Structured Review

Agilent technologies dna microarray scanner
Design of the cassava <t>oligo-DNA</t> <t>microarray.</t>
Dna Microarray Scanner, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 99/100, based on 1473 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/result/dna microarray scanner/product/Agilent technologies
Average 99 stars, based on 1473 article reviews
Price from $9.99 to $1999.99
dna microarray scanner - by Bioz Stars, 2020-04
99/100 stars

Images

1) Product Images from "Transcriptome Analysis Using a High-Density Oligomicroarray under Drought Stress in Various Genotypes of Cassava: An Important Tropical Crop"

Article Title: Transcriptome Analysis Using a High-Density Oligomicroarray under Drought Stress in Various Genotypes of Cassava: An Important Tropical Crop

Journal: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes

doi: 10.1093/dnares/dss016

Design of the cassava oligo-DNA microarray.
Figure Legend Snippet: Design of the cassava oligo-DNA microarray.

Techniques Used: Microarray

2) Product Images from "Transcription factor DUO1 generated by neo-functionalization is associated with evolution of sperm differentiation in plants"

Article Title: Transcription factor DUO1 generated by neo-functionalization is associated with evolution of sperm differentiation in plants

Journal: Nature Communications

doi: 10.1038/s41467-018-07728-3

Characterization of green algal DUO1 orthologs. a Expression profiles of DUO1 orthologs from three Chara species, C. braunii (Cbr), C. australis (Cau), and C. leptospora (Cle) representing two distant clades (subgenera) 41 . Ribosomal protein L6 ( RPL6 ) was used as the internal control. The expression of two flagella component genes ( RSP11 and PACRG ) was also analyzed in C. braunii . Cbr DUO1 gene structure and amplified probed regions are shown in Supplementary Figure 7a . The whole untrimmed images are shown in Supplementary Figure 7b . Oogonia contain the egg. Antheridia contain developing sperm. Thalli are somatic vegetative tissue. b Position weight matrix representations of the top-scoring 8-mer DNA sequences bound by different MYB domains on a protein-binding DNA microarray. CpeDUO1 is DUO1 from Closterium peracerosum-strigosum-littorale complex (conjugating green alga). Numbers denoted on the right side of each motif represent the motif E- and Z-scores 19 . c In vivo transcriptional activation potentials of green algal DUO1 chimeras. DUO1 transcriptional activation potentials were measured by relative luciferase activity (right) ( n = 4; ** p
Figure Legend Snippet: Characterization of green algal DUO1 orthologs. a Expression profiles of DUO1 orthologs from three Chara species, C. braunii (Cbr), C. australis (Cau), and C. leptospora (Cle) representing two distant clades (subgenera) 41 . Ribosomal protein L6 ( RPL6 ) was used as the internal control. The expression of two flagella component genes ( RSP11 and PACRG ) was also analyzed in C. braunii . Cbr DUO1 gene structure and amplified probed regions are shown in Supplementary Figure 7a . The whole untrimmed images are shown in Supplementary Figure 7b . Oogonia contain the egg. Antheridia contain developing sperm. Thalli are somatic vegetative tissue. b Position weight matrix representations of the top-scoring 8-mer DNA sequences bound by different MYB domains on a protein-binding DNA microarray. CpeDUO1 is DUO1 from Closterium peracerosum-strigosum-littorale complex (conjugating green alga). Numbers denoted on the right side of each motif represent the motif E- and Z-scores 19 . c In vivo transcriptional activation potentials of green algal DUO1 chimeras. DUO1 transcriptional activation potentials were measured by relative luciferase activity (right) ( n = 4; ** p

Techniques Used: Expressing, Amplification, Protein Binding, Microarray, In Vivo, Activation Assay, Luciferase, Activity Assay

3) Product Images from "Size effects of single-walled carbon nanotubes on in vivo and in vitro pulmonary toxicity"

Article Title: Size effects of single-walled carbon nanotubes on in vivo and in vitro pulmonary toxicity

Journal: Inhalation Toxicology

doi: 10.3109/08958378.2015.1026620

Effects of CNT-1 and CNT-2 on gene expression in NR8383 cells. Venn diagram showing the number of upregulated and downregulated genes in NR8383 cells exposed to CNT-1 or CNT-2 for 24 h (A). Heat map generated from DNA microarray data reflecting differential expression of genes involved in the response to stimulus (GO: 0050896) in NR8383 cells exposed to CNT-1 or CNT-2 for 24 h. Expression levels are colored blue for low intensity and red for high intensity (see scale at the bottom right corner) (B).
Figure Legend Snippet: Effects of CNT-1 and CNT-2 on gene expression in NR8383 cells. Venn diagram showing the number of upregulated and downregulated genes in NR8383 cells exposed to CNT-1 or CNT-2 for 24 h (A). Heat map generated from DNA microarray data reflecting differential expression of genes involved in the response to stimulus (GO: 0050896) in NR8383 cells exposed to CNT-1 or CNT-2 for 24 h. Expression levels are colored blue for low intensity and red for high intensity (see scale at the bottom right corner) (B).

Techniques Used: Expressing, Generated, Microarray

4) Product Images from "Enrichment of Pluripotent Stem Cell-Derived Hepatocyte-Like Cells by Ammonia Treatment"

Article Title: Enrichment of Pluripotent Stem Cell-Derived Hepatocyte-Like Cells by Ammonia Treatment

Journal: PLoS ONE

doi: 10.1371/journal.pone.0162693

DNA microarray data reveals hepatocyte-like differentiation of ammonia-treated cells. Results of DNA microarray analyses were combined and are presented as a heat map (A) and a principal component analysis (B). (C) Clipped representation from normalized microarray data showing hepatocyte related genes (upper) and control genes (lower). (D) Cell-type specificity of highly-expressed genes in ammonia-treated cells. Cell-type was annotated using GENATLAS (Paris Descartes University; http://genatlas.medecine.univ-paris5.fr/google/gene.php# ). Left; “LIVER” indicates gene with high or predominant expression in organ(s) including the liver. “LIVER (specific)” indicates gene with high liver specific expression. “NON LIVER” indicates genes with high expression levels in organs other than the liver. “NO EXPRESSION” indicates genes without high expression. “UBIQUITOUS” indicates genes with ubiquitous expression (including liver expression). “UNKNOWN” indicates genes with no expression data. Right; breakdown of “NON LIVER”. (E) The top eight factors returned from TRANSFAC analysis of ammonia-treated cells. (F) Quantitative PCR analysis of HNF4A , HNF-3beta ( HNF3b ), and HNF-1alpha ( HNF1A ), gene expression levels in H1 ES cells. Each bar represents mean and SD (n = 3). Values are fold-change relative to the value of HNF4A in undifferentiated cells. *P
Figure Legend Snippet: DNA microarray data reveals hepatocyte-like differentiation of ammonia-treated cells. Results of DNA microarray analyses were combined and are presented as a heat map (A) and a principal component analysis (B). (C) Clipped representation from normalized microarray data showing hepatocyte related genes (upper) and control genes (lower). (D) Cell-type specificity of highly-expressed genes in ammonia-treated cells. Cell-type was annotated using GENATLAS (Paris Descartes University; http://genatlas.medecine.univ-paris5.fr/google/gene.php# ). Left; “LIVER” indicates gene with high or predominant expression in organ(s) including the liver. “LIVER (specific)” indicates gene with high liver specific expression. “NON LIVER” indicates genes with high expression levels in organs other than the liver. “NO EXPRESSION” indicates genes without high expression. “UBIQUITOUS” indicates genes with ubiquitous expression (including liver expression). “UNKNOWN” indicates genes with no expression data. Right; breakdown of “NON LIVER”. (E) The top eight factors returned from TRANSFAC analysis of ammonia-treated cells. (F) Quantitative PCR analysis of HNF4A , HNF-3beta ( HNF3b ), and HNF-1alpha ( HNF1A ), gene expression levels in H1 ES cells. Each bar represents mean and SD (n = 3). Values are fold-change relative to the value of HNF4A in undifferentiated cells. *P

Techniques Used: Microarray, Expressing, Real-time Polymerase Chain Reaction

Microarray data indicating the differentiation tendencies of six pluripotent stem cell lines. Heat maps of DNA microarray analysis (A, C) and the associated principal component analysis (B, D) of undifferentiated cells (A, B) and EB cells (C, D). Hierarchical Clustering; Similarity Measure: Euclidean; Linkage Rule: Complete. (E) Clipped representation from normalized microarray data showing pluripotent stem cell marker genes. (F) Quantitative PCR analysis of expression of endoderm markers Sox7 and Sox17, mesoderm marker Brachyury (T), and neuroectoderm marker NCAM1 in 253G1 cells. Each bar represents mean and SD (n = 3). Values are fold-change relative to the value of Sox7 in undifferentiated cells. *P
Figure Legend Snippet: Microarray data indicating the differentiation tendencies of six pluripotent stem cell lines. Heat maps of DNA microarray analysis (A, C) and the associated principal component analysis (B, D) of undifferentiated cells (A, B) and EB cells (C, D). Hierarchical Clustering; Similarity Measure: Euclidean; Linkage Rule: Complete. (E) Clipped representation from normalized microarray data showing pluripotent stem cell marker genes. (F) Quantitative PCR analysis of expression of endoderm markers Sox7 and Sox17, mesoderm marker Brachyury (T), and neuroectoderm marker NCAM1 in 253G1 cells. Each bar represents mean and SD (n = 3). Values are fold-change relative to the value of Sox7 in undifferentiated cells. *P

Techniques Used: Microarray, Marker, Real-time Polymerase Chain Reaction, Expressing

5) Product Images from "Transcription factor DUO1 generated by neo-functionalization is associated with evolution of sperm differentiation in plants"

Article Title: Transcription factor DUO1 generated by neo-functionalization is associated with evolution of sperm differentiation in plants

Journal: Nature Communications

doi: 10.1038/s41467-018-07728-3

Characterization of green algal DUO1 orthologs. a Expression profiles of DUO1 orthologs from three Chara species, C. braunii (Cbr), C. australis (Cau), and C. leptospora . Ribosomal protein L6 ( RPL6 ) was used as the internal control. The expression of two flagella component genes ( RSP11 and PACRG ) was also analyzed in C. braunii . Cbr DUO1 . Oogonia contain the egg. Antheridia contain developing sperm. Thalli are somatic vegetative tissue. b Position weight matrix representations of the top-scoring 8-mer DNA sequences bound by different MYB domains on a protein-binding DNA microarray. CpeDUO1 is DUO1 from Closterium peracerosum-strigosum-littorale . c In vivo transcriptional activation potentials of green algal DUO1 chimeras. DUO1 transcriptional activation potentials were measured by relative luciferase activity (right) ( n = 4; ** p
Figure Legend Snippet: Characterization of green algal DUO1 orthologs. a Expression profiles of DUO1 orthologs from three Chara species, C. braunii (Cbr), C. australis (Cau), and C. leptospora . Ribosomal protein L6 ( RPL6 ) was used as the internal control. The expression of two flagella component genes ( RSP11 and PACRG ) was also analyzed in C. braunii . Cbr DUO1 . Oogonia contain the egg. Antheridia contain developing sperm. Thalli are somatic vegetative tissue. b Position weight matrix representations of the top-scoring 8-mer DNA sequences bound by different MYB domains on a protein-binding DNA microarray. CpeDUO1 is DUO1 from Closterium peracerosum-strigosum-littorale . c In vivo transcriptional activation potentials of green algal DUO1 chimeras. DUO1 transcriptional activation potentials were measured by relative luciferase activity (right) ( n = 4; ** p

Techniques Used: Expressing, Protein Binding, Microarray, In Vivo, Activation Assay, Luciferase, Activity Assay

6) Product Images from "Transcription factor DUO1 generated by neo-functionalization is associated with evolution of sperm differentiation in plants"

Article Title: Transcription factor DUO1 generated by neo-functionalization is associated with evolution of sperm differentiation in plants

Journal: Nature Communications

doi: 10.1038/s41467-018-07728-3

Characterization of green algal DUO1 orthologs. a Expression profiles of DUO1 orthologs from three Chara species, C. braunii (Cbr), C. australis (Cau), and C. leptospora . Ribosomal protein L6 ( RPL6 ) was used as the internal control. The expression of two flagella component genes ( RSP11 and PACRG ) was also analyzed in C. braunii . Cbr DUO1 . Oogonia contain the egg. Antheridia contain developing sperm. Thalli are somatic vegetative tissue. b Position weight matrix representations of the top-scoring 8-mer DNA sequences bound by different MYB domains on a protein-binding DNA microarray. CpeDUO1 is DUO1 from Closterium peracerosum-strigosum-littorale . c In vivo transcriptional activation potentials of green algal DUO1 chimeras. DUO1 transcriptional activation potentials were measured by relative luciferase activity (right) ( n = 4; ** p
Figure Legend Snippet: Characterization of green algal DUO1 orthologs. a Expression profiles of DUO1 orthologs from three Chara species, C. braunii (Cbr), C. australis (Cau), and C. leptospora . Ribosomal protein L6 ( RPL6 ) was used as the internal control. The expression of two flagella component genes ( RSP11 and PACRG ) was also analyzed in C. braunii . Cbr DUO1 . Oogonia contain the egg. Antheridia contain developing sperm. Thalli are somatic vegetative tissue. b Position weight matrix representations of the top-scoring 8-mer DNA sequences bound by different MYB domains on a protein-binding DNA microarray. CpeDUO1 is DUO1 from Closterium peracerosum-strigosum-littorale . c In vivo transcriptional activation potentials of green algal DUO1 chimeras. DUO1 transcriptional activation potentials were measured by relative luciferase activity (right) ( n = 4; ** p

Techniques Used: Expressing, Protein Binding, Microarray, In Vivo, Activation Assay, Luciferase, Activity Assay

7) Product Images from "In Silico Enhanced Restriction Enzyme Based Methylation Analysis of the Human Glioblastoma Genome Using Agilent 244K CpG Island Microarrays"

Article Title: In Silico Enhanced Restriction Enzyme Based Methylation Analysis of the Human Glioblastoma Genome Using Agilent 244K CpG Island Microarrays

Journal: Frontiers in Neuroscience

doi: 10.3389/neuro.15.005.2009

Schematic diagram of in silico annotated genomic DNA and MSRE method . (A) Using in silico simulation, genomic DNA can be separated into MSRE sensitive and insensitive BfaI fragments (flanked by gray boxes) based on the presence or absence of internal HpaII/MspI sites (CCGG) (blue squares). Microarray probes binding to sensitive fragments are represented with green rectangles. Probes binding to insensitive fragments are represented by blue rectangles. Sensitive fragments can have multiple CCGG sites that can be fully methylated, partially methylated, or completely unmethylated in tandem. Methylated CCGG sites (CC m GG) are indicated with a red dot placed above the blue square. (B) Genomic DNA is fragmented with BfaI, ligated to H12/H24 linkers, digested with HpaII and MspI in parallel, amplified, differentially labeled and co-hybridized to Agilent CpG island arrays. Uncleaved fragments will have high intensities compared to cleaved fragments since only uncleaved fragments are amplified. Fully methylated fragments are cut by MspI but not HpaII, resulting in amplification of HpaII digested fragments only with resultant M -value [log 2 (HpaII/MspI)] > 0. Completely unmethylated or partially methylated (not all CCGGs methylated in tandem) fragments are cut by both MspI and HpaII. With the absence of amplification, these fragments resulting in low signal intensities in both channels (HpaII and MspI ∼ 0) with M = 0. Insensitive fragments should not be cut by either enzyme, resulting in M = 0.
Figure Legend Snippet: Schematic diagram of in silico annotated genomic DNA and MSRE method . (A) Using in silico simulation, genomic DNA can be separated into MSRE sensitive and insensitive BfaI fragments (flanked by gray boxes) based on the presence or absence of internal HpaII/MspI sites (CCGG) (blue squares). Microarray probes binding to sensitive fragments are represented with green rectangles. Probes binding to insensitive fragments are represented by blue rectangles. Sensitive fragments can have multiple CCGG sites that can be fully methylated, partially methylated, or completely unmethylated in tandem. Methylated CCGG sites (CC m GG) are indicated with a red dot placed above the blue square. (B) Genomic DNA is fragmented with BfaI, ligated to H12/H24 linkers, digested with HpaII and MspI in parallel, amplified, differentially labeled and co-hybridized to Agilent CpG island arrays. Uncleaved fragments will have high intensities compared to cleaved fragments since only uncleaved fragments are amplified. Fully methylated fragments are cut by MspI but not HpaII, resulting in amplification of HpaII digested fragments only with resultant M -value [log 2 (HpaII/MspI)] > 0. Completely unmethylated or partially methylated (not all CCGGs methylated in tandem) fragments are cut by both MspI and HpaII. With the absence of amplification, these fragments resulting in low signal intensities in both channels (HpaII and MspI ∼ 0) with M = 0. Insensitive fragments should not be cut by either enzyme, resulting in M = 0.

Techniques Used: In Silico, Microarray, Binding Assay, Methylation, Amplification, Labeling

8) Product Images from "Fibrogenic Activity of MECP2 Is Regulated by Phosphorylation in Hepatic Stellate Cells"

Article Title: Fibrogenic Activity of MECP2 Is Regulated by Phosphorylation in Hepatic Stellate Cells

Journal: Gastroenterology

doi: 10.1053/j.gastro.2019.07.029

Mecp2 regulates DNA replication and repair systems; Has2 is involved in HSC transdifferentiation. ( A ) Heatmap displaying the results of mRNA microarray performed on activated HSCs isolated from 3 control and 3 Mecp2 –/y mice. The top 50 most up-regulated and down-regulated genes are shown. Blue denotes down-regulation; red, up-regulation; white, unchanged. ( B ) Heatmap displaying the most down-regulated genes with a fundamental role in DNA repair responses ( C ) Western blot for MCM2, MCM5, POLD1, PCNA, CCNA2, and GAPDH in WT HSCs after 0, 2, 5, and 8 days in culture. ( D ) IPA was used to form a network of focus genes that are downstream targets of differentially expressed mRNAs. Blue nodes signify that a gene was down-regulated in Mecp2 – /y myofibroblasts; red signifies up-regulation. Symbol shapes signify the nature of the encoded protein, and unshaded symbols signify genes relevant to the pathway but not differentially expressed in our data set. ( E ) mRNA level of Has2 from HSCs, Kupffer cells (KC), and hepatocytes (Hep). ( F ) mRNA levels of Has2, Has1, and Has3 in HSCs after 0, 2, 5, and 8 days in culture. ( G ) Western blot for COL1A1, HAS2, the receptor CD44, α-SMA, and GAPDH in HSCs after 0, 2, 5, and 8 days in culture. ( H ) Schematic showing the silencing experiment: HSCs were cultured for 5 days, then transfected with a cocktail of Has2 targeting siRNA (1 + 3), single Has2 targeting siRNA (3) or a negative control (Con) and harvested 48 hours later on day 7. mRNA levels of Has2, MMP9, MMP13, and transforming growth factor β in control and Has2 siRNA–transfected HSCs. Error bars represent mean ± SEM. Statistical significance was determined by ANOVA; * P
Figure Legend Snippet: Mecp2 regulates DNA replication and repair systems; Has2 is involved in HSC transdifferentiation. ( A ) Heatmap displaying the results of mRNA microarray performed on activated HSCs isolated from 3 control and 3 Mecp2 –/y mice. The top 50 most up-regulated and down-regulated genes are shown. Blue denotes down-regulation; red, up-regulation; white, unchanged. ( B ) Heatmap displaying the most down-regulated genes with a fundamental role in DNA repair responses ( C ) Western blot for MCM2, MCM5, POLD1, PCNA, CCNA2, and GAPDH in WT HSCs after 0, 2, 5, and 8 days in culture. ( D ) IPA was used to form a network of focus genes that are downstream targets of differentially expressed mRNAs. Blue nodes signify that a gene was down-regulated in Mecp2 – /y myofibroblasts; red signifies up-regulation. Symbol shapes signify the nature of the encoded protein, and unshaded symbols signify genes relevant to the pathway but not differentially expressed in our data set. ( E ) mRNA level of Has2 from HSCs, Kupffer cells (KC), and hepatocytes (Hep). ( F ) mRNA levels of Has2, Has1, and Has3 in HSCs after 0, 2, 5, and 8 days in culture. ( G ) Western blot for COL1A1, HAS2, the receptor CD44, α-SMA, and GAPDH in HSCs after 0, 2, 5, and 8 days in culture. ( H ) Schematic showing the silencing experiment: HSCs were cultured for 5 days, then transfected with a cocktail of Has2 targeting siRNA (1 + 3), single Has2 targeting siRNA (3) or a negative control (Con) and harvested 48 hours later on day 7. mRNA levels of Has2, MMP9, MMP13, and transforming growth factor β in control and Has2 siRNA–transfected HSCs. Error bars represent mean ± SEM. Statistical significance was determined by ANOVA; * P

Techniques Used: Microarray, Isolation, Mouse Assay, Western Blot, Indirect Immunoperoxidase Assay, Cell Culture, Transfection, Negative Control

Mecp2 regulates the transcripts controlling myofibroblast DNA replication, cell cycle and integrity, metabolism, and fibrogenesis. ( A ) Western blot for Mecp2 in HSCs from WT or Mecp2 –/y mice. Schematic showing the samples used for lncRNA microarray and RNA microarray. ( B ) Volcano plot and heatmap displaying results of mRNA microarray performed on activated HSCs isolated from 3 control and 3 Mecp2 –/y mice. ( C ) Representation of the groups with 2-fold or greater change in gene expression after the KEGG pathway enrichment analysis. ( D ) Top significantly enriched canonical pathway identified by IPA, showing cell cycle control of chromosomal replication. Blue nodes signify down-regulated gene Mecp2 –/y fibroblasts; red signifies up-regulation. Symbol shapes signify the nature of the encoded protein, and unshaded symbols signify genes relevant to the pathway but not differentially expressed in our data set.
Figure Legend Snippet: Mecp2 regulates the transcripts controlling myofibroblast DNA replication, cell cycle and integrity, metabolism, and fibrogenesis. ( A ) Western blot for Mecp2 in HSCs from WT or Mecp2 –/y mice. Schematic showing the samples used for lncRNA microarray and RNA microarray. ( B ) Volcano plot and heatmap displaying results of mRNA microarray performed on activated HSCs isolated from 3 control and 3 Mecp2 –/y mice. ( C ) Representation of the groups with 2-fold or greater change in gene expression after the KEGG pathway enrichment analysis. ( D ) Top significantly enriched canonical pathway identified by IPA, showing cell cycle control of chromosomal replication. Blue nodes signify down-regulated gene Mecp2 –/y fibroblasts; red signifies up-regulation. Symbol shapes signify the nature of the encoded protein, and unshaded symbols signify genes relevant to the pathway but not differentially expressed in our data set.

