmrR-repressed genes. (A) Data from DNA microarray analysis for selected EmrR-repressed genes are shown as average ratios with standard deviations from three biological replicates comparing transcriptome from C. violaceum ATCC 12472 with Δ emrR mutant. For a complete list of the genes with altered expression levels, see Supplementary Table S4 . (B) Northern blot assays validated several genes as members of the EmrR regulon. Total RNA extracted from C. violaceum ATCC 12472 and Δ emrR mutant were probed for the indicated genes. Levels of rRNA indicated equal RNA loading (bottom panels).

    Article Snippet: DNA Microarray Analysis A detailed description of the custom-designed oligonucleotide microarray slides (Agilent Technologies) was published previously ( ).

    Techniques: Microarray, Mutagenesis, Expressing, Northern Blot

    Microarray result displays for chromosome 16. The second deletion on the patient was observed on chromosome 16q22.2–22.3 bands. The deletion is over 1800 kb detected by more than 1450 molecular markers

    Journal: Molecular Cytogenetics

    Article Title: Identification of novel genomic imbalances in Saudi patients with congenital heart disease

    doi: 10.1186/s13039-018-0356-6

    Figure Lengend Snippet: Microarray result displays for chromosome 16. The second deletion on the patient was observed on chromosome 16q22.2–22.3 bands. The deletion is over 1800 kb detected by more than 1450 molecular markers

    Article Snippet: A custom designed oligonucleotide microarray assay from Agilent (Agilent Technologies, Santa Clara, CA, USA) was utilized for CNV assessment [ ].

    Techniques: Microarray

    Microarray results are displayed for chromosome 2q23.3–24.3 bands. A deletion is seen on 2q24.1 cytoband expanding over more than 249 kb genomic region

    Journal: Molecular Cytogenetics

    Article Title: Identification of novel genomic imbalances in Saudi patients with congenital heart disease

    doi: 10.1186/s13039-018-0356-6

    Figure Lengend Snippet: Microarray results are displayed for chromosome 2q23.3–24.3 bands. A deletion is seen on 2q24.1 cytoband expanding over more than 249 kb genomic region

    Article Snippet: A custom designed oligonucleotide microarray assay from Agilent (Agilent Technologies, Santa Clara, CA, USA) was utilized for CNV assessment [ ].

    Techniques: Microarray

    Distributions of differentially methylated and non-differentially methylated MspI sites in various structural components of the genome based on custom Agilent microarray data. OT: MspI sites not differentially methylated in CVS vs. MBC. CM: MspI sites more hypomethylated in CVS than in MBC. MC: MspI sites more hypomethylated in MBC than in CVS. Data are presented for each chromosome (13, 18, 21), and each type of MspI sites (OT, CM, MC), as the proportions of sites that are located inside (A) gene bodies ( B ) promoter regions ( C ) CGIs and ( D ) exons.

    Journal: PLoS ONE

    Article Title: Structural and Regulatory Characterization of the Placental Epigenome at Its Maternal Interface

    doi: 10.1371/journal.pone.0014723

    Figure Lengend Snippet: Distributions of differentially methylated and non-differentially methylated MspI sites in various structural components of the genome based on custom Agilent microarray data. OT: MspI sites not differentially methylated in CVS vs. MBC. CM: MspI sites more hypomethylated in CVS than in MBC. MC: MspI sites more hypomethylated in MBC than in CVS. Data are presented for each chromosome (13, 18, 21), and each type of MspI sites (OT, CM, MC), as the proportions of sites that are located inside (A) gene bodies ( B ) promoter regions ( C ) CGIs and ( D ) exons.

    Article Snippet: Because the Infinium array generally only targets CpG sites within known CGIs and/or promoter sequences we focused on data generated using the custom Agilent oligonucleotide microarray that is targeted towards every HpaII/MspI recognition sequence (CCGG) on chromosomes 13, 18 and 21 .

    Techniques: Methylation, Microarray

    Distributions of hypomethylated and non-hypomethylated MspI sites in CVS and MBC tissues in various types of genomic regions based on custom Agilent microarray data. CVO: MspI sites not hypomethylated in CVS. CVH: MspI sites hypomethylated in CVS. MBO: MspI sites not hypomethylated in MBC. MBH: MspI sites hypomethylated in MBC. Data are presented for each chromosome (13, 18, 21) and each type of MspI site (CVO, CVH, MBO, MBH), as the proportion that are located inside ( A ) gene bodies ( B ) promoter regions ( C ) CGIs ( D ) exons.

    Journal: PLoS ONE

    Article Title: Structural and Regulatory Characterization of the Placental Epigenome at Its Maternal Interface

    doi: 10.1371/journal.pone.0014723

    Figure Lengend Snippet: Distributions of hypomethylated and non-hypomethylated MspI sites in CVS and MBC tissues in various types of genomic regions based on custom Agilent microarray data. CVO: MspI sites not hypomethylated in CVS. CVH: MspI sites hypomethylated in CVS. MBO: MspI sites not hypomethylated in MBC. MBH: MspI sites hypomethylated in MBC. Data are presented for each chromosome (13, 18, 21) and each type of MspI site (CVO, CVH, MBO, MBH), as the proportion that are located inside ( A ) gene bodies ( B ) promoter regions ( C ) CGIs ( D ) exons.

    Article Snippet: Because the Infinium array generally only targets CpG sites within known CGIs and/or promoter sequences we focused on data generated using the custom Agilent oligonucleotide microarray that is targeted towards every HpaII/MspI recognition sequence (CCGG) on chromosomes 13, 18 and 21 .

    Techniques: Microarray

    Overlap between C. elegans and P. pacificus expression profiles in response to different bacteria. The rectangular boxes represent the entire transcriptomes of C. elegans and P. pacificus genes assayed on our microarrays, and their area of overlap represents the set of 6,126 1∶1 orthologs present on microarrays of both the nematodes. The ovals represent the fraction of differentially expressed genes in each of the subsets. For the 1∶1 orthologs, we assessed the significance of overlap between the genes differentially expressed in response to a given pathogen using a 2×2 Fisher's exact test. Differences or similarities in survival characteristics of the two nematodes when exposed to the same bacteria are reflected in their respective transcriptional responses. (A) On B. thuringiensis DB27, which is highly lethal to C. elegans but not to P. pacificus , only 23 genes are common between the respective expression profiles of the two nematodes, this overlap being statistically not significant. (B) Similarly, S. aureus is more lethal to C. elegans than P. pacificus , and the overlap between the corresponding expression profiles is limited to just 6 orthologs. Although this overlap is statistically significant (p-value = 0.0002), the extent of overlap is too small to be biologically significant. (C) S. marcescens is lethal to both the nematodes and the extent and significance overlap between the orthologs differentially expressed in the corresponding expression profiles is also relatively high (443 common orthologs, p-value = 7.71E–37). (D) On the pathogen X. nematophila , the observed overlap between the expression profiles in the two nematodes is even higher, with 2,093 orthologs regulated in both nematodes (p-value = 6.92E–134).

    Journal: PLoS ONE

    Article Title: System Wide Analysis of the Evolution of Innate Immunity in the Nematode Model Species Caenorhabditis elegans and Pristionchus pacificus

    doi: 10.1371/journal.pone.0044255

    Figure Lengend Snippet: Overlap between C. elegans and P. pacificus expression profiles in response to different bacteria. The rectangular boxes represent the entire transcriptomes of C. elegans and P. pacificus genes assayed on our microarrays, and their area of overlap represents the set of 6,126 1∶1 orthologs present on microarrays of both the nematodes. The ovals represent the fraction of differentially expressed genes in each of the subsets. For the 1∶1 orthologs, we assessed the significance of overlap between the genes differentially expressed in response to a given pathogen using a 2×2 Fisher's exact test. Differences or similarities in survival characteristics of the two nematodes when exposed to the same bacteria are reflected in their respective transcriptional responses. (A) On B. thuringiensis DB27, which is highly lethal to C. elegans but not to P. pacificus , only 23 genes are common between the respective expression profiles of the two nematodes, this overlap being statistically not significant. (B) Similarly, S. aureus is more lethal to C. elegans than P. pacificus , and the overlap between the corresponding expression profiles is limited to just 6 orthologs. Although this overlap is statistically significant (p-value = 0.0002), the extent of overlap is too small to be biologically significant. (C) S. marcescens is lethal to both the nematodes and the extent and significance overlap between the orthologs differentially expressed in the corresponding expression profiles is also relatively high (443 common orthologs, p-value = 7.71E–37). (D) On the pathogen X. nematophila , the observed overlap between the expression profiles in the two nematodes is even higher, with 2,093 orthologs regulated in both nematodes (p-value = 6.92E–134).