Techniques Used: Western Blot, Mouse Assay, Microarray, Isolation, Expressing, Indirect Immunoperoxidase Assay

9) Product Images from "Status of hepatic DNA methylome predetermines and modulates the severity of non-alcoholic fatty liver injury in mice"

Article Title: Status of hepatic DNA methylome predetermines and modulates the severity of non-alcoholic fatty liver injury in mice

Journal: BMC Genomics

doi: 10.1186/s12864-016-2617-2

DNA methylation and H3K4me3 in the normal livers of A/J and WSB/EiJ mice. a MeDIP microarray analysis of CpG island methylation in the normal livers of A/J and WSB/EiJ mice. b ChIP-on-chip analysis of H3K4me3 in the normal livers of A/J and WSB/EiL mice. Heat map illustrating significant differences in hepatic CpG island methylation between A/J and WSB/EiJ control mice. Unsupervised hierarchical clustering analysis was performed using one-way ANOVA with p value cut-off at 0.05. The color bar identifies high-methylated or high H3K4me3-enriched ( red ) and low-methylated or low H3K4me3-enriched ( green ) CpG islands
Figure Legend Snippet: DNA methylation and H3K4me3 in the normal livers of A/J and WSB/EiJ mice. a MeDIP microarray analysis of CpG island methylation in the normal livers of A/J and WSB/EiJ mice. b ChIP-on-chip analysis of H3K4me3 in the normal livers of A/J and WSB/EiL mice. Heat map illustrating significant differences in hepatic CpG island methylation between A/J and WSB/EiJ control mice. Unsupervised hierarchical clustering analysis was performed using one-way ANOVA with p value cut-off at 0.05. The color bar identifies high-methylated or high H3K4me3-enriched ( red ) and low-methylated or low H3K4me3-enriched ( green ) CpG islands

Techniques Used: DNA Methylation Assay, Mouse Assay, Methylated DNA Immunoprecipitation, Microarray, Methylation, Chromatin Immunoprecipitation

MeDIP microarray analysis of CpG island methylation changes in the livers of A/J and WSB/EiJ mice fed a choline- and folate-deficient diet. Heat map illustrating significant differences in hepatic CpG island methylation between A/J ( a ) and WSB/EiJ ( b ) mice fed the CFD diet. Unsupervised hierarchical clustering analysis was performed using one-way ANOVA, with p value cut-off at 0.05. The color bar identifies high-methylated ( red ) and low-methylated ( green ) genes. c Table showing the number of differentially methylated CpG islands in hepatic DNA in A/J and WSB/EiJ mice fed a control or CFD diet. Z-scores were calculated with Agilent Genomic Workbench Light. d Algorithm of analysis of inversely differentially methylated and expressed genes in the livers of A/J and WSB/EiJ mice fed a CFD diet
Figure Legend Snippet: MeDIP microarray analysis of CpG island methylation changes in the livers of A/J and WSB/EiJ mice fed a choline- and folate-deficient diet. Heat map illustrating significant differences in hepatic CpG island methylation between A/J ( a ) and WSB/EiJ ( b ) mice fed the CFD diet. Unsupervised hierarchical clustering analysis was performed using one-way ANOVA, with p value cut-off at 0.05. The color bar identifies high-methylated ( red ) and low-methylated ( green ) genes. c Table showing the number of differentially methylated CpG islands in hepatic DNA in A/J and WSB/EiJ mice fed a control or CFD diet. Z-scores were calculated with Agilent Genomic Workbench Light. d Algorithm of analysis of inversely differentially methylated and expressed genes in the livers of A/J and WSB/EiJ mice fed a CFD diet

Techniques Used: Methylated DNA Immunoprecipitation, Microarray, Methylation, Mouse Assay

10) Product Images from "Status of hepatic DNA methylome predetermines and modulates the severity of non-alcoholic fatty liver injury in mice"

Article Title: Status of hepatic DNA methylome predetermines and modulates the severity of non-alcoholic fatty liver injury in mice

Journal: BMC Genomics

doi: 10.1186/s12864-016-2617-2

DNA methylation and H3K4me3 in the normal livers of A/J and WSB/EiJ mice. a MeDIP microarray analysis of CpG island methylation in the normal livers of A/J and WSB/EiJ mice. b ChIP-on-chip analysis of H3K4me3 in the normal livers of A/J and WSB/EiL mice. Heat map illustrating significant differences in hepatic CpG island methylation between A/J and WSB/EiJ control mice. Unsupervised hierarchical clustering analysis was performed using one-way ANOVA with p value cut-off at 0.05. The color bar identifies high-methylated or high H3K4me3-enriched ( red ) and low-methylated or low H3K4me3-enriched ( green ) CpG islands
Figure Legend Snippet: DNA methylation and H3K4me3 in the normal livers of A/J and WSB/EiJ mice. a MeDIP microarray analysis of CpG island methylation in the normal livers of A/J and WSB/EiJ mice. b ChIP-on-chip analysis of H3K4me3 in the normal livers of A/J and WSB/EiL mice. Heat map illustrating significant differences in hepatic CpG island methylation between A/J and WSB/EiJ control mice. Unsupervised hierarchical clustering analysis was performed using one-way ANOVA with p value cut-off at 0.05. The color bar identifies high-methylated or high H3K4me3-enriched ( red ) and low-methylated or low H3K4me3-enriched ( green ) CpG islands

Techniques Used: DNA Methylation Assay, Mouse Assay, Methylated DNA Immunoprecipitation, Microarray, Methylation, Chromatin Immunoprecipitation

MeDIP microarray analysis of CpG island methylation changes in the livers of A/J and WSB/EiJ mice fed a choline- and folate-deficient diet. Heat map illustrating significant differences in hepatic CpG island methylation between A/J ( a ) and WSB/EiJ ( b ) mice fed the CFD diet. Unsupervised hierarchical clustering analysis was performed using one-way ANOVA, with p value cut-off at 0.05. The color bar identifies high-methylated ( red ) and low-methylated ( green ) genes. c Table showing the number of differentially methylated CpG islands in hepatic DNA in A/J and WSB/EiJ mice fed a control or CFD diet. Z-scores were calculated with Agilent Genomic Workbench Light. d Algorithm of analysis of inversely differentially methylated and expressed genes in the livers of A/J and WSB/EiJ mice fed a CFD diet
Figure Legend Snippet: MeDIP microarray analysis of CpG island methylation changes in the livers of A/J and WSB/EiJ mice fed a choline- and folate-deficient diet. Heat map illustrating significant differences in hepatic CpG island methylation between A/J ( a ) and WSB/EiJ ( b ) mice fed the CFD diet. Unsupervised hierarchical clustering analysis was performed using one-way ANOVA, with p value cut-off at 0.05. The color bar identifies high-methylated ( red ) and low-methylated ( green ) genes. c Table showing the number of differentially methylated CpG islands in hepatic DNA in A/J and WSB/EiJ mice fed a control or CFD diet. Z-scores were calculated with Agilent Genomic Workbench Light. d Algorithm of analysis of inversely differentially methylated and expressed genes in the livers of A/J and WSB/EiJ mice fed a CFD diet

Techniques Used: Methylated DNA Immunoprecipitation, Microarray, Methylation, Mouse Assay

11) Product Images from "The FOXG1/FOXO/SMAD network balances proliferation and differentiation of cortical progenitors and activates Kcnh3 expression in mature neurons"

Article Title: The FOXG1/FOXO/SMAD network balances proliferation and differentiation of cortical progenitors and activates Kcnh3 expression in mature neurons

Journal: Oncotarget

doi: 10.18632/oncotarget.9545

Identification of novel candidate genes regulated through FOXG1/SMAD crosstalk A. Whole mouse genome was screened for genes possessing both Forkhead box- (GTAAACAA) and SMAD4-specific (AGAC) consensus DNA-binding sites in a range of 15 Kb before the TSS and placed not farther than 200 bp from each other. Selected candidate genes fulfilled these criteria and were regulated in our microarray analysis. B. Transcriptional expression of candidate genes was assessed by qRTPCR using E13.5 telencephalic hemispheres from Foxg1 −/− , Tgfbr2 cKO and Tgfb2;Tgfb3 dKO mice. Results are expressed as Log 2 (fold change)±SEM of target gene expression in mutants as compared to respective controls (Ctrl, set as 0). Kcnh3 was found to be regulated in both Foxg1 −/− and Tgfb2;Tgfb3 dKO mice and was thus selected for further analyses. *** p
Figure Legend Snippet: Identification of novel candidate genes regulated through FOXG1/SMAD crosstalk A. Whole mouse genome was screened for genes possessing both Forkhead box- (GTAAACAA) and SMAD4-specific (AGAC) consensus DNA-binding sites in a range of 15 Kb before the TSS and placed not farther than 200 bp from each other. Selected candidate genes fulfilled these criteria and were regulated in our microarray analysis. B. Transcriptional expression of candidate genes was assessed by qRTPCR using E13.5 telencephalic hemispheres from Foxg1 −/− , Tgfbr2 cKO and Tgfb2;Tgfb3 dKO mice. Results are expressed as Log 2 (fold change)±SEM of target gene expression in mutants as compared to respective controls (Ctrl, set as 0). Kcnh3 was found to be regulated in both Foxg1 −/− and Tgfb2;Tgfb3 dKO mice and was thus selected for further analyses. *** p

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

12) Product Images from "Reprogramming Human Endothelial to Hematopoietic Cells Requires Vascular Induction"

Article Title: Reprogramming Human Endothelial to Hematopoietic Cells Requires Vascular Induction

Journal: Nature

doi: 10.1038/nature13547

Analysis of liver and spleen of secondary transplanted mice for signs of malignant transformation and analyses of rEC-MPPs for genetic stability A. Analysis of liver and spleen of secondary transplanted mice for signs of malignant transformation . Repeat analysis of spleen and liver of mice that were engrafted with secondary transplanted hDMEC-derived rEC-hMPP cells 15 weeks post-transplantation for signs of malignant transformation (from Figure 5B ). The level of fibrosis was determined by Masson and PicroSirus stainings. The architectonic geometry of the BM was determined by sequential multi-cross sectional Hematoxylin-Eosin (H E) staining and compared to age control non-transplanted NSG mice. We did not observe any evidence of fibrosis or alteration of the geometry of the spleen or liver of the transplanted mice. Furthermore, no recipient mouse manifested any anatomical or symptomatic evidence of leukemias, lymphomas or myeloproliferative neoplasm (MPN): lymphadenopathy, splenomegaly/organomegaly, illness or hemorrhage. Circulating hCD45 + cells in PB displayed no evidence of lympho/myeloproliferation or dysplasia. Furthermore, microscopic architecture of BM, spleen and liver was normal and without fibrotic remodeling or aberrant deposition of collagen or desmin. All images are acquired at 60x magnification. Top rows of images for each organ are secondary transplants; bottom rows of images for each organ are controls. B. Comparative genomic hybridization analysis (CGH) shows that rEC-hMPPs are genetically stable both in vitro and in vivo . Genomic DNA was extracted from HUVECs, CD45 + rEC-hMPPs (35 days post-transduction) or in CD45 + CD34 + rEC-hMPP sorted from the engrafted NSG BM (24-weeks post-transplantation) and expanded for 72 hours in vitro . A human tumor sample was used as positive control of chromosome rearrangement. Extracted DNA was digested, labeled by random priming and hybridized to the Agilent 1M CGH arrays. The arrays were scanned in an Agilent DNA microarray scanner and obtained data was visualized using Feature Extraction software (version 10.7; Agilent). No genomic abnormalities were identified in CD45 + rEC-hMPPs (or in CD45 + CD34 + rEC-hMPPs engrafted in NSG BM. Hence, rEC-hMPPs remain genetically stable in vitro and in vivo and are not transformed.
Figure Legend Snippet: Analysis of liver and spleen of secondary transplanted mice for signs of malignant transformation and analyses of rEC-MPPs for genetic stability A. Analysis of liver and spleen of secondary transplanted mice for signs of malignant transformation . Repeat analysis of spleen and liver of mice that were engrafted with secondary transplanted hDMEC-derived rEC-hMPP cells 15 weeks post-transplantation for signs of malignant transformation (from Figure 5B ). The level of fibrosis was determined by Masson and PicroSirus stainings. The architectonic geometry of the BM was determined by sequential multi-cross sectional Hematoxylin-Eosin (H E) staining and compared to age control non-transplanted NSG mice. We did not observe any evidence of fibrosis or alteration of the geometry of the spleen or liver of the transplanted mice. Furthermore, no recipient mouse manifested any anatomical or symptomatic evidence of leukemias, lymphomas or myeloproliferative neoplasm (MPN): lymphadenopathy, splenomegaly/organomegaly, illness or hemorrhage. Circulating hCD45 + cells in PB displayed no evidence of lympho/myeloproliferation or dysplasia. Furthermore, microscopic architecture of BM, spleen and liver was normal and without fibrotic remodeling or aberrant deposition of collagen or desmin. All images are acquired at 60x magnification. Top rows of images for each organ are secondary transplants; bottom rows of images for each organ are controls. B. Comparative genomic hybridization analysis (CGH) shows that rEC-hMPPs are genetically stable both in vitro and in vivo . Genomic DNA was extracted from HUVECs, CD45 + rEC-hMPPs (35 days post-transduction) or in CD45 + CD34 + rEC-hMPP sorted from the engrafted NSG BM (24-weeks post-transplantation) and expanded for 72 hours in vitro . A human tumor sample was used as positive control of chromosome rearrangement. Extracted DNA was digested, labeled by random priming and hybridized to the Agilent 1M CGH arrays. The arrays were scanned in an Agilent DNA microarray scanner and obtained data was visualized using Feature Extraction software (version 10.7; Agilent). No genomic abnormalities were identified in CD45 + rEC-hMPPs (or in CD45 + CD34 + rEC-hMPPs engrafted in NSG BM. Hence, rEC-hMPPs remain genetically stable in vitro and in vivo and are not transformed.

Techniques Used: Mouse Assay, Transformation Assay, Derivative Assay, Transplantation Assay, Staining, Hybridization, In Vitro, In Vivo, Transduction, Positive Control, Labeling, Microarray, Software

13) Product Images from "Collagen Type I Improves the Differentiation of Human Embryonic Stem Cells towards Definitive Endoderm"

Article Title: Collagen Type I Improves the Differentiation of Human Embryonic Stem Cells towards Definitive Endoderm

Journal: PLoS ONE

doi: 10.1371/journal.pone.0145389

The microarray screen with combinations of ECMPs demonstrated that the DE differentiation was affected by the ECMPs. ( a ) Schematic overview of the ECMP microarray screen. The ECMP microarray slides were prepared by inkjet spotting and undifferentiated hES cells were subsequently seeded and differentiated towards DE. To assess the differentiation, the samples for immunofluorescence were stained for the markers Oct3/4 (undifferentiated hES cells), Sox17 (DE) and DNA (DAPI), and microscope images were captured using an automated microscope, InCell Analyzer. The images were quantified and the data was analysed. (b ) Fluorescence microscope images of selected spots stained for Oct3/4 (red) and Sox17 (green) (scale bar = 200μm). ( c ) Sox17 z-scores plotted against cell number z-scores for each respective ECMP combination (n = 4). The green square indicate the ECMP combinations giving highest fraction of DE cells, whereas the blue square represents the ECMP combinations giving highest cell number. ( d ) Tables of the ECMP combinations giving to the 10 highest fractions of Sox17 positive cells and top 10 highest cell count respectively. ( e ) Immunofluorescence staining of spots from the protein microarray screen. Images were captured at day 1 (one day after seeding) and day 8 (at the end of the DE differentiation protocol) (Scale bar = 200μm).
Figure Legend Snippet: The microarray screen with combinations of ECMPs demonstrated that the DE differentiation was affected by the ECMPs. ( a ) Schematic overview of the ECMP microarray screen. The ECMP microarray slides were prepared by inkjet spotting and undifferentiated hES cells were subsequently seeded and differentiated towards DE. To assess the differentiation, the samples for immunofluorescence were stained for the markers Oct3/4 (undifferentiated hES cells), Sox17 (DE) and DNA (DAPI), and microscope images were captured using an automated microscope, InCell Analyzer. The images were quantified and the data was analysed. (b ) Fluorescence microscope images of selected spots stained for Oct3/4 (red) and Sox17 (green) (scale bar = 200μm). ( c ) Sox17 z-scores plotted against cell number z-scores for each respective ECMP combination (n = 4). The green square indicate the ECMP combinations giving highest fraction of DE cells, whereas the blue square represents the ECMP combinations giving highest cell number. ( d ) Tables of the ECMP combinations giving to the 10 highest fractions of Sox17 positive cells and top 10 highest cell count respectively. ( e ) Immunofluorescence staining of spots from the protein microarray screen. Images were captured at day 1 (one day after seeding) and day 8 (at the end of the DE differentiation protocol) (Scale bar = 200μm).

Techniques Used: Microarray, Immunofluorescence, Staining, Microscopy, Fluorescence, Cell Counting

14) Product Images from "ICAD Deficiency in Human Colon Cancer and Predisposition to Colon Tumorigenesis: Linkage to Apoptosis Resistance and Genomic Instability"

Article Title: ICAD Deficiency in Human Colon Cancer and Predisposition to Colon Tumorigenesis: Linkage to Apoptosis Resistance and Genomic Instability

Journal: PLoS ONE

doi: 10.1371/journal.pone.0057871

ICAD-deficiency is associated with severe genomic instability in colon of DMH-treated mice. Chromosomal DNA isolated from the different experimental groups was assessed for general chromosomal aberrations using an oligo microarray-based CGH with a chip containing 105,000 mouse genomic probes. DNA from colon tissue of age-matched naïve WT or ICAD −/− mice were used as reference controls. Test and reference DNA were labeled by random priming with Cy5-dUTP and Cy3-dUTP, respectively, using the Agilent Genomic DNA Labeling Kit Plus. The individually labeled test and reference samples were concentrated and then combined. Following probe denaturation and pre-annealing with mouse Cot-1 DNA, hybridization was performed as described in the methods. Data including Copy Number Variations were obtained by Agilent Feature Extraction software 9 and analyzed with Agilent Genomic Workbench software 5.0, using the statistical algorithms z score and ADM-2 according to sensitivity threshold respectively at 2.5 and 6.0 and a moving average window of 0.2 Mb. ( A ) Depiction of amplifications (pink) and deletions (green) throughout the 19 somatic chromosomes and the X and Y chromosomes. ( B ) Quantitative assessment of total aberrations (left panel); the right panel represents data attained when stringency was increased and a cutoff of a 3-fold change was applied; p
Figure Legend Snippet: ICAD-deficiency is associated with severe genomic instability in colon of DMH-treated mice. Chromosomal DNA isolated from the different experimental groups was assessed for general chromosomal aberrations using an oligo microarray-based CGH with a chip containing 105,000 mouse genomic probes. DNA from colon tissue of age-matched naïve WT or ICAD −/− mice were used as reference controls. Test and reference DNA were labeled by random priming with Cy5-dUTP and Cy3-dUTP, respectively, using the Agilent Genomic DNA Labeling Kit Plus. The individually labeled test and reference samples were concentrated and then combined. Following probe denaturation and pre-annealing with mouse Cot-1 DNA, hybridization was performed as described in the methods. Data including Copy Number Variations were obtained by Agilent Feature Extraction software 9 and analyzed with Agilent Genomic Workbench software 5.0, using the statistical algorithms z score and ADM-2 according to sensitivity threshold respectively at 2.5 and 6.0 and a moving average window of 0.2 Mb. ( A ) Depiction of amplifications (pink) and deletions (green) throughout the 19 somatic chromosomes and the X and Y chromosomes. ( B ) Quantitative assessment of total aberrations (left panel); the right panel represents data attained when stringency was increased and a cutoff of a 3-fold change was applied; p

Techniques Used: Mouse Assay, Isolation, Microarray, Chromatin Immunoprecipitation, Labeling, DNA Labeling, DNA Hybridization, Software

15) Product Images from "Rex1/Zfp42 is dispensable for pluripotency in mouse ES cells"

Article Title: Rex1/Zfp42 is dispensable for pluripotency in mouse ES cells

Journal: BMC Developmental Biology

doi: 10.1186/1471-213X-8-45

Gene expression profile in Rex1 KO ES cells . A . DNA microarray analysis of Rex1 KO ES cells. Scatter-plot of log-ratios of relative expression levels were shown for wild-type (EB5) versus Rex1 KO (HP3) ES cells. B . QPCR analyses of expressions of the putative Rex1 target genes. Three independent clones with each genotypes were cultured with LIF for 4 days, analyzed separately with normalization by the amount of Gapdh , and plotted with standard deviation against the expression level in undifferentiated wild-type ES cells (wt), set as 1.0.
Figure Legend Snippet: Gene expression profile in Rex1 KO ES cells . A . DNA microarray analysis of Rex1 KO ES cells. Scatter-plot of log-ratios of relative expression levels were shown for wild-type (EB5) versus Rex1 KO (HP3) ES cells. B . QPCR analyses of expressions of the putative Rex1 target genes. Three independent clones with each genotypes were cultured with LIF for 4 days, analyzed separately with normalization by the amount of Gapdh , and plotted with standard deviation against the expression level in undifferentiated wild-type ES cells (wt), set as 1.0.

Techniques Used: Expressing, Microarray, Real-time Polymerase Chain Reaction, Clone Assay, Cell Culture, Standard Deviation

16) Product Images from "Active DNA demethylation in human postmitotic cells correlates with activating histone modifications, but not transcription levels"

Article Title: Active DNA demethylation in human postmitotic cells correlates with activating histone modifications, but not transcription levels

Journal: Genome Biology

doi: 10.1186/gb-2010-11-6-r63

Identification of differentially DNA methylated regions . The fragmented genomes of macrophages (MAC) and immature dendritic cells (iDC) are separated into unmethylated (CpG) and methylated (mCpG) pools. Each pool is directly labeled using fluorescent dyes and each pool of one cell type is compared to the corresponding pool of the other cell type on a global promoter microarray. Microarray images are analyzed in combination to identify regions that show a reciprocal hybridization behavior. Representative scatter plots of CpG and mCpG pool hybridizations are shown. Probes enriched in the unmethylated pool of iDCs (red spots) were enriched in the methylated pool of macrophages (blue spots) and indicated the presence of DNA methylated regions. The reciprocal signal intensity ratios served as internal control for the reliability of microarray data.
Figure Legend Snippet: Identification of differentially DNA methylated regions . The fragmented genomes of macrophages (MAC) and immature dendritic cells (iDC) are separated into unmethylated (CpG) and methylated (mCpG) pools. Each pool is directly labeled using fluorescent dyes and each pool of one cell type is compared to the corresponding pool of the other cell type on a global promoter microarray. Microarray images are analyzed in combination to identify regions that show a reciprocal hybridization behavior. Representative scatter plots of CpG and mCpG pool hybridizations are shown. Probes enriched in the unmethylated pool of iDCs (red spots) were enriched in the methylated pool of macrophages (blue spots) and indicated the presence of DNA methylated regions. The reciprocal signal intensity ratios served as internal control for the reliability of microarray data.

Techniques Used: Methylation, Labeling, Microarray, Hybridization

Comparison of MCIp microarray and MassARRAY EpiTYPER data. (a-c) Diagrams at the top show signal ratios of microarray probes for both independent experiments (donor A in blue, donor B in red) corresponding to their chromosomal localization. Typical DMRs are enriched in the hypomethylated fraction of one cell type and in the hypermethylated region of the other one, resulting in a mirror inverted image. Orange-colored zones indicate sequence regions validated via bisulfite conversion. Middle panels schematically present the chromosomal location of DMRs (orange boxes). Regions analyzed by MALDI TOF MS of bisulfite-converted DNA are indicated at the bottom. White circles represent detectable CpGs while grey circles (or grey boxes in the heat map below) show CpGs not measured by MS. Heat maps depict the methylation status of individual CpGs as shades of blue with each box representing a single CpG. Data of at least six independent donors were averaged.
Figure Legend Snippet: Comparison of MCIp microarray and MassARRAY EpiTYPER data. (a-c) Diagrams at the top show signal ratios of microarray probes for both independent experiments (donor A in blue, donor B in red) corresponding to their chromosomal localization. Typical DMRs are enriched in the hypomethylated fraction of one cell type and in the hypermethylated region of the other one, resulting in a mirror inverted image. Orange-colored zones indicate sequence regions validated via bisulfite conversion. Middle panels schematically present the chromosomal location of DMRs (orange boxes). Regions analyzed by MALDI TOF MS of bisulfite-converted DNA are indicated at the bottom. White circles represent detectable CpGs while grey circles (or grey boxes in the heat map below) show CpGs not measured by MS. Heat maps depict the methylation status of individual CpGs as shades of blue with each box representing a single CpG. Data of at least six independent donors were averaged.

Techniques Used: Microarray, Sequencing, Mass Spectrometry, Methylation

17) Product Images from "SPEN, a new player in primary cilia formation and cell migration in breast cancer"

Article Title: SPEN, a new player in primary cilia formation and cell migration in breast cancer

Journal: Breast Cancer Research : BCR

doi: 10.1186/s13058-017-0897-3

SPEN is coexpressed with RFX3 in breast cancer. a Growth curve of MCF10A cells treated with siRNA control or siRNA for SPEN . Data points represent the mean fluorescence values (±SEM) of three experiments performed in quadruplicates. b Cell cycle analyses performed with MCF10A cells treated with siRNA control or siRNA for SPEN . Bar graph represents the mean percentage of cells (±SEM) in each phase of the cell cycle in three independent experiments. c Growth curve of Hs578T cells treated with siRNA control or siRNA for SPEN . Data points represent the mean fluorescence values (±SEM) of three experiments performed in quadruplicates. d Cell cycle analyses performed with Hs578T cells treated with siRNA control or siRNA for SPEN . Bar graph represents the mean percentage of cells (±SEM) in each phase of the cell cycle in three independent experiments. e Venn diagram showing the intersection of the list of genes coexpressed with SPEN in T47D clones, genes downregulated by SPEN knockdown in MCF10A cells, and a curated list of genes involved in ciliary biology. The microarray data for this study can be found on ArrayExpress under the accession numbers [E-MTAB-4974 and E-MTAB-4975]. f Dot plot showing that SPEN and RFX3 RNA expression levels are strongly correlated in a cohort of 82 primary tumors from patients with triple-negative breast cancer. g Representative immunoblot (IB) showing RFX3 protein levels in T47D-CTL and T47D-SPEN as well as immunoprecipitated (IP) RFX3 protein levels in MCF10A and Hs578T cells treated with siRNA control or siRNA against SPEN . h Endpoint PCR performed on DNA immunoprecipitating with SPEN in T47D-SPEN and T47D-CTL, showing an interaction of SPEN with the RFX3 promoter in T47D-SPEN but not in T47D-CTL cells. *** P ≤ 0.005; ** P ≤ 0.01; * P ≤ 0.05. siRNA Small interfering RNA, SPEN Split ends
Figure Legend Snippet: SPEN is coexpressed with RFX3 in breast cancer. a Growth curve of MCF10A cells treated with siRNA control or siRNA for SPEN . Data points represent the mean fluorescence values (±SEM) of three experiments performed in quadruplicates. b Cell cycle analyses performed with MCF10A cells treated with siRNA control or siRNA for SPEN . Bar graph represents the mean percentage of cells (±SEM) in each phase of the cell cycle in three independent experiments. c Growth curve of Hs578T cells treated with siRNA control or siRNA for SPEN . Data points represent the mean fluorescence values (±SEM) of three experiments performed in quadruplicates. d Cell cycle analyses performed with Hs578T cells treated with siRNA control or siRNA for SPEN . Bar graph represents the mean percentage of cells (±SEM) in each phase of the cell cycle in three independent experiments. e Venn diagram showing the intersection of the list of genes coexpressed with SPEN in T47D clones, genes downregulated by SPEN knockdown in MCF10A cells, and a curated list of genes involved in ciliary biology. The microarray data for this study can be found on ArrayExpress under the accession numbers [E-MTAB-4974 and E-MTAB-4975]. f Dot plot showing that SPEN and RFX3 RNA expression levels are strongly correlated in a cohort of 82 primary tumors from patients with triple-negative breast cancer. g Representative immunoblot (IB) showing RFX3 protein levels in T47D-CTL and T47D-SPEN as well as immunoprecipitated (IP) RFX3 protein levels in MCF10A and Hs578T cells treated with siRNA control or siRNA against SPEN . h Endpoint PCR performed on DNA immunoprecipitating with SPEN in T47D-SPEN and T47D-CTL, showing an interaction of SPEN with the RFX3 promoter in T47D-SPEN but not in T47D-CTL cells. *** P ≤ 0.005; ** P ≤ 0.01; * P ≤ 0.05. siRNA Small interfering RNA, SPEN Split ends

Techniques Used: Fluorescence, Clone Assay, Microarray, RNA Expression, CTL Assay, Immunoprecipitation, Polymerase Chain Reaction, Small Interfering RNA

18) Product Images from "Transient PP2A inhibition alleviates normal tissue stem cell susceptibility to cell death during radiotherapy"

Article Title: Transient PP2A inhibition alleviates normal tissue stem cell susceptibility to cell death during radiotherapy

Journal: Cell Death & Disease

doi: 10.1038/s41419-018-0559-0

PP2A is constitutively overexpressed in stem cells in vivo and in culture. a The number of genes up- or downregulated more than two-fold is compared between ES and ED cells as well as among irradiated ES and ED cells collected early (15 min; RE, radiation early) or late (4 h; RL, radiation late) after 10 Gy IR using microarray analysis. b PP2A and GAPDH were detected in lysates of ES and ED cells using immunoblot. c Tissue sections obtained from testis of WT C57BL/6 mice were stained with Oct4, PP2A, and DNA labeled with DAPI. d Tissue sections of the dentate gyrus of hippocampus obtained from brains of WT C57BL/6 mice were stained with SOX2, PP2A, and DNA labeled with DAPI. e ES and ED were co-plated and stained with SOX2, PP2A, and DNA labeled with DAPI. Cells were stained after 0 Gy treatment. f ES and ED were co-plated and stained with SOX2, PP2A, and DNA labeled with DAPI. Cells were stained 30 min after 6 Gy treatment. Scale bars indicate 10 μm
Figure Legend Snippet: PP2A is constitutively overexpressed in stem cells in vivo and in culture. a The number of genes up- or downregulated more than two-fold is compared between ES and ED cells as well as among irradiated ES and ED cells collected early (15 min; RE, radiation early) or late (4 h; RL, radiation late) after 10 Gy IR using microarray analysis. b PP2A and GAPDH were detected in lysates of ES and ED cells using immunoblot. c Tissue sections obtained from testis of WT C57BL/6 mice were stained with Oct4, PP2A, and DNA labeled with DAPI. d Tissue sections of the dentate gyrus of hippocampus obtained from brains of WT C57BL/6 mice were stained with SOX2, PP2A, and DNA labeled with DAPI. e ES and ED were co-plated and stained with SOX2, PP2A, and DNA labeled with DAPI. Cells were stained after 0 Gy treatment. f ES and ED were co-plated and stained with SOX2, PP2A, and DNA labeled with DAPI. Cells were stained 30 min after 6 Gy treatment. Scale bars indicate 10 μm

Techniques Used: In Vivo, Irradiation, Microarray, Mouse Assay, Staining, Labeling

19) Product Images from "Epigenetic Modulation of Gene Expression during Keratinocyte Differentiation"

Article Title: Epigenetic Modulation of Gene Expression during Keratinocyte Differentiation

Journal: Annals of Dermatology

doi: 10.5021/ad.2012.24.3.261

Scatter plot of the methylation microarray. Genomic DNA was isolated from the T1 and T4 fractions, labeled with Cy3 and Cy5, then applied to the methylation microarray chip. After hybridization, the microarray slide was scanned and analyzed. Each gene was spotted according to its signal intensity.
Figure Legend Snippet: Scatter plot of the methylation microarray. Genomic DNA was isolated from the T1 and T4 fractions, labeled with Cy3 and Cy5, then applied to the methylation microarray chip. After hybridization, the microarray slide was scanned and analyzed. Each gene was spotted according to its signal intensity.

Techniques Used: Methylation, Microarray, Isolation, Labeling, Chromatin Immunoprecipitation, Hybridization

20) Product Images from "Binding and entry of peste des petits ruminants virus into caprine endometrial epithelial cells profoundly affect early cellular gene expression"

Article Title: Binding and entry of peste des petits ruminants virus into caprine endometrial epithelial cells profoundly affect early cellular gene expression

Journal: Veterinary Research

doi: 10.1186/s13567-018-0504-3

Comparison of DNA microarray and real-time PCR data. DNA microarray results and qRT–PCR quantification of the changes in expression levels of 10 selected cellular genes in goat endometrial epithelial cells at 1 h after exposure to PPRV. Data are expressed as fold changes in cellular gene expression. A Upregulated genes identified in the DNA microarray and qRT–PCR experiments after PPRV exposure for 1 and 24 h. B Downregulated genes identified in the DNA microarray and qRT–PCR experiments after exposure to PPRV for 24 h. Data are expressed as mean ± SD ( n = 3).
Figure Legend Snippet: Comparison of DNA microarray and real-time PCR data. DNA microarray results and qRT–PCR quantification of the changes in expression levels of 10 selected cellular genes in goat endometrial epithelial cells at 1 h after exposure to PPRV. Data are expressed as fold changes in cellular gene expression. A Upregulated genes identified in the DNA microarray and qRT–PCR experiments after PPRV exposure for 1 and 24 h. B Downregulated genes identified in the DNA microarray and qRT–PCR experiments after exposure to PPRV for 24 h. Data are expressed as mean ± SD ( n = 3).

Techniques Used: Microarray, Real-time Polymerase Chain Reaction, Quantitative RT-PCR, Expressing

21) Product Images from "Gene Expression Profiling of IL-17A-Treated Synovial Fibroblasts from the Human Temporomandibular Joint"

Article Title: Gene Expression Profiling of IL-17A-Treated Synovial Fibroblasts from the Human Temporomandibular Joint

Journal: Mediators of Inflammation

doi: 10.1155/2015/436067

Scatter plots of microarray analysis. Of the 50,739 genes on the DNA microarray, the 27,583 genes that were expressed in synovial fibroblasts were compared between synovial fibroblasts treated with IL-17A and nontreated control. Of these 27,583 genes, 1,710 genes (389 upregulated genes and 1321 downregulated genes) showed a greater than twofold difference between IL-17A-treated and control cells.
Figure Legend Snippet: Scatter plots of microarray analysis. Of the 50,739 genes on the DNA microarray, the 27,583 genes that were expressed in synovial fibroblasts were compared between synovial fibroblasts treated with IL-17A and nontreated control. Of these 27,583 genes, 1,710 genes (389 upregulated genes and 1321 downregulated genes) showed a greater than twofold difference between IL-17A-treated and control cells.

Techniques Used: Microarray

22) Product Images from "Dynamics of the transcriptome response of cultured human embryonic stem cells to ionizing radiation exposure"

Article Title: Dynamics of the transcriptome response of cultured human embryonic stem cells to ionizing radiation exposure

Journal: Mutation research

doi: 10.1016/j.mrfmmm.2011.02.008

3.7. Real-time PCR validation of DNA microarray results
Figure Legend Snippet: 3.7. Real-time PCR validation of DNA microarray results

Techniques Used: Real-time Polymerase Chain Reaction, Microarray

23) Product Images from "Genetic characterization of clinical and agri-food isolates of multi drug resistant Salmonella enterica serovar Heidelberg from Canada"

Article Title: Genetic characterization of clinical and agri-food isolates of multi drug resistant Salmonella enterica serovar Heidelberg from Canada

Journal: BMC Microbiology

doi: 10.1186/1471-2180-8-89

DNA microarray-based comparative genomics of S . Heidelberg. Array probes represent the linear order of S . Typhimurium LT2 coding sequences from left to right, and with the Salmonella genomic island 1 (SGI1) present at the far-left side. White denotes similarity to LT2, green denotes putative divergence and red represents putative duplication or copy number change. The region STM0691–0704 which was putatively divergent between S . Heidelberg strains is represented by
Figure Legend Snippet: DNA microarray-based comparative genomics of S . Heidelberg. Array probes represent the linear order of S . Typhimurium LT2 coding sequences from left to right, and with the Salmonella genomic island 1 (SGI1) present at the far-left side. White denotes similarity to LT2, green denotes putative divergence and red represents putative duplication or copy number change. The region STM0691–0704 which was putatively divergent between S . Heidelberg strains is represented by "A". Clusters of bacteriophage-related determinants that are divergent in S . Heidelberg compared to S . Typhimurium: B, STM0892–0929 (Fels-1 prophage); C, STM2584–2636 (Gifsy-1 prophage); D, STM2694–2739 (Fels-2 prophage).

Techniques Used: Microarray

24) Product Images from "Rabies Virus Nucleoprotein Functions To Evade Activation of the RIG-I-Mediated Antiviral Response ▿"

Article Title: Rabies Virus Nucleoprotein Functions To Evade Activation of the RIG-I-Mediated Antiviral Response ▿

Journal: Journal of Virology

doi: 10.1128/JVI.02220-09

Comparison of the gene expressions of SYM-I cells infected with Ni, Ni-CE, and CE(NiN) strains using a DNA microarray. SYM-I cells were infected with Ni, Ni-CE, and CE(NiN) strains at an MOI of 2. After 24 h, the total cellular RNA was extracted and used for DNA microarray analysis. The data were normalized by GeneSpring GX software. (A) Cluster analysis of genes of SYM-I cells infected with each virus. The expression pattern of genes involved in “host-pathogen interaction” is represented as a hierarchical clustering, using Cluster and Java TreeView. Genes shown in red are upregulated, and those shown in green are downregulated relative to mock-infected cells. (B) Expression levels of 10 host immunity-related genes, most of which were differentially expressed in Ni-CE- and CE(NiN)-infected cells. Each bar represents the fold change in expression compared to the expression level of each gene in mock-infected cells.
Figure Legend Snippet: Comparison of the gene expressions of SYM-I cells infected with Ni, Ni-CE, and CE(NiN) strains using a DNA microarray. SYM-I cells were infected with Ni, Ni-CE, and CE(NiN) strains at an MOI of 2. After 24 h, the total cellular RNA was extracted and used for DNA microarray analysis. The data were normalized by GeneSpring GX software. (A) Cluster analysis of genes of SYM-I cells infected with each virus. The expression pattern of genes involved in “host-pathogen interaction” is represented as a hierarchical clustering, using Cluster and Java TreeView. Genes shown in red are upregulated, and those shown in green are downregulated relative to mock-infected cells. (B) Expression levels of 10 host immunity-related genes, most of which were differentially expressed in Ni-CE- and CE(NiN)-infected cells. Each bar represents the fold change in expression compared to the expression level of each gene in mock-infected cells.