    Article Snippet: For P. pacificus experiments, we used our custom designed oligonucleotide microarrays manufactured by Agilent Technologies, which contain ∼93,000 unique probes for the ∼23,000 P. pacificus predicted genes (NCBI GEO accession GPL14372, see for design details of custom microarrays).

    Techniques: Expressing, Significance Assay

    Comparison of RT-qPCR and microarray results. Values represent fold change (Log 2 ) in transcript copy number relative to controls. Red and green highlighted cells represent statistically significant increases and decreases in copy number, respectively.

    Journal: Physiological Genomics

    Article Title: From raw materials to validated system: the construction of a genomic library and microarray to interpret systemic perturbations in Northern bobwhite

    doi: 10.1152/physiolgenomics.00022.2010

    Figure Lengend Snippet: Comparison of RT-qPCR and microarray results. Values represent fold change (Log 2 ) in transcript copy number relative to controls. Red and green highlighted cells represent statistically significant increases and decreases in copy number, respectively.

    Article Snippet: We created a 15,000-probe microarray using a 8 × 15K custom oligonucleotide microarray platform (Agilent Technologies, Santa Clara, CA).

    Techniques: Quantitative RT-PCR, Microarray

    Results of microarray analyses identifying significant differential expression of transcripts relative to controls in response to a 60 day (d) exposure to 2,6-dinitrotoluene (2,6-DNT). A and B : comparison of the results of a parametric t -test ( P value

    Journal: Physiological Genomics

    Article Title: From raw materials to validated system: the construction of a genomic library and microarray to interpret systemic perturbations in Northern bobwhite

    doi: 10.1152/physiolgenomics.00022.2010

    Figure Lengend Snippet: Results of microarray analyses identifying significant differential expression of transcripts relative to controls in response to a 60 day (d) exposure to 2,6-dinitrotoluene (2,6-DNT). A and B : comparison of the results of a parametric t -test ( P value

    Article Snippet: We created a 15,000-probe microarray using a 8 × 15K custom oligonucleotide microarray platform (Agilent Technologies, Santa Clara, CA).

    Techniques: Microarray, Expressing

    Clustering analysis of the expression balance between the sense and antisense genes, or the coding and noncoding genes in ES cells, fibroblast cells, brain, heart, and testis. A, B, C was based on the microarray data obtained with the oligo dT priming method, whereas the random priming method was used for the data in D, E , and F . ( A,D ) Clustering with the data of the pairs consisting of the coding genes only. When the sense gene expression is threefold more than the antisense gene expression, the color is shown in red. In the reversed situation, the color is shown in green. ( B,E ) Clustering with the data of the pairs consisting of the noncoding genes only. The coloring is the same as found in A . ( C,F ) Clustering with the data of the pairs consisting of the coding and noncoding genes. When the noncoding gene expression is threefold more than the coding gene expression, the color is shown in red. Note that this figure is intended to show the ratio between sense and antisense, or noncoding and coding expression. The absolute expression values for each gene are found in Supplemental Table 1.

    Journal: Genome Research

    Article Title: Disclosing hidden transcripts: Mouse natural sense-antisense transcripts tend to be poly(A) negative and nuclear localized

    doi: 10.1101/gr.3155905

    Figure Lengend Snippet: Clustering analysis of the expression balance between the sense and antisense genes, or the coding and noncoding genes in ES cells, fibroblast cells, brain, heart, and testis. A, B, C was based on the microarray data obtained with the oligo dT priming method, whereas the random priming method was used for the data in D, E , and F . ( A,D ) Clustering with the data of the pairs consisting of the coding genes only. When the sense gene expression is threefold more than the antisense gene expression, the color is shown in red. In the reversed situation, the color is shown in green. ( B,E ) Clustering with the data of the pairs consisting of the noncoding genes only. The coloring is the same as found in A . ( C,F ) Clustering with the data of the pairs consisting of the coding and noncoding genes. When the noncoding gene expression is threefold more than the coding gene expression, the color is shown in red. Note that this figure is intended to show the ratio between sense and antisense, or noncoding and coding expression. The absolute expression values for each gene are found in Supplemental Table 1.

    Article Snippet: DNAFORM (Japan), and Agilent Technologies manufactured custom oligo DNA microarray chips by using this information.

    Techniques: Expressing, Microarray

    Microarray and Northern hybridization analysis of representative SAT pair. ( A ) Mapping patterns of sense (coding, 6330439J10) and antisense (noncoding, A230019L24) genes in the genome. The positions of exons are indicated as filled columns. The directions of transcription are indicated with arrows. In this figure, information associated with sense genes is shown in blue and that for antisense genes in red. ( B ) Microarray signal intensities obtained with samples labeled by oligo dT priming. ( C ) Microarray signal intensities obtained with samples labeled by random-nanomer priming. ( D,E ) Northern hybridization of sense (6330439J10) and antisense (A230019L24) genes. In each lane, 20 μg of total RNA or 1 μg of mRNA was loaded. In the Northern blot figures, the positions of 18S and 28S ribosomal RNA are indicated by arrowheads at the left edges of the blots.

    Journal: Genome Research

    Article Title: Disclosing hidden transcripts: Mouse natural sense-antisense transcripts tend to be poly(A) negative and nuclear localized

    doi: 10.1101/gr.3155905

    Figure Lengend Snippet: Microarray and Northern hybridization analysis of representative SAT pair. ( A ) Mapping patterns of sense (coding, 6330439J10) and antisense (noncoding, A230019L24) genes in the genome. The positions of exons are indicated as filled columns. The directions of transcription are indicated with arrows. In this figure, information associated with sense genes is shown in blue and that for antisense genes in red. ( B ) Microarray signal intensities obtained with samples labeled by oligo dT priming. ( C ) Microarray signal intensities obtained with samples labeled by random-nanomer priming. ( D,E ) Northern hybridization of sense (6330439J10) and antisense (A230019L24) genes. In each lane, 20 μg of total RNA or 1 μg of mRNA was loaded. In the Northern blot figures, the positions of 18S and 28S ribosomal RNA are indicated by arrowheads at the left edges of the blots.

    Article Snippet: DNAFORM (Japan), and Agilent Technologies manufactured custom oligo DNA microarray chips by using this information.

    Techniques: Microarray, Northern Blot, Hybridization, Labeling

    Overall expression of sense and antisense genes as determined by using an oligo DNA microarray. The combined expression of one SAT pair is represented by a dot. The expression in ES cells is presented in A and B , and that in fibroblast cells is presented in C and D . The pairs consisting of coding and noncoding genes are shown in A and C ( x -axis, noncoding gene; y -axis, coding gene), whereas the pairs consisting of both coding genes are shown in B and D .

    Journal: Genome Research

    Article Title: Disclosing hidden transcripts: Mouse natural sense-antisense transcripts tend to be poly(A) negative and nuclear localized

    doi: 10.1101/gr.3155905

    Figure Lengend Snippet: Overall expression of sense and antisense genes as determined by using an oligo DNA microarray. The combined expression of one SAT pair is represented by a dot. The expression in ES cells is presented in A and B , and that in fibroblast cells is presented in C and D . The pairs consisting of coding and noncoding genes are shown in A and C ( x -axis, noncoding gene; y -axis, coding gene), whereas the pairs consisting of both coding genes are shown in B and D .

    Article Snippet: DNAFORM (Japan), and Agilent Technologies manufactured custom oligo DNA microarray chips by using this information.

    Techniques: Expressing, Microarray

    Average signal intensities on microarray chips after oligo dT priming were compared with those from random priming methods. In every cell type and tissue analyzed, the average signal intensity of SAT genes was higher than that of typical genes (ESTs) when the random priming method was used for sample labeling. The change in signal intensity after the change from oligo dT priming to random priming is shown at the top of the bars.