Techniques Used: Infection, Microarray, Software, Expressing

Validation by real-time RT-PCR of DNA microarray results for IFN -β (A), IFN -λ 1 (B), CXCL10 (C), and CCL5 (D). The assay was performed with the same total RNA used in the DNA microarray experiment. Expression levels of genes were normalized to mRNA levels of GAPDH . Each bar represents the mean (± the SD) of three independent replicates. *, Significant difference ( P
Figure Legend Snippet: Validation by real-time RT-PCR of DNA microarray results for IFN -β (A), IFN -λ 1 (B), CXCL10 (C), and CCL5 (D). The assay was performed with the same total RNA used in the DNA microarray experiment. Expression levels of genes were normalized to mRNA levels of GAPDH . Each bar represents the mean (± the SD) of three independent replicates. *, Significant difference ( P

Techniques Used: Quantitative RT-PCR, Microarray, Expressing

25) Product Images from "Transcription factor DUO1 generated by neo-functionalization is associated with evolution of sperm differentiation in plants"

Article Title: Transcription factor DUO1 generated by neo-functionalization is associated with evolution of sperm differentiation in plants

Journal: Nature Communications

doi: 10.1038/s41467-018-07728-3

Characterization of green algal DUO1 orthologs. a Expression profiles of DUO1 orthologs from three Chara species, C. braunii (Cbr), C. australis (Cau), and C. leptospora (Cle) representing two distant clades (subgenera) 41 . Ribosomal protein L6 ( RPL6 ) was used as the internal control. The expression of two flagella component genes ( RSP11 and PACRG ) was also analyzed in C. braunii . Cbr DUO1 gene structure and amplified probed regions are shown in Supplementary Figure 7a . The whole untrimmed images are shown in Supplementary Figure 7b . Oogonia contain the egg. Antheridia contain developing sperm. Thalli are somatic vegetative tissue. b Position weight matrix representations of the top-scoring 8-mer DNA sequences bound by different MYB domains on a protein-binding DNA microarray. CpeDUO1 is DUO1 from Closterium peracerosum-strigosum-littorale complex (conjugating green alga). Numbers denoted on the right side of each motif represent the motif E- and Z-scores 19 . c In vivo transcriptional activation potentials of green algal DUO1 chimeras. DUO1 transcriptional activation potentials were measured by relative luciferase activity (right) ( n = 4; ** p
Figure Legend Snippet: Characterization of green algal DUO1 orthologs. a Expression profiles of DUO1 orthologs from three Chara species, C. braunii (Cbr), C. australis (Cau), and C. leptospora (Cle) representing two distant clades (subgenera) 41 . Ribosomal protein L6 ( RPL6 ) was used as the internal control. The expression of two flagella component genes ( RSP11 and PACRG ) was also analyzed in C. braunii . Cbr DUO1 gene structure and amplified probed regions are shown in Supplementary Figure 7a . The whole untrimmed images are shown in Supplementary Figure 7b . Oogonia contain the egg. Antheridia contain developing sperm. Thalli are somatic vegetative tissue. b Position weight matrix representations of the top-scoring 8-mer DNA sequences bound by different MYB domains on a protein-binding DNA microarray. CpeDUO1 is DUO1 from Closterium peracerosum-strigosum-littorale complex (conjugating green alga). Numbers denoted on the right side of each motif represent the motif E- and Z-scores 19 . c In vivo transcriptional activation potentials of green algal DUO1 chimeras. DUO1 transcriptional activation potentials were measured by relative luciferase activity (right) ( n = 4; ** p

Techniques Used: Expressing, Amplification, Protein Binding, Microarray, In Vivo, Activation Assay, Luciferase, Activity Assay

26) Product Images from "High Throughput Determination of TGF?1/SMAD3 Targets in A549 Lung Epithelial Cells"

Article Title: High Throughput Determination of TGF?1/SMAD3 Targets in A549 Lung Epithelial Cells

Journal: PLoS ONE

doi: 10.1371/journal.pone.0020319

FOXA2 promoter as a direct target of SMAD3. A: ChIP promoter binding profile of FOXA2 , baseline (left) and after 30 min 2 ng/ml TGFβ1 stimulation (right). Each bar height indicates respective array signal intensity for that probe. Values from the three promoter array replicates are shown (green, blue, purple, respectively). If the binding was statistically significant, the binding curve (red) is also included and shows the fitted peak shape. B: Heat map illustration specifically of FOXA2 ChIP binding values (left) with respective gene expression microarray intensities with and without SIS3 treatment (right and far right, respectively). The microarray expression values are plotted in a bar graph (bottom) and show significant repression (white bars) of FOXA2 during a time course of TGFβ1 treatment that is largely abolished by SIS3 treatment (black bars). C: Electrophoretic mobility shift assay shows specific binding of the SMAD3 protein (lanes 2-4) and nuclear extract from TGFβ1-stimulated A549 cells (lanes 5-7). Lanes 3/6 and 4/7 contain non-labeled competitor FOXA2 promoter sequence DNA, 40 ng and 200 ng, respectively. Lane 8 contains a polyclonal Ab against SMAD3 and has a supershift band (3).
Figure Legend Snippet: FOXA2 promoter as a direct target of SMAD3. A: ChIP promoter binding profile of FOXA2 , baseline (left) and after 30 min 2 ng/ml TGFβ1 stimulation (right). Each bar height indicates respective array signal intensity for that probe. Values from the three promoter array replicates are shown (green, blue, purple, respectively). If the binding was statistically significant, the binding curve (red) is also included and shows the fitted peak shape. B: Heat map illustration specifically of FOXA2 ChIP binding values (left) with respective gene expression microarray intensities with and without SIS3 treatment (right and far right, respectively). The microarray expression values are plotted in a bar graph (bottom) and show significant repression (white bars) of FOXA2 during a time course of TGFβ1 treatment that is largely abolished by SIS3 treatment (black bars). C: Electrophoretic mobility shift assay shows specific binding of the SMAD3 protein (lanes 2-4) and nuclear extract from TGFβ1-stimulated A549 cells (lanes 5-7). Lanes 3/6 and 4/7 contain non-labeled competitor FOXA2 promoter sequence DNA, 40 ng and 200 ng, respectively. Lane 8 contains a polyclonal Ab against SMAD3 and has a supershift band (3).

Techniques Used: Chromatin Immunoprecipitation, Binding Assay, Expressing, Microarray, Electrophoretic Mobility Shift Assay, Labeling, Sequencing

27) Product Images from "Bcl-2-Enhanced Efficacy of Microtubule-Targeting Chemotherapy through Bim Overexpression: Implications for Cancer Treatment 1"

Article Title: Bcl-2-Enhanced Efficacy of Microtubule-Targeting Chemotherapy through Bim Overexpression: Implications for Cancer Treatment 1

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

doi:

Bim mRNA and protein expression is induced in Bcl-2-overexpressing A549 cells. (A) Differences in gene expression profiles of Bcl-2 family members in A549 Bcl-2 cells versus A549 pUse cells, using DNA microarray analysis. Protein expression change in
Figure Legend Snippet: Bim mRNA and protein expression is induced in Bcl-2-overexpressing A549 cells. (A) Differences in gene expression profiles of Bcl-2 family members in A549 Bcl-2 cells versus A549 pUse cells, using DNA microarray analysis. Protein expression change in

Techniques Used: Expressing, Microarray

28) Product Images from "Ruler Arrays Reveal Haploid Genomic Structural Variation"

Article Title: Ruler Arrays Reveal Haploid Genomic Structural Variation

Journal: PLoS ONE

doi: 10.1371/journal.pone.0043210

The ruler array method uses a digest-ligate-extend protocol to generate a labeled DNA sample to detect distances between genomic points. (a) One or more restriction enzymes digest the input DNA sample, leaving a set of sticky ends. (b) An adapter DNA molecule is ligated to the ends, providing a biotin moiety for purification of the ligated material and an initiation site for the polymerase extensions. (c) The ligated material is purified using streptavidin coated beads. (d) Primers, DNA polymerase, and labeled nucleotides are added and primer extensions occur. (e) An extension terminates either upon reaching the end of the template molecule or randomly due to the polymerase’s processivity. Since the output material includes many partial extension products, sequences close to the restriction site occur more frequently than do sequences far from the restriction site. When the labeled sample is hybridized to the microarray, probes close to the restriction site yield correspondingly higher intensities than the distal probes. When this material is labeled (the polymerase may incorporate labeled bases or modified bases or the product may be labeled with a system like ULS) and hybridized to a microarray, probes near the restriction site in the genome will observe a high intensity while probes farther away observe lower intensities.
Figure Legend Snippet: The ruler array method uses a digest-ligate-extend protocol to generate a labeled DNA sample to detect distances between genomic points. (a) One or more restriction enzymes digest the input DNA sample, leaving a set of sticky ends. (b) An adapter DNA molecule is ligated to the ends, providing a biotin moiety for purification of the ligated material and an initiation site for the polymerase extensions. (c) The ligated material is purified using streptavidin coated beads. (d) Primers, DNA polymerase, and labeled nucleotides are added and primer extensions occur. (e) An extension terminates either upon reaching the end of the template molecule or randomly due to the polymerase’s processivity. Since the output material includes many partial extension products, sequences close to the restriction site occur more frequently than do sequences far from the restriction site. When the labeled sample is hybridized to the microarray, probes close to the restriction site yield correspondingly higher intensities than the distal probes. When this material is labeled (the polymerase may incorporate labeled bases or modified bases or the product may be labeled with a system like ULS) and hybridized to a microarray, probes near the restriction site in the genome will observe a high intensity while probes farther away observe lower intensities.

Techniques Used: Labeling, Purification, Microarray, Modification

29) Product Images from "A regulatory module controlling stress-induced cell cycle arrest in Arabidopsis"

Article Title: A regulatory module controlling stress-induced cell cycle arrest in Arabidopsis

Journal: eLife

doi: 10.7554/eLife.43944

ANAC044 and ANAC085 are not required for HR-mediated DNA repair. ( A ) Transcriptional response of DNA repair-related genes to bleomycin. Five-day-old seedlings of WT, sog1-101 and anac044-1 anac085-1 were treated with or without 0.6 µg/ml bleomycin for 10 hr. Total RNA was extracted from root tips and subjected to microarray analysis. Purple and green colours indicate up- and down-regulation, respectively, of genes by bleomycin treatment. ( B ) HR assay. The GUS reporter constructs before and after HR are shown (upper panel). Two-week-old plants of WT, sog1-101 and anac044-1 anac085-1 carrying the GUS reporter construct were irradiated with or without gamma rays (50 Gy), and grown for 3 days. Numbers of blue spots on leaves were counted. Data are presented as mean ± SD (n = 50). Different letters indicate significant differences between samples (Student’s t -test, p
Figure Legend Snippet: ANAC044 and ANAC085 are not required for HR-mediated DNA repair. ( A ) Transcriptional response of DNA repair-related genes to bleomycin. Five-day-old seedlings of WT, sog1-101 and anac044-1 anac085-1 were treated with or without 0.6 µg/ml bleomycin for 10 hr. Total RNA was extracted from root tips and subjected to microarray analysis. Purple and green colours indicate up- and down-regulation, respectively, of genes by bleomycin treatment. ( B ) HR assay. The GUS reporter constructs before and after HR are shown (upper panel). Two-week-old plants of WT, sog1-101 and anac044-1 anac085-1 carrying the GUS reporter construct were irradiated with or without gamma rays (50 Gy), and grown for 3 days. Numbers of blue spots on leaves were counted. Data are presented as mean ± SD (n = 50). Different letters indicate significant differences between samples (Student’s t -test, p

Techniques Used: Microarray, Construct, Irradiation

30) Product Images from "Enhanced anticancer activity of a combination of docetaxel and Aneustat (OMN54) in a patient‐derived, advanced prostate cancer tissue xenograft model), Enhanced anticancer activity of a combination of docetaxel and Aneustat (OMN54) in a patient‐derived, advanced prostate cancer tissue xenograft model"

Article Title: Enhanced anticancer activity of a combination of docetaxel and Aneustat (OMN54) in a patient‐derived, advanced prostate cancer tissue xenograft model), Enhanced anticancer activity of a combination of docetaxel and Aneustat (OMN54) in a patient‐derived, advanced prostate cancer tissue xenograft model

Journal: Molecular Oncology

doi: 10.1016/j.molonc.2013.12.004

Effects of treatment of LTL‐313H xenografts with docetaxel + Aneustat on expression of cancer hallmark‐mediating genes as revealed via DNA microarray analysis. (A) Up‐regulated (red) and down‐regulated (blue) genes. (B) Down‐regulated (green) glycolysis‐associated genes. Additional information is presented in the Supplementary Table S2.
Figure Legend Snippet: Effects of treatment of LTL‐313H xenografts with docetaxel + Aneustat on expression of cancer hallmark‐mediating genes as revealed via DNA microarray analysis. (A) Up‐regulated (red) and down‐regulated (blue) genes. (B) Down‐regulated (green) glycolysis‐associated genes. Additional information is presented in the Supplementary Table S2.

Techniques Used: Expressing, Microarray

31) Product Images from "Analysis of Genes with Alternatively Spliced Transcripts in the Leaf, Root, Panicle and Seed of Rice Using a Long Oligomer Microarray and RNA-Seq"

Article Title: Analysis of Genes with Alternatively Spliced Transcripts in the Leaf, Root, Panicle and Seed of Rice Using a Long Oligomer Microarray and RNA-Seq

Journal: Molecules and Cells

doi: 10.14348/molcells.2017.2297

Design of the feature probes of the rice alternatively spliced transcript detection microarray (ASDM) (A) Probes are positioned and over-scaled based on the genome features in RAP-DB (rapdb.dna.affrc.go.jp). Four probes are collectively indicated as R for the locus Os08g0482700 covering 60 bp of the CDS and 90 bp of the 3′ UTR. Additionally, a 60-bp feature probe (UniqExonJ) was designed by joining 30-bp-long spliced transcripts from two regions (arrow heads) in the CDS for each exon for Os08t0482700-01 . Thus, the probe represents a unique junction of two exons of Os08t0482700-01 and is indicated as Os08t0482700-01_UE in the intensity file. The Os08t0482700-02 transcript has three unique regions compared to Os08t0482700-01 : part of the 5′ UTR, the CDS and part of a 3′ UTR, designated as UniqExonU, UniqExon, and UniqExonD, respectively. Three 60-bp-long target probes were designed according to these regions. (B) Signal intensities and transcript numbers for rice ASDM (top) and RNA-Seq (bottom), respectively. Exons in RNA-Seq are designated according to the exon partition by dexseq_prepare_annotation.py ( Anders et al., 2012 ). Exon bins are indicated by suffixing E and numeral generated by exonic_part_number attribute ( Supplementary Table S4 ). (C) Confirmation of expression by semi-quantitative RT-PCR.
Figure Legend Snippet: Design of the feature probes of the rice alternatively spliced transcript detection microarray (ASDM) (A) Probes are positioned and over-scaled based on the genome features in RAP-DB (rapdb.dna.affrc.go.jp). Four probes are collectively indicated as R for the locus Os08g0482700 covering 60 bp of the CDS and 90 bp of the 3′ UTR. Additionally, a 60-bp feature probe (UniqExonJ) was designed by joining 30-bp-long spliced transcripts from two regions (arrow heads) in the CDS for each exon for Os08t0482700-01 . Thus, the probe represents a unique junction of two exons of Os08t0482700-01 and is indicated as Os08t0482700-01_UE in the intensity file. The Os08t0482700-02 transcript has three unique regions compared to Os08t0482700-01 : part of the 5′ UTR, the CDS and part of a 3′ UTR, designated as UniqExonU, UniqExon, and UniqExonD, respectively. Three 60-bp-long target probes were designed according to these regions. (B) Signal intensities and transcript numbers for rice ASDM (top) and RNA-Seq (bottom), respectively. Exons in RNA-Seq are designated according to the exon partition by dexseq_prepare_annotation.py ( Anders et al., 2012 ). Exon bins are indicated by suffixing E and numeral generated by exonic_part_number attribute ( Supplementary Table S4 ). (C) Confirmation of expression by semi-quantitative RT-PCR.

Techniques Used: Microarray, RNA Sequencing Assay, Generated, Expressing, Quantitative RT-PCR

32) Product Images from "Combination of IAP Antagonists and TNF-α-Armed Oncolytic Viruses Induce Tumor Vascular Shutdown and Tumor Regression"

Article Title: Combination of IAP Antagonists and TNF-α-Armed Oncolytic Viruses Induce Tumor Vascular Shutdown and Tumor Regression

Journal: Molecular Therapy Oncolytics

doi: 10.1016/j.omto.2018.06.002

Combination Treatment of SMC and TNF-α-Armed Oncolytic VSV Induces Vascular Shutdown and Tumor Cell Death (A) EMT6-bearing mice were treated with vehicle or 50 mg/kg of the SMC LCL161 orally and PBS or 1 × 10 7 PFU of VSVΔ51-TNF-α intratumorally for 24 hr and injected with fluorescent microspheres (i.v.) for 5 min. Tumor sections were scanned using the Agilent Technologies DNA microarray scanner. Scale bar, 200 μm. (B) Quantification of perfused microspheres described in (A). One-way ANOVA, *p
Figure Legend Snippet: Combination Treatment of SMC and TNF-α-Armed Oncolytic VSV Induces Vascular Shutdown and Tumor Cell Death (A) EMT6-bearing mice were treated with vehicle or 50 mg/kg of the SMC LCL161 orally and PBS or 1 × 10 7 PFU of VSVΔ51-TNF-α intratumorally for 24 hr and injected with fluorescent microspheres (i.v.) for 5 min. Tumor sections were scanned using the Agilent Technologies DNA microarray scanner. Scale bar, 200 μm. (B) Quantification of perfused microspheres described in (A). One-way ANOVA, *p

Techniques Used: Mouse Assay, Injection, Microarray

33) Product Images from "Integrated Genomic and Epigenomic Analysis of Breast Cancer Brain Metastasis"

Article Title: Integrated Genomic and Epigenomic Analysis of Breast Cancer Brain Metastasis

Journal: PLoS ONE

doi: 10.1371/journal.pone.0085448

DNA Copy Number Analysis of Breast Brain Metastasis. GISTIC analysis was conducted on Agilent SurePrint G3 Human CGH Microarray data for 15 breast brain metastases. Significant false discovery rates (Q-values) for amplified (red) and deleted (blue) regions are plotted genome-wide. Annotations for a few of the significant regions are shown. Focal amplifications and deletions are annotated in boldface, and broad amplifications and deletions are annotated in non-boldface. Q-values for deleted and amplified genes are displayed along the x-axis on top and bottom of the figure, respectively.
Figure Legend Snippet: DNA Copy Number Analysis of Breast Brain Metastasis. GISTIC analysis was conducted on Agilent SurePrint G3 Human CGH Microarray data for 15 breast brain metastases. Significant false discovery rates (Q-values) for amplified (red) and deleted (blue) regions are plotted genome-wide. Annotations for a few of the significant regions are shown. Focal amplifications and deletions are annotated in boldface, and broad amplifications and deletions are annotated in non-boldface. Q-values for deleted and amplified genes are displayed along the x-axis on top and bottom of the figure, respectively.

Techniques Used: Microarray, Amplification, Genome Wide

34) Product Images from "OsTGA2 confers disease resistance to rice against leaf blight by regulating expression levels of disease related genes via interaction with NH1"

Article Title: OsTGA2 confers disease resistance to rice against leaf blight by regulating expression levels of disease related genes via interaction with NH1

Journal: PLoS ONE

doi: 10.1371/journal.pone.0206910

Identification of DNA binding sequences of OsTGA2. (A and B) Identification of DNA-binding sequences of OsTGA2. (A) Summary of putative OsTGA2 DNA binding sequences. Q9 protein-binding microarray analysis was performed using OsTGA2-DsRed fusion protein. A total of 113 probe sequences that produced high signal intensities were selected for further analysis. (B) Signal intensities of TGACGTA sequence and single nucleotide substitution derivatives using Q9 protein-binding microarray. W, Wild-type sequence; 1 to 9, single nucleotide substitution variants (number corresponds to the position of the nucleotide substitution). One probe set that was irrelevant to GGGAAA sequences was used as negative control (N). (C) Sequence logo of TGA binding site based on the information weight matrix model. The height of each letter within a stack is proportional to its frequency at that position in the binding site. Letters are sorted with the most frequent one on the top. The sequence logo was created using WebLogo software ( http://weblogo.berkeley.edu ). (D) Rice TGA2 binds to TGACGT sequences in gel mobility shift assay. Nucleotide sequences of oligonucleotides used as probe and competitors are depicted. Unlabeled wild-type (Wt) and mutated (M1, M2, M3) oligonucleotides were included as competitors.
Figure Legend Snippet: Identification of DNA binding sequences of OsTGA2. (A and B) Identification of DNA-binding sequences of OsTGA2. (A) Summary of putative OsTGA2 DNA binding sequences. Q9 protein-binding microarray analysis was performed using OsTGA2-DsRed fusion protein. A total of 113 probe sequences that produced high signal intensities were selected for further analysis. (B) Signal intensities of TGACGTA sequence and single nucleotide substitution derivatives using Q9 protein-binding microarray. W, Wild-type sequence; 1 to 9, single nucleotide substitution variants (number corresponds to the position of the nucleotide substitution). One probe set that was irrelevant to GGGAAA sequences was used as negative control (N). (C) Sequence logo of TGA binding site based on the information weight matrix model. The height of each letter within a stack is proportional to its frequency at that position in the binding site. Letters are sorted with the most frequent one on the top. The sequence logo was created using WebLogo software ( http://weblogo.berkeley.edu ). (D) Rice TGA2 binds to TGACGT sequences in gel mobility shift assay. Nucleotide sequences of oligonucleotides used as probe and competitors are depicted. Unlabeled wild-type (Wt) and mutated (M1, M2, M3) oligonucleotides were included as competitors.

Techniques Used: Binding Assay, Protein Binding, Microarray, Produced, Sequencing, Negative Control, Software, Mobility Shift

35) Product Images from "Leukemia inhibitory factor via the Toll-like receptor 5 signaling pathway involves aggravation of cachexia induced by human gastric cancer-derived 85As2 cells in rats"

Article Title: Leukemia inhibitory factor via the Toll-like receptor 5 signaling pathway involves aggravation of cachexia induced by human gastric cancer-derived 85As2 cells in rats

Journal: Oncotarget

doi: 10.18632/oncotarget.26190

Increased gene expression of Toll-like receptor (TLR) 5 signaling in 85As2 cells compared to in MKN45cl85 cells The increased gene expression of the TLR signaling pathway in 85As2 cells compared to MKN45cl85 cells was demonstrated by MetaCore analysis of the DNA microarray. Red represents increased gene expression and blue represents decreased gene expression in 85As2 cells compared to MKN45cl85 cells.
Figure Legend Snippet: Increased gene expression of Toll-like receptor (TLR) 5 signaling in 85As2 cells compared to in MKN45cl85 cells The increased gene expression of the TLR signaling pathway in 85As2 cells compared to MKN45cl85 cells was demonstrated by MetaCore analysis of the DNA microarray. Red represents increased gene expression and blue represents decreased gene expression in 85As2 cells compared to MKN45cl85 cells.

Techniques Used: Expressing, Microarray

36) Product Images from "Combination of IAP Antagonists and TNF-α-Armed Oncolytic Viruses Induce Tumor Vascular Shutdown and Tumor Regression"

Article Title: Combination of IAP Antagonists and TNF-α-Armed Oncolytic Viruses Induce Tumor Vascular Shutdown and Tumor Regression

Journal: Molecular Therapy Oncolytics

doi: 10.1016/j.omto.2018.06.002

Combination Treatment of SMC and TNF-α-Armed Oncolytic VSV Induces Vascular Shutdown and Tumor Cell Death (A) EMT6-bearing mice were treated with vehicle or 50 mg/kg of the SMC LCL161 orally and PBS or 1 × 10 7 PFU of VSVΔ51-TNF-α intratumorally for 24 hr and injected with fluorescent microspheres (i.v.) for 5 min. Tumor sections were scanned using the Agilent Technologies DNA microarray scanner. Scale bar, 200 μm. (B) Quantification of perfused microspheres described in (A). One-way ANOVA, *p
Figure Legend Snippet: Combination Treatment of SMC and TNF-α-Armed Oncolytic VSV Induces Vascular Shutdown and Tumor Cell Death (A) EMT6-bearing mice were treated with vehicle or 50 mg/kg of the SMC LCL161 orally and PBS or 1 × 10 7 PFU of VSVΔ51-TNF-α intratumorally for 24 hr and injected with fluorescent microspheres (i.v.) for 5 min. Tumor sections were scanned using the Agilent Technologies DNA microarray scanner. Scale bar, 200 μm. (B) Quantification of perfused microspheres described in (A). One-way ANOVA, *p

Techniques Used: Mouse Assay, Injection, Microarray

37) Product Images from "Leukemia inhibitory factor via the Toll-like receptor 5 signaling pathway involves aggravation of cachexia induced by human gastric cancer-derived 85As2 cells in rats"

Article Title: Leukemia inhibitory factor via the Toll-like receptor 5 signaling pathway involves aggravation of cachexia induced by human gastric cancer-derived 85As2 cells in rats

Journal: Oncotarget

doi: 10.18632/oncotarget.26190

Increased gene expression of Toll-like receptor (TLR) 5 signaling in 85As2 cells compared to in MKN45cl85 cells The increased gene expression of the TLR signaling pathway in 85As2 cells compared to MKN45cl85 cells was demonstrated by MetaCore analysis of the DNA microarray. Red represents increased gene expression and blue represents decreased gene expression in 85As2 cells compared to MKN45cl85 cells.
Figure Legend Snippet: Increased gene expression of Toll-like receptor (TLR) 5 signaling in 85As2 cells compared to in MKN45cl85 cells The increased gene expression of the TLR signaling pathway in 85As2 cells compared to MKN45cl85 cells was demonstrated by MetaCore analysis of the DNA microarray. Red represents increased gene expression and blue represents decreased gene expression in 85As2 cells compared to MKN45cl85 cells.

Techniques Used: Expressing, Microarray

38) Product Images from "SIRT6 Depletion Suppresses Tumor Growth by Promoting Cellular Senescence Induced by DNA Damage in HCC"

Article Title: SIRT6 Depletion Suppresses Tumor Growth by Promoting Cellular Senescence Induced by DNA Damage in HCC

Journal: PLoS ONE

doi: 10.1371/journal.pone.0165835

Effect of SIRT6 knockdown on DNA damage and cell cycle progression. (A) Expression of γ-H2AX was assessed by immunocytochemistry using a confocal microscope. (B) Cells with over 10 foci were quantified by counting cells from the randomly obtained images. The quantified cells were compared in the histogram. The scale bar indicates 30 μM. (C) The expression of indicated proteins was assessed by western blotting. Cells for western blotting and immunocytochemistry were harvested or fixed 5 days after viral transduction. (D) Propidium iodide staining was performed to determine the cell cycle distribution in Hep3B cells 5 days after infection with lentiviruses containing NC or shSIRT6. The numbers of Hep3B cells at the G1, S, and G2/M phases were quantified by FACS analysis. The Modifit program was used for data analysis. (E) Expression of cell cycle-related proteins and SIRT6 were assessed by western blotting. Cells for microarray, RT-PCR, and western blotting were harvested 5 days after viral transduction. All data are representative of three independent experiments. (F) Representative FACS analysis of BrdU incorporation. (G) Cell proliferation rate of NC and shSIRT6-depleted cells as quantified by FACS analysis of four independently performed experiments. (** P
Figure Legend Snippet: Effect of SIRT6 knockdown on DNA damage and cell cycle progression. (A) Expression of γ-H2AX was assessed by immunocytochemistry using a confocal microscope. (B) Cells with over 10 foci were quantified by counting cells from the randomly obtained images. The quantified cells were compared in the histogram. The scale bar indicates 30 μM. (C) The expression of indicated proteins was assessed by western blotting. Cells for western blotting and immunocytochemistry were harvested or fixed 5 days after viral transduction. (D) Propidium iodide staining was performed to determine the cell cycle distribution in Hep3B cells 5 days after infection with lentiviruses containing NC or shSIRT6. The numbers of Hep3B cells at the G1, S, and G2/M phases were quantified by FACS analysis. The Modifit program was used for data analysis. (E) Expression of cell cycle-related proteins and SIRT6 were assessed by western blotting. Cells for microarray, RT-PCR, and western blotting were harvested 5 days after viral transduction. All data are representative of three independent experiments. (F) Representative FACS analysis of BrdU incorporation. (G) Cell proliferation rate of NC and shSIRT6-depleted cells as quantified by FACS analysis of four independently performed experiments. (** P

Techniques Used: Expressing, Immunocytochemistry, Microscopy, Western Blot, Transduction, Staining, Infection, FACS, Microarray, Reverse Transcription Polymerase Chain Reaction, BrdU Incorporation Assay

39) Product Images from "Improved genome-wide localization by ChIP-chip using double-round T7 RNA polymerase-based amplification"

Article Title: Improved genome-wide localization by ChIP-chip using double-round T7 RNA polymerase-based amplification

Journal: Nucleic Acids Research

doi: 10.1093/nar/gkm1144

Double-round T7 amplification results in reduced technical variation compared to LM-PCR. Histograms of averaged binding ratios of four hybridizations with double-T7 ( A ) or LM-PCR amplified samples ( B ) across all DNA microarray probes. ( C ) Overview plot of chromosome 7 showing locations of array probes (black) and genes (green). Graphs of binding ratios of input versus ChIP show the background and binding signals for double-round T7 amplification (double-T7) (top) and LM-PCR (bottom). ( D ) Enlargement of indicated regions in (C).
Figure Legend Snippet: Double-round T7 amplification results in reduced technical variation compared to LM-PCR. Histograms of averaged binding ratios of four hybridizations with double-T7 ( A ) or LM-PCR amplified samples ( B ) across all DNA microarray probes. ( C ) Overview plot of chromosome 7 showing locations of array probes (black) and genes (green). Graphs of binding ratios of input versus ChIP show the background and binding signals for double-round T7 amplification (double-T7) (top) and LM-PCR (bottom). ( D ) Enlargement of indicated regions in (C).

Techniques Used: Amplification, Polymerase Chain Reaction, Binding Assay, Microarray, Chromatin Immunoprecipitation

40) Product Images from "A functional in vitro model of heterotypic interactions reveals a role for interferon-positive carcinoma associated fibroblasts in breast cancer"

Article Title: A functional in vitro model of heterotypic interactions reveals a role for interferon-positive carcinoma associated fibroblasts in breast cancer

Journal: BMC Cancer

doi: 10.1186/s12885-015-1117-0

Hierarchical clustering of CAFs reveals interferon positive CAF subset. (A) Hierarchical clustering (HCL) of the 23 CAFs. DNA microarray data were filtered for genes that were 2-fold above or below the mean for that gene in a minimum of 3 samples. This resulted in a total of 2506 genes which are shown clustered above. (B) Magnification of the gene cluster highlighted by the red bar in Figure 1A. Further inspection of this cluster shows the upregulation of many type-one interferon genes in addition to a host of cytokines in five of the CAFs analyzed. (C) An IFN-β ELISA of DMEM (2% FBS) cultured with sub-confluent fibroblasts (3 normal breast fibroblast, 3 IFN-negative CAFs and 3 IFN-positive CAFs) for 48 hours. IFN-β ligand was only detected in the 3 IFN-positive CAF supernatents. (D) Q-RT-PCR analysis on frozen whole tumor sections corresponding to two IFN-positive and two IFN-negative CAFs. The IFN-positive CAFs (T35 and T44) showed a greatly increased level of both IFN markers IFN-β and OAS2 relative to the IFN-negative tumors (T77 and T79) (p
Figure Legend Snippet: Hierarchical clustering of CAFs reveals interferon positive CAF subset. (A) Hierarchical clustering (HCL) of the 23 CAFs. DNA microarray data were filtered for genes that were 2-fold above or below the mean for that gene in a minimum of 3 samples. This resulted in a total of 2506 genes which are shown clustered above. (B) Magnification of the gene cluster highlighted by the red bar in Figure 1A. Further inspection of this cluster shows the upregulation of many type-one interferon genes in addition to a host of cytokines in five of the CAFs analyzed. (C) An IFN-β ELISA of DMEM (2% FBS) cultured with sub-confluent fibroblasts (3 normal breast fibroblast, 3 IFN-negative CAFs and 3 IFN-positive CAFs) for 48 hours. IFN-β ligand was only detected in the 3 IFN-positive CAF supernatents. (D) Q-RT-PCR analysis on frozen whole tumor sections corresponding to two IFN-positive and two IFN-negative CAFs. The IFN-positive CAFs (T35 and T44) showed a greatly increased level of both IFN markers IFN-β and OAS2 relative to the IFN-negative tumors (T77 and T79) (p

Techniques Used: Microarray, Enzyme-linked Immunosorbent Assay, Cell Culture, Reverse Transcription Polymerase Chain Reaction

41) Product Images from "Open chromatin structures regulate the efficiencies of pre-RC formation and replication initiation in Epstein-Barr virus"

Article Title: Open chromatin structures regulate the efficiencies of pre-RC formation and replication initiation in Epstein-Barr virus

Journal: The Journal of Cell Biology

doi: 10.1083/jcb.201109105

Scheme of the EBV genome and experimental design for the analyses of pre-RC and SNS zones as well as mapping of MR profiles. (A) Scheme of the circular EBV genome. In addition to the latent origins oriP (blue box) and the 14-kbp “Raji origin” (blue line), the lytic origin (oriLyt) is shown. The latent EBV nuclear antigens 1, 2, 3A–C, EBNA-LP genes (turquoise), and LMP1 and -2 (purple) are depicted, including their transcripts and promoters. The EBER1 and -2 and the miRNAs regions (BART and BARF) are indicated (green lines). The Raji genome harbors two deletions (red Δ, nt 86,000–89,000 and 163,978–166,635). These regions do not produce array signals in comparison to the reference strain type I used for the design of the EBV microarray. (B) Chart of the experimental set up to map pre-RC zones (left), MNase profiles (central), and SNS DNA (right). (C) Cell cycle phases of logarithmically growing Raji cells were separated by centrifugal elutriation. The DNA content of the different fractions was determined by FACS analysis (top, I–VI). The FACS profiles of one out of three experiments are shown. The quality of coprecipitated DNA was determined by quantitative PCR. The histograms show the mean values of three independent Orc2 (bottom left) and Mcm3 (bottom right) immunoprecipitations. The enrichments of Orc2 (red bars) and Mcm3 enrichments (blue bars) at the DS region are shown. The black bars indicate the enrichments of Orc2 and Mcm3 to a reference site. Error bars indicate mean ± SEM.
Figure Legend Snippet: Scheme of the EBV genome and experimental design for the analyses of pre-RC and SNS zones as well as mapping of MR profiles. (A) Scheme of the circular EBV genome. In addition to the latent origins oriP (blue box) and the 14-kbp “Raji origin” (blue line), the lytic origin (oriLyt) is shown. The latent EBV nuclear antigens 1, 2, 3A–C, EBNA-LP genes (turquoise), and LMP1 and -2 (purple) are depicted, including their transcripts and promoters. The EBER1 and -2 and the miRNAs regions (BART and BARF) are indicated (green lines). The Raji genome harbors two deletions (red Δ, nt 86,000–89,000 and 163,978–166,635). These regions do not produce array signals in comparison to the reference strain type I used for the design of the EBV microarray. (B) Chart of the experimental set up to map pre-RC zones (left), MNase profiles (central), and SNS DNA (right). (C) Cell cycle phases of logarithmically growing Raji cells were separated by centrifugal elutriation. The DNA content of the different fractions was determined by FACS analysis (top, I–VI). The FACS profiles of one out of three experiments are shown. The quality of coprecipitated DNA was determined by quantitative PCR. The histograms show the mean values of three independent Orc2 (bottom left) and Mcm3 (bottom right) immunoprecipitations. The enrichments of Orc2 (red bars) and Mcm3 enrichments (blue bars) at the DS region are shown. The black bars indicate the enrichments of Orc2 and Mcm3 to a reference site. Error bars indicate mean ± SEM.

Techniques Used: Microarray, FACS, Real-time Polymerase Chain Reaction

42) Product Images from "Integrated Genomic and Epigenomic Analysis of Breast Cancer Brain Metastasis"

Article Title: Integrated Genomic and Epigenomic Analysis of Breast Cancer Brain Metastasis

Journal: PLoS ONE

doi: 10.1371/journal.pone.0085448

DNA Copy Number Analysis of Breast Brain Metastasis. GISTIC analysis was conducted on Agilent SurePrint G3 Human CGH Microarray data for 15 breast brain metastases. Significant false discovery rates (Q-values) for amplified (red) and deleted (blue) regions are plotted genome-wide. Annotations for a few of the significant regions are shown. Focal amplifications and deletions are annotated in boldface, and broad amplifications and deletions are annotated in non-boldface. Q-values for deleted and amplified genes are displayed along the x-axis on top and bottom of the figure, respectively.
Figure Legend Snippet: DNA Copy Number Analysis of Breast Brain Metastasis. GISTIC analysis was conducted on Agilent SurePrint G3 Human CGH Microarray data for 15 breast brain metastases. Significant false discovery rates (Q-values) for amplified (red) and deleted (blue) regions are plotted genome-wide. Annotations for a few of the significant regions are shown. Focal amplifications and deletions are annotated in boldface, and broad amplifications and deletions are annotated in non-boldface. Q-values for deleted and amplified genes are displayed along the x-axis on top and bottom of the figure, respectively.

Techniques Used: Microarray, Amplification, Genome Wide

43) Product Images from "Derivation of iPSCs after Culture of Human Dental Pulp Cells under Defined Conditions"

Article Title: Derivation of iPSCs after Culture of Human Dental Pulp Cells under Defined Conditions

Journal: PLoS ONE

doi: 10.1371/journal.pone.0115392

Microarray analysis of gene expression. Scatter plots compared the embryonic stem cell marker genes expression between chemically defined culture conditions (MSCGM-CD) and normal culture conditions (MSCGM) determined by DNA microarray. The green lines indicate the diagonal and 2-fold changes between the two samples. Black and red circles indicate the expression levels of some embryonic stem cell marker genes ( S3 Table ).
Figure Legend Snippet: Microarray analysis of gene expression. Scatter plots compared the embryonic stem cell marker genes expression between chemically defined culture conditions (MSCGM-CD) and normal culture conditions (MSCGM) determined by DNA microarray. The green lines indicate the diagonal and 2-fold changes between the two samples. Black and red circles indicate the expression levels of some embryonic stem cell marker genes ( S3 Table ).

Techniques Used: Microarray, Expressing, Marker

44) Product Images from "Chapter 9 - Methylation Analysis by Microarray"

Article Title: Chapter 9 - Methylation Analysis by Microarray

Journal: Methods in molecular biology (Clifton, N.J.)

doi: 10.1007/978-1-60327-192-9_9

DMH protocol outline. A DNA sonication: genomic DNA is fragmented to ~500–800 bp in length. Gel shows typical DNA smears of good and bad samples. B End blunting and linker ligation: sonicated DNA is end-repaired and used as a template for linker-adapters attachment. Gel shows a good sample (smear pattern similar to the sonicated DNA) and a bad sample (smear pattern has high MW masses that are not seen in the sonicated DNA). C Methylation Sensitive Restriction: The Linker ligated fragments are digested with any restriction enzyme which recognizes a sequence containing a CG di-nucleotide and is only able to digest the DNA if it lacks a methylated cytosine. D Linker-mediated PCR: The fragments which survive digestion are amplified using primers complimentary to the linker sequence. As depicted, fragments containing unmethylated or partially methylated sites will not be amplified. E Dye Labeling: Klenow fragments are used to incorporate amino-allyl dUTPs (aa-dUTPs) into the amplified fragments. These aa-dUTPs then serve as attachment sites for the Cy dyes. F Microarray Outcomes: After the test sample and control sample are mixed at equal concentrations, they are allowed to hybridize to the microarray potentially giving any of the following outcomes for each probe: 1 (pseudo-red) hypermethylation of test sample as compared to the control sample; 2 (pseudo-green) hypomethylation of test sample; 3 (pseudo-yellow) equal methylation of both samples; 4 (no signal above background) no hybridization to the probes can be caused by poor interaction between the probe and fragment, or fragments not seen because they are unmethylated and digested.
Figure Legend Snippet: DMH protocol outline. A DNA sonication: genomic DNA is fragmented to ~500–800 bp in length. Gel shows typical DNA smears of good and bad samples. B End blunting and linker ligation: sonicated DNA is end-repaired and used as a template for linker-adapters attachment. Gel shows a good sample (smear pattern similar to the sonicated DNA) and a bad sample (smear pattern has high MW masses that are not seen in the sonicated DNA). C Methylation Sensitive Restriction: The Linker ligated fragments are digested with any restriction enzyme which recognizes a sequence containing a CG di-nucleotide and is only able to digest the DNA if it lacks a methylated cytosine. D Linker-mediated PCR: The fragments which survive digestion are amplified using primers complimentary to the linker sequence. As depicted, fragments containing unmethylated or partially methylated sites will not be amplified. E Dye Labeling: Klenow fragments are used to incorporate amino-allyl dUTPs (aa-dUTPs) into the amplified fragments. These aa-dUTPs then serve as attachment sites for the Cy dyes. F Microarray Outcomes: After the test sample and control sample are mixed at equal concentrations, they are allowed to hybridize to the microarray potentially giving any of the following outcomes for each probe: 1 (pseudo-red) hypermethylation of test sample as compared to the control sample; 2 (pseudo-green) hypomethylation of test sample; 3 (pseudo-yellow) equal methylation of both samples; 4 (no signal above background) no hybridization to the probes can be caused by poor interaction between the probe and fragment, or fragments not seen because they are unmethylated and digested.

Techniques Used: Sonication, Ligation, Methylation, Sequencing, Polymerase Chain Reaction, Amplification, Labeling, Microarray, Hybridization

45) Product Images from "A New Microarray System to Detect Streptococcus pneumoniae Serotypes"

Article Title: A New Microarray System to Detect Streptococcus pneumoniae Serotypes

Journal: Journal of Biomedicine and Biotechnology

doi: 10.1155/2011/352736

(a) Microarray oligonucleotide probes layout. Oligonucleotides 1 to 222 are provided in Tables 2 and 3 . P represents S. pneumoniae housekeeping genes and 16S rDNA positive control oligonucleotides. N indicates negative control oligonucleotides designed from housekeeping genes of other bacterial species. E denotes empty spot. (b) Scanned microarray images of S. pneumoniae genomic DNA hybridized with 6 samples (serotype 3, 9V, 11A, 19F, 22F and 22A). The numbers correspond to the spot identifiers given in Tables 2 and 3 , and Figure 1(a) P indicates positive spot.
Figure Legend Snippet: (a) Microarray oligonucleotide probes layout. Oligonucleotides 1 to 222 are provided in Tables 2 and 3 . P represents S. pneumoniae housekeeping genes and 16S rDNA positive control oligonucleotides. N indicates negative control oligonucleotides designed from housekeeping genes of other bacterial species. E denotes empty spot. (b) Scanned microarray images of S. pneumoniae genomic DNA hybridized with 6 samples (serotype 3, 9V, 11A, 19F, 22F and 22A). The numbers correspond to the spot identifiers given in Tables 2 and 3 , and Figure 1(a) P indicates positive spot.

Techniques Used: Microarray, Positive Control, Negative Control

46) Product Images from "Binding and entry of peste des petits ruminants virus into caprine endometrial epithelial cells profoundly affect early cellular gene expression"

Article Title: Binding and entry of peste des petits ruminants virus into caprine endometrial epithelial cells profoundly affect early cellular gene expression

Journal: Veterinary Research

doi: 10.1186/s13567-018-0504-3

Comparison of DNA microarray and real-time PCR data. DNA microarray results and qRT–PCR quantification of the changes in expression levels of 10 selected cellular genes in goat endometrial epithelial cells at 1 h after exposure to PPRV. Data are expressed as fold changes in cellular gene expression. A Upregulated genes identified in the DNA microarray and qRT–PCR experiments after PPRV exposure for 1 and 24 h. B Downregulated genes identified in the DNA microarray and qRT–PCR experiments after exposure to PPRV for 24 h. Data are expressed as mean ± SD ( n = 3).
Figure Legend Snippet: Comparison of DNA microarray and real-time PCR data. DNA microarray results and qRT–PCR quantification of the changes in expression levels of 10 selected cellular genes in goat endometrial epithelial cells at 1 h after exposure to PPRV. Data are expressed as fold changes in cellular gene expression. A Upregulated genes identified in the DNA microarray and qRT–PCR experiments after PPRV exposure for 1 and 24 h. B Downregulated genes identified in the DNA microarray and qRT–PCR experiments after exposure to PPRV for 24 h. Data are expressed as mean ± SD ( n = 3).