    Journal: Genome Research

    Article Title: Disclosing hidden transcripts: Mouse natural sense-antisense transcripts tend to be poly(A) negative and nuclear localized

    doi: 10.1101/gr.3155905

    Figure Lengend Snippet: Average signal intensities on microarray chips after oligo dT priming were compared with those from random priming methods. In every cell type and tissue analyzed, the average signal intensity of SAT genes was higher than that of typical genes (ESTs) when the random priming method was used for sample labeling. The change in signal intensity after the change from oligo dT priming to random priming is shown at the top of the bars.

    Article Snippet: DNAFORM (Japan), and Agilent Technologies manufactured custom oligo DNA microarray chips by using this information.

    Techniques: Microarray, Labeling

    FES expression is regulated by promoter methylation in human melanomas. ( A ) Analysis of FES expression in 474 melanoma clinical samples from the TCGA cohort. The left panel shows FES mRNA levels ordered from the highest (red) to the lowest (green). The middle panel shows DNA methylation profile obtained from 19 array probes located in the CpG sites of FES . The schematic above shows a representation of the FES locus, with UTR regions in white and exons in black. CpG positions are shown as red stripes. The right panel depicts the copy number status of the FES locus split into cases that show loss (in blue) and gain (in red) and samples in which the CNA status of FES was not assessed (in gray). ( B ) FES expression in short-term melanoma cultures (MM) and 3 normal melanocyte cultures (NM). Upper graph shows expression of FES mRNA levels as determined by RT-qPCR. Values are normalized to the mean RNA level of normal melanocytes, which was set to 1. Error bars show mean ± SD ( n = 2). The middle panel shows Western blot analysis of FES. Actin served as a loading control. The bottom panel shows methylation profile of short-term melanoma cultures and normal melanocytes as determined by bisulfite sequencing of 20 CpG sites located at positions ranging from –72 to +115 from the FES ′ TSS. BRAF V600E (B) and NRAS Q61K,L,R (N) mutational status is indicated on top of the sample name. ( C ) Expression of FES in MM031 cell culture after treatment with demethylating agent decitabine or its vehicle. The upper panel shows FES mRNA levels assessed by qRT-PCR. Western blot analysis in the 2 lower panels shows FES protein levels. GAPDH served as a loading control.

    Journal: The Journal of Clinical Investigation

    Article Title: Comparative oncogenomics identifies tyrosine kinase FES as a tumor suppressor in melanoma

    doi: 10.1172/JCI91291

    Figure Lengend Snippet: FES expression is regulated by promoter methylation in human melanomas. ( A ) Analysis of FES expression in 474 melanoma clinical samples from the TCGA cohort. The left panel shows FES mRNA levels ordered from the highest (red) to the lowest (green). The middle panel shows DNA methylation profile obtained from 19 array probes located in the CpG sites of FES . The schematic above shows a representation of the FES locus, with UTR regions in white and exons in black. CpG positions are shown as red stripes. The right panel depicts the copy number status of the FES locus split into cases that show loss (in blue) and gain (in red) and samples in which the CNA status of FES was not assessed (in gray). ( B ) FES expression in short-term melanoma cultures (MM) and 3 normal melanocyte cultures (NM). Upper graph shows expression of FES mRNA levels as determined by RT-qPCR. Values are normalized to the mean RNA level of normal melanocytes, which was set to 1. Error bars show mean ± SD ( n = 2). The middle panel shows Western blot analysis of FES. Actin served as a loading control. The bottom panel shows methylation profile of short-term melanoma cultures and normal melanocytes as determined by bisulfite sequencing of 20 CpG sites located at positions ranging from –72 to +115 from the FES ′ TSS. BRAF V600E (B) and NRAS Q61K,L,R (N) mutational status is indicated on top of the sample name. ( C ) Expression of FES in MM031 cell culture after treatment with demethylating agent decitabine or its vehicle. The upper panel shows FES mRNA levels assessed by qRT-PCR. Western blot analysis in the 2 lower panels shows FES protein levels. GAPDH served as a loading control.

    Article Snippet: Illumina’s NextSeq library Prep Kit (Illumina) was used to prepare the library from 1000 ng of RNA and the library quality was monitored on an HS DNA chip (Bioanalyzer, Agilent).

    Techniques: Expressing, Methylation, DNA Methylation Assay, Quantitative RT-PCR, Western Blot, Methylation Sequencing, Cell Culture