Techniques Used: Microarray, Real-time Polymerase Chain Reaction, Quantitative RT-PCR, Expressing

47) Product Images from "OMICS in Ecology: Systems Level Analyses of Halobacterium salinarum Reveal Large-scale Temperature-Mediated Changes and a Requirement of CctA for Thermotolerance"

Article Title: OMICS in Ecology: Systems Level Analyses of Halobacterium salinarum Reveal Large-scale Temperature-Mediated Changes and a Requirement of CctA for Thermotolerance

Journal: OMICS : a Journal of Integrative Biology

doi: 10.1089/omi.2012.0117

Protein changes supported by ancillary DNA microarray data
Figure Legend Snippet: Protein changes supported by ancillary DNA microarray data

Techniques Used: Microarray

48) Product Images from "Transient PP2A inhibition alleviates normal tissue stem cell susceptibility to cell death during radiotherapy"

Article Title: Transient PP2A inhibition alleviates normal tissue stem cell susceptibility to cell death during radiotherapy

Journal: Cell Death & Disease

doi: 10.1038/s41419-018-0559-0

PP2A is constitutively overexpressed in stem cells in vivo and in culture. a The number of genes up- or downregulated more than two-fold is compared between ES and ED cells as well as among irradiated ES and ED cells collected early (15 min; RE, radiation early) or late (4 h; RL, radiation late) after 10 Gy IR using microarray analysis. b PP2A and GAPDH were detected in lysates of ES and ED cells using immunoblot. c Tissue sections obtained from testis of WT C57BL/6 mice were stained with Oct4, PP2A, and DNA labeled with DAPI. d Tissue sections of the dentate gyrus of hippocampus obtained from brains of WT C57BL/6 mice were stained with SOX2, PP2A, and DNA labeled with DAPI. e ES and ED were co-plated and stained with SOX2, PP2A, and DNA labeled with DAPI. Cells were stained after 0 Gy treatment. f ES and ED were co-plated and stained with SOX2, PP2A, and DNA labeled with DAPI. Cells were stained 30 min after 6 Gy treatment. Scale bars indicate 10 μm
Figure Legend Snippet: PP2A is constitutively overexpressed in stem cells in vivo and in culture. a The number of genes up- or downregulated more than two-fold is compared between ES and ED cells as well as among irradiated ES and ED cells collected early (15 min; RE, radiation early) or late (4 h; RL, radiation late) after 10 Gy IR using microarray analysis. b PP2A and GAPDH were detected in lysates of ES and ED cells using immunoblot. c Tissue sections obtained from testis of WT C57BL/6 mice were stained with Oct4, PP2A, and DNA labeled with DAPI. d Tissue sections of the dentate gyrus of hippocampus obtained from brains of WT C57BL/6 mice were stained with SOX2, PP2A, and DNA labeled with DAPI. e ES and ED were co-plated and stained with SOX2, PP2A, and DNA labeled with DAPI. Cells were stained after 0 Gy treatment. f ES and ED were co-plated and stained with SOX2, PP2A, and DNA labeled with DAPI. Cells were stained 30 min after 6 Gy treatment. Scale bars indicate 10 μm

Techniques Used: In Vivo, Irradiation, Microarray, Mouse Assay, Staining, Labeling

49) Product Images from "Genome-wide copy number profiling of single cells in S-phase reveals DNA-replication domains"

Article Title: Genome-wide copy number profiling of single cells in S-phase reveals DNA-replication domains

Journal: Nucleic Acids Research

doi: 10.1093/nar/gks1352

Log2 intensity ratios in S-phase cells oscillate according to predicted replication timing. For each single-cell and multi-cell control sample, a heat map of the mean log2 intensity ratio per replication domain across all autosomes is depicted in a circosplot. The colour-code legend of the heat map is depicted at the bottom of the figure. In each circosplot, the outermost circle depicts the predicted replication timing pattern as published by Ryba et al. ( 28 ) (early replicating domains in green; late replicating domains in red; replication domains covered by five or more microarray probes are marked by a blue bar on the outside). This is followed (from the outside to the inside of the circosplot) by the heat maps representing all single-cell log2 intensity ratio data (one cell per rim) and subsequently by the heat maps reflecting all multi-cell control log2 intensity ratio data (one multi-cell control per rim). ( a and b ) All S-phase single-cell and multi-cell samples. The top circosplot depicts the chromosomes 1 to 8 (a), bottom circosplot chromosomes 9 to 22 (b). The 14 S-phase single cell samples are shown in the following order (outside to inside): S1.3, S1.2, S3.1, S7.5, S7.6, S1.4, S7.7, S1.1, S7.1, S7.4, S4.1, S4.2, S7.2 and S7.3; followed by S-phase multi-cell control samples. ( c and d ) All G1- and G2/M-phase single-cell and multi- cell samples. Top circosplot depicts the chromosomes 1 to 8 (c), bottom circosplot chromosomes 9 to 22 (d). The 16 single-cell samples are shown in the following order (outside to inside): G1.1, G1.2, G1.3, G1.4, G3.1, G4.1, G7.1, G7.2, M1.1, M1.2, M1.3, M3.1, M3.2, M4.1, M7.1 and M7.2; followed by G1- and G2/M-phase multi-cell control samples. The oscillating pattern of consecutive positive and negative log2 intensity ratios genome wide orchestrated by early and late DNA replication in S-phase single cells can be clearly observed, and is concordant with the pattern in multi-cell controls. In contrast, the G1-phase and G2/M-phase single cells do not demonstrate such genome wide oscillation of log2 intensity ratios in accordance with the replication timing pattern. Similar observations can be made for the multi-cell controls. Three specific regions for which the log2 intensity plots are shown in Supplementary Figure S5 at high resolution are marked by a black box.
Figure Legend Snippet: Log2 intensity ratios in S-phase cells oscillate according to predicted replication timing. For each single-cell and multi-cell control sample, a heat map of the mean log2 intensity ratio per replication domain across all autosomes is depicted in a circosplot. The colour-code legend of the heat map is depicted at the bottom of the figure. In each circosplot, the outermost circle depicts the predicted replication timing pattern as published by Ryba et al. ( 28 ) (early replicating domains in green; late replicating domains in red; replication domains covered by five or more microarray probes are marked by a blue bar on the outside). This is followed (from the outside to the inside of the circosplot) by the heat maps representing all single-cell log2 intensity ratio data (one cell per rim) and subsequently by the heat maps reflecting all multi-cell control log2 intensity ratio data (one multi-cell control per rim). ( a and b ) All S-phase single-cell and multi-cell samples. The top circosplot depicts the chromosomes 1 to 8 (a), bottom circosplot chromosomes 9 to 22 (b). The 14 S-phase single cell samples are shown in the following order (outside to inside): S1.3, S1.2, S3.1, S7.5, S7.6, S1.4, S7.7, S1.1, S7.1, S7.4, S4.1, S4.2, S7.2 and S7.3; followed by S-phase multi-cell control samples. ( c and d ) All G1- and G2/M-phase single-cell and multi- cell samples. Top circosplot depicts the chromosomes 1 to 8 (c), bottom circosplot chromosomes 9 to 22 (d). The 16 single-cell samples are shown in the following order (outside to inside): G1.1, G1.2, G1.3, G1.4, G3.1, G4.1, G7.1, G7.2, M1.1, M1.2, M1.3, M3.1, M3.2, M4.1, M7.1 and M7.2; followed by G1- and G2/M-phase multi-cell control samples. The oscillating pattern of consecutive positive and negative log2 intensity ratios genome wide orchestrated by early and late DNA replication in S-phase single cells can be clearly observed, and is concordant with the pattern in multi-cell controls. In contrast, the G1-phase and G2/M-phase single cells do not demonstrate such genome wide oscillation of log2 intensity ratios in accordance with the replication timing pattern. Similar observations can be made for the multi-cell controls. Three specific regions for which the log2 intensity plots are shown in Supplementary Figure S5 at high resolution are marked by a black box.

Techniques Used: Microarray, Genome Wide

50) Product Images from "Combination of IAP Antagonists and TNF-α-Armed Oncolytic Viruses Induce Tumor Vascular Shutdown and Tumor Regression"

Article Title: Combination of IAP Antagonists and TNF-α-Armed Oncolytic Viruses Induce Tumor Vascular Shutdown and Tumor Regression

Journal: Molecular Therapy Oncolytics

doi: 10.1016/j.omto.2018.06.002

Combination Treatment of SMC and TNF-α-Armed Oncolytic VSV Induces Vascular Shutdown and Tumor Cell Death (A) EMT6-bearing mice were treated with vehicle or 50 mg/kg of the SMC LCL161 orally and PBS or 1 × 10 7 PFU of VSVΔ51-TNF-α intratumorally for 24 hr and injected with fluorescent microspheres (i.v.) for 5 min. Tumor sections were scanned using the Agilent Technologies DNA microarray scanner. Scale bar, 200 μm. (B) Quantification of perfused microspheres described in (A). One-way ANOVA, *p
Figure Legend Snippet: Combination Treatment of SMC and TNF-α-Armed Oncolytic VSV Induces Vascular Shutdown and Tumor Cell Death (A) EMT6-bearing mice were treated with vehicle or 50 mg/kg of the SMC LCL161 orally and PBS or 1 × 10 7 PFU of VSVΔ51-TNF-α intratumorally for 24 hr and injected with fluorescent microspheres (i.v.) for 5 min. Tumor sections were scanned using the Agilent Technologies DNA microarray scanner. Scale bar, 200 μm. (B) Quantification of perfused microspheres described in (A). One-way ANOVA, *p

Techniques Used: Mouse Assay, Injection, Microarray

51) Product Images from "Embryonic MicroRNA-369 Controls Metabolic Splicing Factors and Urges Cellular Reprograming"

Article Title: Embryonic MicroRNA-369 Controls Metabolic Splicing Factors and Urges Cellular Reprograming

Journal: PLoS ONE

doi: 10.1371/journal.pone.0132789

Role of transcripts located at mouse chromosome 12F1 in Oct4 deprivation-induced differentiated ESCs. A) Mouse genomic regions involving Dlk1 , Meg3 , Rian , Mirg , and Dio3 . miR-369 locations and ChIP-PCR primer positions are shown. B) Microarray analysis of miR expression level in undifferentiated ESCs (WT ES) and differentiated ESCs (WT EB D7). C) H3K4 tri-methylation in ESCs is shown at various time points indicated as: day 0 (Blue), 3 (Red), and 7 (Green). D) H3K9 tri-methylation in ESCs is shown at various time points indicated as: day 0 (Blue), 3 (Red), and 7 (Green). E) H3K27 tri-methylation in ESCs is shown at various time points indicated as: day 0 (Blue), 3 (Red), and 7 (Green). F) H3K79 tri-methylation in ESCs is shown at various time points indicated as: day 0 (Blue), 3 (Red), and 7 (Green). Vertical axis indicates relative amount of DNA.
Figure Legend Snippet: Role of transcripts located at mouse chromosome 12F1 in Oct4 deprivation-induced differentiated ESCs. A) Mouse genomic regions involving Dlk1 , Meg3 , Rian , Mirg , and Dio3 . miR-369 locations and ChIP-PCR primer positions are shown. B) Microarray analysis of miR expression level in undifferentiated ESCs (WT ES) and differentiated ESCs (WT EB D7). C) H3K4 tri-methylation in ESCs is shown at various time points indicated as: day 0 (Blue), 3 (Red), and 7 (Green). D) H3K9 tri-methylation in ESCs is shown at various time points indicated as: day 0 (Blue), 3 (Red), and 7 (Green). E) H3K27 tri-methylation in ESCs is shown at various time points indicated as: day 0 (Blue), 3 (Red), and 7 (Green). F) H3K79 tri-methylation in ESCs is shown at various time points indicated as: day 0 (Blue), 3 (Red), and 7 (Green). Vertical axis indicates relative amount of DNA.

Techniques Used: Chromatin Immunoprecipitation, Polymerase Chain Reaction, Microarray, Expressing, Methylation

52) Product Images from "Combination of IAP Antagonists and TNF-α-Armed Oncolytic Viruses Induce Tumor Vascular Shutdown and Tumor Regression"

Article Title: Combination of IAP Antagonists and TNF-α-Armed Oncolytic Viruses Induce Tumor Vascular Shutdown and Tumor Regression

Journal: Molecular Therapy Oncolytics

doi: 10.1016/j.omto.2018.06.002

Combination Treatment of SMC and TNF-α-Armed Oncolytic VSV Induces Vascular Shutdown and Tumor Cell Death (A) EMT6-bearing mice were treated with vehicle or 50 mg/kg of the SMC LCL161 orally and PBS or 1 × 10 7 PFU of VSVΔ51-TNF-α intratumorally for 24 hr and injected with fluorescent microspheres (i.v.) for 5 min. Tumor sections were scanned using the Agilent Technologies DNA microarray scanner. Scale bar, 200 μm. (B) Quantification of perfused microspheres described in (A). One-way ANOVA, *p
Figure Legend Snippet: Combination Treatment of SMC and TNF-α-Armed Oncolytic VSV Induces Vascular Shutdown and Tumor Cell Death (A) EMT6-bearing mice were treated with vehicle or 50 mg/kg of the SMC LCL161 orally and PBS or 1 × 10 7 PFU of VSVΔ51-TNF-α intratumorally for 24 hr and injected with fluorescent microspheres (i.v.) for 5 min. Tumor sections were scanned using the Agilent Technologies DNA microarray scanner. Scale bar, 200 μm. (B) Quantification of perfused microspheres described in (A). One-way ANOVA, *p

Techniques Used: Mouse Assay, Injection, Microarray

53) Product Images from "Genome-wide transcriptomic analysis of the effects of sub-ambient atmospheric oxygen and elevated atmospheric carbon dioxide levels on gametophytes of the moss, Physcomitrella patens"

Article Title: Genome-wide transcriptomic analysis of the effects of sub-ambient atmospheric oxygen and elevated atmospheric carbon dioxide levels on gametophytes of the moss, Physcomitrella patens

Journal: Journal of Experimental Botany

doi: 10.1093/jxb/erv197

RT-PCR validation of microarray data. RNA was extracted from gametophytes and semi-quantitative RT-PCR was performed using primers designed to amplify a selection of genes identified as being differentially expressed in microarray experiments under conditions of sub-ambient O 2 , elevated CO 2 , and low O 2 –high CO 2 . The corresponding fold-change as identified from microarray experiments is indicated below each gel band. Amplified DNA was run on a 1% (w/v) agarose gel and stained with ethidium bromide before visualization under UV illumination. Images shown are representative of three independent biological replicates.
Figure Legend Snippet: RT-PCR validation of microarray data. RNA was extracted from gametophytes and semi-quantitative RT-PCR was performed using primers designed to amplify a selection of genes identified as being differentially expressed in microarray experiments under conditions of sub-ambient O 2 , elevated CO 2 , and low O 2 –high CO 2 . The corresponding fold-change as identified from microarray experiments is indicated below each gel band. Amplified DNA was run on a 1% (w/v) agarose gel and stained with ethidium bromide before visualization under UV illumination. Images shown are representative of three independent biological replicates.

Techniques Used: Reverse Transcription Polymerase Chain Reaction, Microarray, Quantitative RT-PCR, Selection, Amplification, Agarose Gel Electrophoresis, Staining

54) Product Images from "Transcriptional profiling of the effect of lipopolysaccharide (LPS) pretreatment in blood from probiotics-treated dairy cows"

Article Title: Transcriptional profiling of the effect of lipopolysaccharide (LPS) pretreatment in blood from probiotics-treated dairy cows

Journal: Genomics Data

doi: 10.1016/j.gdata.2016.08.016

Microarray analysis in lipopolysaccharide treated blood from cows orally administered with probiotics for 60 days. The DNA microarray experiment was performed using the Agilent Bovine v2 4x44K gene expression microarray slides. Raw and normalized average data from the microarray analysis are available at NCBI GEO repository under the accession number: GSE75240 .
Figure Legend Snippet: Microarray analysis in lipopolysaccharide treated blood from cows orally administered with probiotics for 60 days. The DNA microarray experiment was performed using the Agilent Bovine v2 4x44K gene expression microarray slides. Raw and normalized average data from the microarray analysis are available at NCBI GEO repository under the accession number: GSE75240 .

Techniques Used: Microarray, Expressing

55) Product Images from "Genome-Wide Responses of the Model Archaeon Halobacterium sp. Strain NRC-1 to Oxygen Limitation"

Article Title: Genome-Wide Responses of the Model Archaeon Halobacterium sp. Strain NRC-1 to Oxygen Limitation

Journal: Journal of Bacteriology

doi: 10.1128/JB.01153-12

Genome-wide transcriptomic data comparing Halobacterium sp. NRC-1 grown (A) aerobically ( y axis) versus anaerobically with arginine ( x axis) or (B) anaerobically with TMAO ( y axis) versus arginine ( x axis). DNA microarray data (fluorescence units) were
Figure Legend Snippet: Genome-wide transcriptomic data comparing Halobacterium sp. NRC-1 grown (A) aerobically ( y axis) versus anaerobically with arginine ( x axis) or (B) anaerobically with TMAO ( y axis) versus arginine ( x axis). DNA microarray data (fluorescence units) were

Techniques Used: Genome Wide, Microarray, Fluorescence

56) Product Images from "In-Depth Investigation of Archival and Prospectively Collected Samples Reveals No Evidence for XMRV Infection in Prostate Cancer"

Article Title: In-Depth Investigation of Archival and Prospectively Collected Samples Reveals No Evidence for XMRV Infection in Prostate Cancer

Journal: PLoS ONE

doi: 10.1371/journal.pone.0044954

Detection of XMRV in Prostate Cancer Tissues and Archival RNA Extracts by Microarray. Samples were analyzed using the ViroChip, a pan-viral DNA detection microarray (x-axis). The heat map shows a selected cluster consisting of 96 gammaretrovirus probes (y-axis) and corresponding to the same cluster observed in the 2006 study by Urisman, et al [1] . The red color saturation indicates the normalized magnitude of hybridization intensity. Microarrays corresponding to key samples are highlighted (arrows). Only prostate cancer samples VP35 and VP42 were found to be consistently positive for XMRV from both total and polyA RNA [1] .
Figure Legend Snippet: Detection of XMRV in Prostate Cancer Tissues and Archival RNA Extracts by Microarray. Samples were analyzed using the ViroChip, a pan-viral DNA detection microarray (x-axis). The heat map shows a selected cluster consisting of 96 gammaretrovirus probes (y-axis) and corresponding to the same cluster observed in the 2006 study by Urisman, et al [1] . The red color saturation indicates the normalized magnitude of hybridization intensity. Microarrays corresponding to key samples are highlighted (arrows). Only prostate cancer samples VP35 and VP42 were found to be consistently positive for XMRV from both total and polyA RNA [1] .

Techniques Used: Microarray, Hybridization

57) Product Images from "Discovery and Characterization of Novel Vascular and Hematopoietic Genes Downstream of Etsrp in Zebrafish"

Article Title: Discovery and Characterization of Novel Vascular and Hematopoietic Genes Downstream of Etsrp in Zebrafish

Journal: PLoS ONE

doi: 10.1371/journal.pone.0004994

Ectopic induction of microarray identified genes by etsrp overexpression. Ectopic gene expression was examined at 80% epiboly to tailbud stages in flk1:gfp transgenic embryos injected with 30 pg etsrp -mcherry DNA at the one cell stage. Embryos exhibiting both red and green fluorescence were selected for analysis. Representative control embryos are on the left and etsrp overexpressing (OE) embryos are on the right side of each panel. Represented genes: (A) krml2 ; (B) yrk ; (C) lrrp33 ; (D) similar to hemicentin ; (E) hapln1b ; (F) sh3gl3 ; (G) rasgrp3 ; (H) similar to costimulatory protein ; (I) tem8 ; (J) ldb2 ; (K) arhgap23 ; (L) est:AI721944 ; (M) fgd5 ; and (N) est:AW019729 . Note that there is a low level of endogenous expression in the control embryos for the two EST's, L and N, at the polster (arrows). Ratios in bottom right hand corner in panels represent the number of embryos with ectopic induction of total embryos processed and scored in the injected groups; control embryos never displayed ectopic induction. All embryos are in lateral view, and those at tail bud stage are oriented with anterior to the left. Scale bar: 250 µm.
Figure Legend Snippet: Ectopic induction of microarray identified genes by etsrp overexpression. Ectopic gene expression was examined at 80% epiboly to tailbud stages in flk1:gfp transgenic embryos injected with 30 pg etsrp -mcherry DNA at the one cell stage. Embryos exhibiting both red and green fluorescence were selected for analysis. Representative control embryos are on the left and etsrp overexpressing (OE) embryos are on the right side of each panel. Represented genes: (A) krml2 ; (B) yrk ; (C) lrrp33 ; (D) similar to hemicentin ; (E) hapln1b ; (F) sh3gl3 ; (G) rasgrp3 ; (H) similar to costimulatory protein ; (I) tem8 ; (J) ldb2 ; (K) arhgap23 ; (L) est:AI721944 ; (M) fgd5 ; and (N) est:AW019729 . Note that there is a low level of endogenous expression in the control embryos for the two EST's, L and N, at the polster (arrows). Ratios in bottom right hand corner in panels represent the number of embryos with ectopic induction of total embryos processed and scored in the injected groups; control embryos never displayed ectopic induction. All embryos are in lateral view, and those at tail bud stage are oriented with anterior to the left. Scale bar: 250 µm.

Techniques Used: Microarray, Over Expression, Expressing, Transgenic Assay, Injection, Fluorescence

58) Product Images from "Novel DNA Microarray System for Analysis of Nascent mRNAs"

Article Title: Novel DNA Microarray System for Analysis of Nascent mRNAs

Journal: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes

doi: 10.1093/dnares/dsn015

DNA microarray analyses of nascent RNAs. ( A ) FT210 cells were synchronized in the G 2 phase by incubation at 39 °C for 17 h. Cell cycle profiles of asynchronous cells and G 2 -arrested cells were analyzed by propidium iodide staining and flow cytometry. ( B ) Scatter plots comparing the expression profiles of asynchronous cells with those of G 2 -arrested cells in a nascent RNA profile (left panel) and a steady-state RNA profile (right panel). ( C ) The Venn diagrams show the overlap of genes whose expression levels changed more than twofold in the nascent RNA profile and the steady-state RNA profile.
Figure Legend Snippet: DNA microarray analyses of nascent RNAs. ( A ) FT210 cells were synchronized in the G 2 phase by incubation at 39 °C for 17 h. Cell cycle profiles of asynchronous cells and G 2 -arrested cells were analyzed by propidium iodide staining and flow cytometry. ( B ) Scatter plots comparing the expression profiles of asynchronous cells with those of G 2 -arrested cells in a nascent RNA profile (left panel) and a steady-state RNA profile (right panel). ( C ) The Venn diagrams show the overlap of genes whose expression levels changed more than twofold in the nascent RNA profile and the steady-state RNA profile.

Techniques Used: Microarray, Incubation, Staining, Flow Cytometry, Cytometry, Expressing

( A ) Eluted RNAs were converted to cDNA, and cDNA was amplified by TS-PCR. ( B ) Validation with quantitative RT–PCR of the DNA microarray data using each amplification method. Genes expressed at various levels in the non-amplification method, TS-PCR amplification method, and T7 in vitro transcription (IVT) amplification method were confirmed using quantitative RT–PCR. Quantitative RT–PCR was performed using the total RNA of these transcription factors. Gapd was used as the control. The same total RNA was used for quantitative RT–PCR and DNA microarray experiments. The ratio of the total target RNA levels was normalized by using those of the Tbp ( Mus musculus TATA box binding protein) gene, and the fold change for each gene in the differentiated ES cells compared to the control ES cells was calculated. Error bars represent standard deviations of log (base 2) of ratio. ( C ) Amplified cDNA labeled with Cy3/Cy5 underwent self-self hybridization.
Figure Legend Snippet: ( A ) Eluted RNAs were converted to cDNA, and cDNA was amplified by TS-PCR. ( B ) Validation with quantitative RT–PCR of the DNA microarray data using each amplification method. Genes expressed at various levels in the non-amplification method, TS-PCR amplification method, and T7 in vitro transcription (IVT) amplification method were confirmed using quantitative RT–PCR. Quantitative RT–PCR was performed using the total RNA of these transcription factors. Gapd was used as the control. The same total RNA was used for quantitative RT–PCR and DNA microarray experiments. The ratio of the total target RNA levels was normalized by using those of the Tbp ( Mus musculus TATA box binding protein) gene, and the fold change for each gene in the differentiated ES cells compared to the control ES cells was calculated. Error bars represent standard deviations of log (base 2) of ratio. ( C ) Amplified cDNA labeled with Cy3/Cy5 underwent self-self hybridization.

Techniques Used: Amplification, Polymerase Chain Reaction, Quantitative RT-PCR, Microarray, In Vitro, Binding Assay, Labeling, Hybridization

59) Product Images from "Limited genetic diversity in Salmonella enterica Serovar Enteritidis PT13"

Article Title: Limited genetic diversity in Salmonella enterica Serovar Enteritidis PT13

Journal: BMC Microbiology

doi: 10.1186/1471-2180-7-87

DNA microarray-based comparative genomics of S . Enteritidis PT13. Array probes represent the linear order of S . Typhimurium LT2 coding sequences from left to right, with the custom Salmonella genomic island 1 (SGI1) at the far-left side. White denotes similarity to LT2, green denotes putative divergence and red represents putative duplication or copy number change. Clusters of bacteriophage-related determinants that are divergent in S . Enteritidis compared to S . Typhimurium: A, STM893–929 (Fels-1 prophage); B, STM1005–1024 (Gifsy-2 prophage); C, STM2230–2240 (putative phage); D, STM2589–2636 (Gifsy-1 prophage); E, STM2732–2772 (Fels-2 prophage); F, STM4198–4218 (putative phage).
Figure Legend Snippet: DNA microarray-based comparative genomics of S . Enteritidis PT13. Array probes represent the linear order of S . Typhimurium LT2 coding sequences from left to right, with the custom Salmonella genomic island 1 (SGI1) at the far-left side. White denotes similarity to LT2, green denotes putative divergence and red represents putative duplication or copy number change. Clusters of bacteriophage-related determinants that are divergent in S . Enteritidis compared to S . Typhimurium: A, STM893–929 (Fels-1 prophage); B, STM1005–1024 (Gifsy-2 prophage); C, STM2230–2240 (putative phage); D, STM2589–2636 (Gifsy-1 prophage); E, STM2732–2772 (Fels-2 prophage); F, STM4198–4218 (putative phage).

Techniques Used: Microarray

Related Articles

Centrifugation:

Article Title: Transcription factor DUO1 generated by neo-functionalization is associated with evolution of sperm differentiation in plants
Article Snippet: .. The slide was spun dry by centrifugation (1 min at 500 rpm) and scanned at 2 μm resolution in a Agilent’s DNA Microarray Scanner for monitoring the amount of dsDNA. .. The binding mixture obtained from cleared bacterial lysates was adjusted to 175 μl and to contain 2% milk and 0.89 μg of denatured salmon sperm DNA (ssDNA).

Article Title: Transcription factor DUO1 generated by neo-functionalization is associated with evolution of sperm differentiation in plants
Article Snippet: Slides were then washed three times PBS-1% Tween 20 (5 min), three times in PBS-0.01% Triton X-100 (5 min) and spun dry by centrifugation. .. DNA microarrays were scanned in a DNA Microarray Scanner at 2-μm resolution and quantified with Feature Extraction 9.0 software (Agilent Technologies).

Amplification:

Article Title: Size effects of single-walled carbon nanotubes on in vivo and in vitro pulmonary toxicity
Article Snippet: Cyanine-3-labeled cRNA was prepared from RNA using the One-Color Low RNA Input Linear Amplification PLUS Kit (Agilent Technologies, Santa Clara, CA), according to the instructions of the manufacturer, followed by RNeasy column purification (Qiagen, Tokyo, Japan). .. Each labeled cRNA probe was used separately for hybridization to a 4 × 44 K Whole Rat Genome Microarray Kit (G4131F; Agilent Technologies, Santa Clara, CA), and hybridization was performed at 65 °C for 17 h. Hybridized microarray slides were washed according to the instructions of the manufacturer and were scanned with an Agilent DNA Microarray Scanner (G2565BA; Agilent Technologies, Santa Clara, CA) at 5-μm resolution.

Article Title: Enrichment of Pluripotent Stem Cell-Derived Hepatocyte-Like Cells by Ammonia Treatment
Article Snippet: DNA microarray Total RNA was amplified and labeled with Cy3 using Agilent Low Input Quick Amp Labeling Kit, one-color (Agilent Technologies, Palo Alto, CA). .. For each hybridization reaction, 1.65 μg of fragmented Cy3-labeled cRNA was incubated with an Agilent Human GE 8x60K Microarray (Design ID: 028004) at 65°C for 17 h. Washed microarrays were scanned using an Agilent DNA microarray scanner.

Article Title: Fibrogenic Activity of MECP2 Is Regulated by Phosphorylation in Hepatic Stellate Cells
Article Snippet: Each sample was amplified and transcribed into fluorescent complementary RNA along the entire length of the transcripts without 3′ bias by using a random priming method. .. After the slides were washed, the arrays were scanned by the Agilent DNA Microarray Scanner (part no. G2505C).

Article Title: Status of hepatic DNA methylome predetermines and modulates the severity of non-alcoholic fatty liver injury in mice
Article Snippet: Amplified immunoprecipitated DNA and input DNA samples were labeled with cyanine 3-dUTP and cyanine 5-dUTP, respectively, using an Agilent Genomic DNA Labeling Kit Plus (Agilent Technologies, Santa Clara, CA, USA). .. Microarrays were scanned on an Agilent DNA microarray scanner and the resulting images were analyzed with Agilent Feature Extraction Software (Version 10.7.3).

Whole Genome Amplification:

Article Title: Status of hepatic DNA methylome predetermines and modulates the severity of non-alcoholic fatty liver injury in mice
Article Snippet: Sheared by sonication and purified, immunoprecipitated DNA and input DNA were amplified by a GenomePlex® Complete Whole Genome Amplification kit (Sigma-Aldrich, St. Louis, MO, USA). .. Microarrays were scanned on an Agilent DNA microarray scanner and the resulting images were analyzed with Agilent Feature Extraction Software (Version 10.7.3).

Positive Control:

Article Title: Reprogramming Human Endothelial to Hematopoietic Cells Requires Vascular Induction
Article Snippet: As a positive control of chromosomal rearrangements we used a CGH array of a leukemic cell line with a duplication of the chromosome 7 and a deletion of the chromosome 10. .. The arrays were scanned in an Agilent DNA microarray scanner and obtained data was visualized using Feature Extraction software (version 10.7; Agilent).

Synthesized:

Article Title: Transcription factor DUO1 generated by neo-functionalization is associated with evolution of sperm differentiation in plants
Article Snippet: Second strand of DNA was synthesized in a primer extension reaction with 32 U Thermo Sequenase Polymerase (USB), 163 μM dNTPs, 1.63 μM Cy5-dUTP (GE Healthcare) and 1.17 μM oligonucleotide primer (5′-CAGCACGGACAACGGAACACAGAC-3′) in a 900 μl total volume reaction. .. The slide was spun dry by centrifugation (1 min at 500 rpm) and scanned at 2 μm resolution in a Agilent’s DNA Microarray Scanner for monitoring the amount of dsDNA.

Article Title: Transcription factor DUO1 generated by neo-functionalization is associated with evolution of sperm differentiation in plants
Article Snippet: We used the nPBM11 design containing 167,773 different oligonucleotide probes synthesized in an Agilent’s SurePrint G3 4 × 180k format (Agilent Technologies). .. DNA microarrays were scanned in a DNA Microarray Scanner at 2-μm resolution and quantified with Feature Extraction 9.0 software (Agilent Technologies).

Construct:

Article Title: Transcription factor DUO1 generated by neo-functionalization is associated with evolution of sperm differentiation in plants
Article Snippet: Pellets corresponding to 25 ml of induced E. coli culture for each construct were stored at −80 °C and resuspended in 1 ml 1× binding buffer prior to DNA-binding assay . .. The slide was spun dry by centrifugation (1 min at 500 rpm) and scanned at 2 μm resolution in a Agilent’s DNA Microarray Scanner for monitoring the amount of dsDNA.

DNA Binding Assay:

Article Title: Transcription factor DUO1 generated by neo-functionalization is associated with evolution of sperm differentiation in plants
Article Snippet: Pellets corresponding to 25 ml of induced E. coli culture for each construct were stored at −80 °C and resuspended in 1 ml 1× binding buffer prior to DNA-binding assay . .. The slide was spun dry by centrifugation (1 min at 500 rpm) and scanned at 2 μm resolution in a Agilent’s DNA Microarray Scanner for monitoring the amount of dsDNA.

Microarray:

Article Title: The FOXG1/FOXO/SMAD network balances proliferation and differentiation of cortical progenitors and activates Kcnh3 expression in mature neurons
Article Snippet: .. Cy3 intensities were detected by one-color scanning using an “Agilent DNA Microarray Scanner (G250B)” at 5 μm resolution. .. Microarray data analysis Intensity data were extracted using Agilent's Feature Extraction (FE) software (version 9.5.3.1) including a quality control based on internal controls using Agilent's protocol GE1107 Sep09.

Article Title: Transcription factor DUO1 generated by neo-functionalization is associated with evolution of sperm differentiation in plants
Article Snippet: .. The slide was spun dry by centrifugation (1 min at 500 rpm) and scanned at 2 μm resolution in a Agilent’s DNA Microarray Scanner for monitoring the amount of dsDNA. .. The binding mixture obtained from cleared bacterial lysates was adjusted to 175 μl and to contain 2% milk and 0.89 μg of denatured salmon sperm DNA (ssDNA).

Article Title: Size effects of single-walled carbon nanotubes on in vivo and in vitro pulmonary toxicity
Article Snippet: .. Each labeled cRNA probe was used separately for hybridization to a 4 × 44 K Whole Rat Genome Microarray Kit (G4131F; Agilent Technologies, Santa Clara, CA), and hybridization was performed at 65 °C for 17 h. Hybridized microarray slides were washed according to the instructions of the manufacturer and were scanned with an Agilent DNA Microarray Scanner (G2565BA; Agilent Technologies, Santa Clara, CA) at 5-μm resolution. .. The scanned images were analyzed numerically using Agilent Feature Extraction Software, version 10.7.3.1 (Agilent Technologies, Santa Clara, CA).

Article Title: Status of hepatic DNA methylome predetermines and modulates the severity of non-alcoholic fatty liver injury in mice
Article Snippet: .. Microarrays were scanned on an Agilent DNA microarray scanner and the resulting images were analyzed with Agilent Feature Extraction Software (Version 10.7.3). .. The combined Z-score for each probe was calculated with Agilent Genomic Workbench Light (Version 6.0).

Article Title: Enrichment of Pluripotent Stem Cell-Derived Hepatocyte-Like Cells by Ammonia Treatment
Article Snippet: .. For each hybridization reaction, 1.65 μg of fragmented Cy3-labeled cRNA was incubated with an Agilent Human GE 8x60K Microarray (Design ID: 028004) at 65°C for 17 h. Washed microarrays were scanned using an Agilent DNA microarray scanner. .. Data analysis of microarray Intensity values of each scanned feature were quantified using Agilent feature extraction software version 10.7.3.1.

Article Title: Reprogramming Human Endothelial to Hematopoietic Cells Requires Vascular Induction
Article Snippet: .. The arrays were scanned in an Agilent DNA microarray scanner and obtained data was visualized using Feature Extraction software (version 10.7; Agilent). .. Differentiation and reprogramming of human embryonic stem cells (hES) We used a transgenic hES reporter line that specifically identifies differentiated EC derivatives via a fluorescent reporter driven by a fragment of the human VE-cadherin promoter , .

Article Title: Transcriptome Analysis Using a High-Density Oligomicroarray under Drought Stress in Various Genotypes of Cassava: An Important Tropical Crop
Article Snippet: .. Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4 × 44 K array slides. .. Signal intensities were detected from the obtained digital images using Feature Extraction software (Ver.

Article Title: Transcription factor DUO1 generated by neo-functionalization is associated with evolution of sperm differentiation in plants
Article Snippet: .. DNA microarrays were scanned in a DNA Microarray Scanner at 2-μm resolution and quantified with Feature Extraction 9.0 software (Agilent Technologies). ..

Article Title: Fibrogenic Activity of MECP2 Is Regulated by Phosphorylation in Hepatic Stellate Cells
Article Snippet: .. After the slides were washed, the arrays were scanned by the Agilent DNA Microarray Scanner (part no. G2505C). .. The acquired array images were analyzed by Agilent Feature Extraction software, version 11.0.1.1.

Article Title: In Silico Enhanced Restriction Enzyme Based Methylation Analysis of the Human Glioblastoma Genome Using Agilent 244K CpG Island Microarrays
Article Snippet: .. Data analysis Hybridized microarrays were scanned with an Agilent DNA Microarray Scanner (UCLA Microarray Core) to create an image file. .. From this file, Cy-5 (HpaII digested) and Cy-3 (MspI digested) intensities for each probe were determined by the Agilent Feature Extraction 9.1 software using the CGH protocol v4.95 Feb07 (Agilent Technologies).

Incubation:

Article Title: Transcription factor DUO1 generated by neo-functionalization is associated with evolution of sperm differentiation in plants
Article Snippet: The slide was then rapidly transferred to wash solution (1× PBS, 0.01% Triton X-100), incubated at 37 °C for 10 min with agitation and rinsed in 1× Phosphate Buffered Saline (PBS) for 3 min at room temperature. .. The slide was spun dry by centrifugation (1 min at 500 rpm) and scanned at 2 μm resolution in a Agilent’s DNA Microarray Scanner for monitoring the amount of dsDNA.

Article Title: Size effects of single-walled carbon nanotubes on in vivo and in vitro pulmonary toxicity
Article Snippet: Cells incubated in the presence or absence of CNT-1 or CNT-2 (n = 4) were collected, and the total RNA was extracted from the cells using the RNeasy Mini Kit (Qiagen, Tokyo, Japan), following the instructions of the manufacturer. .. Each labeled cRNA probe was used separately for hybridization to a 4 × 44 K Whole Rat Genome Microarray Kit (G4131F; Agilent Technologies, Santa Clara, CA), and hybridization was performed at 65 °C for 17 h. Hybridized microarray slides were washed according to the instructions of the manufacturer and were scanned with an Agilent DNA Microarray Scanner (G2565BA; Agilent Technologies, Santa Clara, CA) at 5-μm resolution.

Article Title: Enrichment of Pluripotent Stem Cell-Derived Hepatocyte-Like Cells by Ammonia Treatment
Article Snippet: .. For each hybridization reaction, 1.65 μg of fragmented Cy3-labeled cRNA was incubated with an Agilent Human GE 8x60K Microarray (Design ID: 028004) at 65°C for 17 h. Washed microarrays were scanned using an Agilent DNA microarray scanner. .. Data analysis of microarray Intensity values of each scanned feature were quantified using Agilent feature extraction software version 10.7.3.1.

Article Title: Transcription factor DUO1 generated by neo-functionalization is associated with evolution of sperm differentiation in plants
Article Snippet: DNA–protein complexes were incubated with 16 μg of Rabbit polyclonal to Maltose Binding Protein (Abcam) in PBS-2% milk for 16 h at room temperature. .. DNA microarrays were scanned in a DNA Microarray Scanner at 2-μm resolution and quantified with Feature Extraction 9.0 software (Agilent Technologies).

Expressing:

Article Title: The FOXG1/FOXO/SMAD network balances proliferation and differentiation of cortical progenitors and activates Kcnh3 expression in mature neurons
Article Snippet: Paragraph title: Gene expression profiling ... Cy3 intensities were detected by one-color scanning using an “Agilent DNA Microarray Scanner (G250B)” at 5 μm resolution.

Modification:

Article Title: Transcription factor DUO1 generated by neo-functionalization is associated with evolution of sperm differentiation in plants
Article Snippet: DNA microarrays were scanned in a DNA Microarray Scanner at 2-μm resolution and quantified with Feature Extraction 9.0 software (Agilent Technologies). .. Perl scripts were modified to adapt them to nPBM11 microarray dimensions and to input files generated by Feature Extraction software.

Hybridization:

Article Title: Transcription factor DUO1 generated by neo-functionalization is associated with evolution of sperm differentiation in plants
Article Snippet: DNA microarray was incubated with the mixture in a hybridization oven for 10 min at 85 °C, the temperature gradually reduced up to 60 °C during 30 min and hold at this temperature for 90 min. .. The slide was spun dry by centrifugation (1 min at 500 rpm) and scanned at 2 μm resolution in a Agilent’s DNA Microarray Scanner for monitoring the amount of dsDNA.

Article Title: Size effects of single-walled carbon nanotubes on in vivo and in vitro pulmonary toxicity
Article Snippet: .. Each labeled cRNA probe was used separately for hybridization to a 4 × 44 K Whole Rat Genome Microarray Kit (G4131F; Agilent Technologies, Santa Clara, CA), and hybridization was performed at 65 °C for 17 h. Hybridized microarray slides were washed according to the instructions of the manufacturer and were scanned with an Agilent DNA Microarray Scanner (G2565BA; Agilent Technologies, Santa Clara, CA) at 5-μm resolution. .. The scanned images were analyzed numerically using Agilent Feature Extraction Software, version 10.7.3.1 (Agilent Technologies, Santa Clara, CA).

Article Title: Enrichment of Pluripotent Stem Cell-Derived Hepatocyte-Like Cells by Ammonia Treatment
Article Snippet: .. For each hybridization reaction, 1.65 μg of fragmented Cy3-labeled cRNA was incubated with an Agilent Human GE 8x60K Microarray (Design ID: 028004) at 65°C for 17 h. Washed microarrays were scanned using an Agilent DNA microarray scanner. .. Data analysis of microarray Intensity values of each scanned feature were quantified using Agilent feature extraction software version 10.7.3.1.

Article Title: Reprogramming Human Endothelial to Hematopoietic Cells Requires Vascular Induction
Article Snippet: Paragraph title: Comparative Genomic Hybridization (CGH) ... The arrays were scanned in an Agilent DNA microarray scanner and obtained data was visualized using Feature Extraction software (version 10.7; Agilent).

Article Title: Transcriptome Analysis Using a High-Density Oligomicroarray under Drought Stress in Various Genotypes of Cassava: An Important Tropical Crop
Article Snippet: Paragraph title: Microarray hybridization ... Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4 × 44 K array slides.

Article Title: Fibrogenic Activity of MECP2 Is Regulated by Phosphorylation in Hepatic Stellate Cells
Article Snippet: The labeled complementary RNAs were purified, and 1 μg of each labeled complementary RNA was hybridized onto the Mouse LncRNA Array v2.0 (8 × 60,000, Arraystar) for 17 hours at 65°C in an Agilent (Santa Clara, CA) Hybridization Oven. .. After the slides were washed, the arrays were scanned by the Agilent DNA Microarray Scanner (part no. G2505C).

Generated:

Article Title: Transcription factor DUO1 generated by neo-functionalization is associated with evolution of sperm differentiation in plants
Article Snippet: DNA microarrays were scanned in a DNA Microarray Scanner at 2-μm resolution and quantified with Feature Extraction 9.0 software (Agilent Technologies). .. Perl scripts were modified to adapt them to nPBM11 microarray dimensions and to input files generated by Feature Extraction software.

DNA Labeling:

Article Title: Status of hepatic DNA methylome predetermines and modulates the severity of non-alcoholic fatty liver injury in mice
Article Snippet: Immunoprecipitated DNA and input DNA samples were labeled with cyanine 3-dUTP and cyanine 5-dUTP, respectively, using an Agilent Genomic DNA Labeling Kit Plus (Agilent Technologies, Santa Clara, CA, USA). .. Microarrays were scanned on an Agilent DNA microarray scanner and the resulting images were analyzed with Agilent Feature Extraction Software (Version 10.7.3).

Sonication:

Article Title: Transcription factor DUO1 generated by neo-functionalization is associated with evolution of sperm differentiation in plants
Article Snippet: Bacterial lysates were sonicated twice for 30 s, and centrifuged twice at 20,000× g to obtain cleared extracts of soluble proteins. .. The slide was spun dry by centrifugation (1 min at 500 rpm) and scanned at 2 μm resolution in a Agilent’s DNA Microarray Scanner for monitoring the amount of dsDNA.

Article Title: Status of hepatic DNA methylome predetermines and modulates the severity of non-alcoholic fatty liver injury in mice
Article Snippet: Sheared by sonication and purified, immunoprecipitated DNA and input DNA were amplified by a GenomePlex® Complete Whole Genome Amplification kit (Sigma-Aldrich, St. Louis, MO, USA). .. Microarrays were scanned on an Agilent DNA microarray scanner and the resulting images were analyzed with Agilent Feature Extraction Software (Version 10.7.3).

Binding Assay:

Article Title: Transcription factor DUO1 generated by neo-functionalization is associated with evolution of sperm differentiation in plants
Article Snippet: Pellets corresponding to 25 ml of induced E. coli culture for each construct were stored at −80 °C and resuspended in 1 ml 1× binding buffer prior to DNA-binding assay . .. The slide was spun dry by centrifugation (1 min at 500 rpm) and scanned at 2 μm resolution in a Agilent’s DNA Microarray Scanner for monitoring the amount of dsDNA.

Article Title: Transcription factor DUO1 generated by neo-functionalization is associated with evolution of sperm differentiation in plants
Article Snippet: DNA–protein complexes were incubated with 16 μg of Rabbit polyclonal to Maltose Binding Protein (Abcam) in PBS-2% milk for 16 h at room temperature. .. DNA microarrays were scanned in a DNA Microarray Scanner at 2-μm resolution and quantified with Feature Extraction 9.0 software (Agilent Technologies).

Methylated DNA Immunoprecipitation:

Article Title: Status of hepatic DNA methylome predetermines and modulates the severity of non-alcoholic fatty liver injury in mice
Article Snippet: All DNA samples from control and CFD diet-fed A/J and WSB/EiJ mice in the MeDIP microarray experiment were processed simultaneously. .. Microarrays were scanned on an Agilent DNA microarray scanner and the resulting images were analyzed with Agilent Feature Extraction Software (Version 10.7.3).

DNA Extraction:

Article Title: Reprogramming Human Endothelial to Hematopoietic Cells Requires Vascular Induction
Article Snippet: Before DNA extraction, CD45+ CD34+ rEC-hMPPs sorted from the BM were expanded for 72 hours in vitro . .. The arrays were scanned in an Agilent DNA microarray scanner and obtained data was visualized using Feature Extraction software (version 10.7; Agilent).

Methylation:

Article Title: Status of hepatic DNA methylome predetermines and modulates the severity of non-alcoholic fatty liver injury in mice
Article Snippet: Paragraph title: Methylated DNA immunoprecipitation microarray analysis ... Microarrays were scanned on an Agilent DNA microarray scanner and the resulting images were analyzed with Agilent Feature Extraction Software (Version 10.7.3).

Isolation:

Article Title: Fibrogenic Activity of MECP2 Is Regulated by Phosphorylation in Hepatic Stellate Cells
Article Snippet: Microarray and Computational Analysis RNA was purified from total RNA after removal of ribosomal RNA (mRNA-ONLY Eukaryotic mRNA Isolation Kit; Epicentre Bio, Madison, WI). .. After the slides were washed, the arrays were scanned by the Agilent DNA Microarray Scanner (part no. G2505C).

Labeling:

Article Title: Size effects of single-walled carbon nanotubes on in vivo and in vitro pulmonary toxicity
Article Snippet: .. Each labeled cRNA probe was used separately for hybridization to a 4 × 44 K Whole Rat Genome Microarray Kit (G4131F; Agilent Technologies, Santa Clara, CA), and hybridization was performed at 65 °C for 17 h. Hybridized microarray slides were washed according to the instructions of the manufacturer and were scanned with an Agilent DNA Microarray Scanner (G2565BA; Agilent Technologies, Santa Clara, CA) at 5-μm resolution. .. The scanned images were analyzed numerically using Agilent Feature Extraction Software, version 10.7.3.1 (Agilent Technologies, Santa Clara, CA).

Article Title: Status of hepatic DNA methylome predetermines and modulates the severity of non-alcoholic fatty liver injury in mice
Article Snippet: The labeled immunoprecipitated DNA and input DNA were co-hybridized to Agilent Mouse 2 × 105 K CpG Island Microarrays, containing ~97,652 oligonucleotide probes covering 16,030 CpG islands, according to the manufacturer’s protocol. .. Microarrays were scanned on an Agilent DNA microarray scanner and the resulting images were analyzed with Agilent Feature Extraction Software (Version 10.7.3).

Article Title: Enrichment of Pluripotent Stem Cell-Derived Hepatocyte-Like Cells by Ammonia Treatment
Article Snippet: DNA microarray Total RNA was amplified and labeled with Cy3 using Agilent Low Input Quick Amp Labeling Kit, one-color (Agilent Technologies, Palo Alto, CA). .. For each hybridization reaction, 1.65 μg of fragmented Cy3-labeled cRNA was incubated with an Agilent Human GE 8x60K Microarray (Design ID: 028004) at 65°C for 17 h. Washed microarrays were scanned using an Agilent DNA microarray scanner.

Article Title: Reprogramming Human Endothelial to Hematopoietic Cells Requires Vascular Induction
Article Snippet: Extracted DNA was digested, labeled by random priming and hybridized to the Agilent 1M CGH arrays. .. The arrays were scanned in an Agilent DNA microarray scanner and obtained data was visualized using Feature Extraction software (version 10.7; Agilent).

Article Title: Transcriptome Analysis Using a High-Density Oligomicroarray under Drought Stress in Various Genotypes of Cassava: An Important Tropical Crop
Article Snippet: Microarray hybridization Cyanine-3 (Cy3)-labeled cRNA was prepared from 0.5 μg of total RNA using the Quick Amp Labeling kit (Agilent Technologies) according to the manufacturer's instructions ( http://www.chem.agilent.com/Library/usermanuals/Public/G4140-90040_GeneExpression_One-color_v6.5.pdf ), followed by RNeasy column purification (Qiagen). .. Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4 × 44 K array slides.

Article Title: Transcription factor DUO1 generated by neo-functionalization is associated with evolution of sperm differentiation in plants
Article Snippet: Labeling of DNA–protein complexes were performed by incubating the microarrays with 0.4 μg of goat anti-rabbit IgG DyLight 549 conjugated (Pierce) in PBS-2% milk for 3 h at room temperature, followed by the same washes as before and the slides dried for scanning. .. DNA microarrays were scanned in a DNA Microarray Scanner at 2-μm resolution and quantified with Feature Extraction 9.0 software (Agilent Technologies).

Article Title: Fibrogenic Activity of MECP2 Is Regulated by Phosphorylation in Hepatic Stellate Cells
Article Snippet: The labeled complementary RNAs were purified, and 1 μg of each labeled complementary RNA was hybridized onto the Mouse LncRNA Array v2.0 (8 × 60,000, Arraystar) for 17 hours at 65°C in an Agilent (Santa Clara, CA) Hybridization Oven. .. After the slides were washed, the arrays were scanned by the Agilent DNA Microarray Scanner (part no. G2505C).

Purification:

Article Title: Size effects of single-walled carbon nanotubes on in vivo and in vitro pulmonary toxicity
Article Snippet: Cyanine-3-labeled cRNA was prepared from RNA using the One-Color Low RNA Input Linear Amplification PLUS Kit (Agilent Technologies, Santa Clara, CA), according to the instructions of the manufacturer, followed by RNeasy column purification (Qiagen, Tokyo, Japan). .. Each labeled cRNA probe was used separately for hybridization to a 4 × 44 K Whole Rat Genome Microarray Kit (G4131F; Agilent Technologies, Santa Clara, CA), and hybridization was performed at 65 °C for 17 h. Hybridized microarray slides were washed according to the instructions of the manufacturer and were scanned with an Agilent DNA Microarray Scanner (G2565BA; Agilent Technologies, Santa Clara, CA) at 5-μm resolution.

Article Title: Status of hepatic DNA methylome predetermines and modulates the severity of non-alcoholic fatty liver injury in mice
Article Snippet: The labeled DNA samples were purified using Amicon Ultra-0.5 30 kDa columns (Millipore, Billerica, MA, USA) and eluted with 22 μL of 10 mM Tris, 1 mM EDTA buffer, pH 8.0. .. Microarrays were scanned on an Agilent DNA microarray scanner and the resulting images were analyzed with Agilent Feature Extraction Software (Version 10.7.3).

Article Title: Transcriptome Analysis Using a High-Density Oligomicroarray under Drought Stress in Various Genotypes of Cassava: An Important Tropical Crop
Article Snippet: Microarray hybridization Cyanine-3 (Cy3)-labeled cRNA was prepared from 0.5 μg of total RNA using the Quick Amp Labeling kit (Agilent Technologies) according to the manufacturer's instructions ( http://www.chem.agilent.com/Library/usermanuals/Public/G4140-90040_GeneExpression_One-color_v6.5.pdf ), followed by RNeasy column purification (Qiagen). .. Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4 × 44 K array slides.

Article Title: Fibrogenic Activity of MECP2 Is Regulated by Phosphorylation in Hepatic Stellate Cells
Article Snippet: The labeled complementary RNAs were purified, and 1 μg of each labeled complementary RNA was hybridized onto the Mouse LncRNA Array v2.0 (8 × 60,000, Arraystar) for 17 hours at 65°C in an Agilent (Santa Clara, CA) Hybridization Oven. .. After the slides were washed, the arrays were scanned by the Agilent DNA Microarray Scanner (part no. G2505C).

Lysis:

Article Title: Size effects of single-walled carbon nanotubes on in vivo and in vitro pulmonary toxicity
Article Snippet: RNA extraction and DNA microarray experiments Right lungs (n = 4 per group per time point) were homogenized using the QIAzol Lysis Reagent and a TissueRuptor (Qiagen, Tokyo, Japan). .. Each labeled cRNA probe was used separately for hybridization to a 4 × 44 K Whole Rat Genome Microarray Kit (G4131F; Agilent Technologies, Santa Clara, CA), and hybridization was performed at 65 °C for 17 h. Hybridized microarray slides were washed according to the instructions of the manufacturer and were scanned with an Agilent DNA Microarray Scanner (G2565BA; Agilent Technologies, Santa Clara, CA) at 5-μm resolution.

Mouse Assay:

Article Title: The FOXG1/FOXO/SMAD network balances proliferation and differentiation of cortical progenitors and activates Kcnh3 expression in mature neurons
Article Snippet: Gene expression profiling Gene expression profiles of Foxg1−/− mice (n = 3) and wild-type control mice (n = 2) were analyzed using Agilent's Whole Mouse Genome Microarray (026655). .. Cy3 intensities were detected by one-color scanning using an “Agilent DNA Microarray Scanner (G250B)” at 5 μm resolution.

Article Title: Status of hepatic DNA methylome predetermines and modulates the severity of non-alcoholic fatty liver injury in mice
Article Snippet: All DNA samples from control and CFD diet-fed A/J and WSB/EiJ mice in the MeDIP microarray experiment were processed simultaneously. .. Microarrays were scanned on an Agilent DNA microarray scanner and the resulting images were analyzed with Agilent Feature Extraction Software (Version 10.7.3).

Article Title: Reprogramming Human Endothelial to Hematopoietic Cells Requires Vascular Induction
Article Snippet: Comparative Genomic Hybridization (CGH) Genomic DNA was extracted from HUVECs, FACS sorted CD45+ rEC-hMPPs, and CD45+ CD34+ rEC-hMPPs sorted from the BM of the NSG mice. .. The arrays were scanned in an Agilent DNA microarray scanner and obtained data was visualized using Feature Extraction software (version 10.7; Agilent).

Chromatin Immunoprecipitation:

Article Title: Status of hepatic DNA methylome predetermines and modulates the severity of non-alcoholic fatty liver injury in mice
Article Snippet: Paragraph title: Histone H3 K4 me3 chromatin immunoprecipitation microarray analysis ... Microarrays were scanned on an Agilent DNA microarray scanner and the resulting images were analyzed with Agilent Feature Extraction Software (Version 10.7.3).

Software:

Article Title: Size effects of single-walled carbon nanotubes on in vivo and in vitro pulmonary toxicity
Article Snippet: Each labeled cRNA probe was used separately for hybridization to a 4 × 44 K Whole Rat Genome Microarray Kit (G4131F; Agilent Technologies, Santa Clara, CA), and hybridization was performed at 65 °C for 17 h. Hybridized microarray slides were washed according to the instructions of the manufacturer and were scanned with an Agilent DNA Microarray Scanner (G2565BA; Agilent Technologies, Santa Clara, CA) at 5-μm resolution. .. The scanned images were analyzed numerically using Agilent Feature Extraction Software, version 10.7.3.1 (Agilent Technologies, Santa Clara, CA).

Article Title: Status of hepatic DNA methylome predetermines and modulates the severity of non-alcoholic fatty liver injury in mice
Article Snippet: .. Microarrays were scanned on an Agilent DNA microarray scanner and the resulting images were analyzed with Agilent Feature Extraction Software (Version 10.7.3). .. The combined Z-score for each probe was calculated with Agilent Genomic Workbench Light (Version 6.0).

Article Title: Reprogramming Human Endothelial to Hematopoietic Cells Requires Vascular Induction
Article Snippet: .. The arrays were scanned in an Agilent DNA microarray scanner and obtained data was visualized using Feature Extraction software (version 10.7; Agilent). .. Differentiation and reprogramming of human embryonic stem cells (hES) We used a transgenic hES reporter line that specifically identifies differentiated EC derivatives via a fluorescent reporter driven by a fragment of the human VE-cadherin promoter , .

Article Title: Transcriptome Analysis Using a High-Density Oligomicroarray under Drought Stress in Various Genotypes of Cassava: An Important Tropical Crop
Article Snippet: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4 × 44 K array slides. .. Signal intensities were detected from the obtained digital images using Feature Extraction software (Ver.

Article Title: Transcription factor DUO1 generated by neo-functionalization is associated with evolution of sperm differentiation in plants
Article Snippet: .. DNA microarrays were scanned in a DNA Microarray Scanner at 2-μm resolution and quantified with Feature Extraction 9.0 software (Agilent Technologies). ..

Article Title: Fibrogenic Activity of MECP2 Is Regulated by Phosphorylation in Hepatic Stellate Cells
Article Snippet: After the slides were washed, the arrays were scanned by the Agilent DNA Microarray Scanner (part no. G2505C). .. The acquired array images were analyzed by Agilent Feature Extraction software, version 11.0.1.1.

Article Title: In Silico Enhanced Restriction Enzyme Based Methylation Analysis of the Human Glioblastoma Genome Using Agilent 244K CpG Island Microarrays
Article Snippet: Data analysis Hybridized microarrays were scanned with an Agilent DNA Microarray Scanner (UCLA Microarray Core) to create an image file. .. From this file, Cy-5 (HpaII digested) and Cy-3 (MspI digested) intensities for each probe were determined by the Agilent Feature Extraction 9.1 software using the CGH protocol v4.95 Feb07 (Agilent Technologies).

RNA Extraction:

Article Title: Size effects of single-walled carbon nanotubes on in vivo and in vitro pulmonary toxicity
Article Snippet: Paragraph title: RNA extraction and DNA microarray experiments ... Each labeled cRNA probe was used separately for hybridization to a 4 × 44 K Whole Rat Genome Microarray Kit (G4131F; Agilent Technologies, Santa Clara, CA), and hybridization was performed at 65 °C for 17 h. Hybridized microarray slides were washed according to the instructions of the manufacturer and were scanned with an Agilent DNA Microarray Scanner (G2565BA; Agilent Technologies, Santa Clara, CA) at 5-μm resolution.

In Vitro:

Article Title: Enrichment of Pluripotent Stem Cell-Derived Hepatocyte-Like Cells by Ammonia Treatment
Article Snippet: Total RNA (100 ng) was transcribed to double-strand cDNA using a poly dT-T7 primer and cDNA products were then used as templates for in vitro transcription to generate fluorescent cRNA. .. For each hybridization reaction, 1.65 μg of fragmented Cy3-labeled cRNA was incubated with an Agilent Human GE 8x60K Microarray (Design ID: 028004) at 65°C for 17 h. Washed microarrays were scanned using an Agilent DNA microarray scanner.

Article Title: Reprogramming Human Endothelial to Hematopoietic Cells Requires Vascular Induction
Article Snippet: Before DNA extraction, CD45+ CD34+ rEC-hMPPs sorted from the BM were expanded for 72 hours in vitro . .. The arrays were scanned in an Agilent DNA microarray scanner and obtained data was visualized using Feature Extraction software (version 10.7; Agilent).

Protein Binding:

Article Title: Transcription factor DUO1 generated by neo-functionalization is associated with evolution of sperm differentiation in plants
Article Snippet: Paragraph title: Protein-binding DNA microarray assay ... The slide was spun dry by centrifugation (1 min at 500 rpm) and scanned at 2 μm resolution in a Agilent’s DNA Microarray Scanner for monitoring the amount of dsDNA.

Spectrophotometry:

Article Title: Size effects of single-walled carbon nanotubes on in vivo and in vitro pulmonary toxicity
Article Snippet: RNA was quantified using a NanoDrop 2000 spectrophotometer (Thermo Fisher Scientific Inc., Waltham, MA), and sample qualities were monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA). .. Each labeled cRNA probe was used separately for hybridization to a 4 × 44 K Whole Rat Genome Microarray Kit (G4131F; Agilent Technologies, Santa Clara, CA), and hybridization was performed at 65 °C for 17 h. Hybridized microarray slides were washed according to the instructions of the manufacturer and were scanned with an Agilent DNA Microarray Scanner (G2565BA; Agilent Technologies, Santa Clara, CA) at 5-μm resolution.

Article Title: Transcriptome Analysis Using a High-Density Oligomicroarray under Drought Stress in Various Genotypes of Cassava: An Important Tropical Crop
Article Snippet: Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer. .. Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4 × 44 K array slides.

Immunoprecipitation:

Article Title: Status of hepatic DNA methylome predetermines and modulates the severity of non-alcoholic fatty liver injury in mice
Article Snippet: Paragraph title: Methylated DNA immunoprecipitation microarray analysis ... Microarrays were scanned on an Agilent DNA microarray scanner and the resulting images were analyzed with Agilent Feature Extraction Software (Version 10.7.3).

FACS:

Article Title: Reprogramming Human Endothelial to Hematopoietic Cells Requires Vascular Induction
Article Snippet: Comparative Genomic Hybridization (CGH) Genomic DNA was extracted from HUVECs, FACS sorted CD45+ rEC-hMPPs, and CD45+ CD34+ rEC-hMPPs sorted from the BM of the NSG mice. .. The arrays were scanned in an Agilent DNA microarray scanner and obtained data was visualized using Feature Extraction software (version 10.7; Agilent).

Similar Products

  • Logo
  • About
  • News
  • Press Release
  • Team
  • Advisors
  • Partners
  • Contact
  • Bioz Stars
  • Bioz vStars
  • 99
    Agilent technologies dna microarray scanner
    Design of the cassava <t>oligo-DNA</t> <t>microarray.</t>
    Dna Microarray Scanner, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 99/100, based on 1473 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/dna microarray scanner/product/Agilent technologies
    Average 99 stars, based on 1473 article reviews
    Price from $9.99 to $1999.99
    dna microarray scanner - by Bioz Stars, 2020-04
    99/100 stars
      Buy from Supplier

    91
    Agilent technologies g2505b dna microarray scanner
    Gene networks involved in the metabolic adaptation to hyperoxia in tightly synchronized P. falciparum cultures . Using PS 6.0™ software and <t>microarray</t> expression data, gene networks were built and genes modulated in response to hyperoxia are represented. (A) Representation of metabolic interrelations related to adaptative hyperoxia exposure. Energetic metabolism: aspartate carbamoyltransferase (P13_0240), carbamoyl-phosphate synthetase (PF13_0044), glutamine-fructose-6-phosphate transaminase (PF10_0245), glucose-6-phosphate dehydrogenase (PF14_0511), acetyl-CoA synthetase (PFF1350c), gapdh (PF14_0598) - Signal transduction: regulatory sub-unit of cAMP-dependent protein kinase (PFL1110c), catalytic sub-unit of cAMP-dependent protein kinase (PFI1685w), ser thr protein kinase (PF13_0085) - Translation: citrate synthase (PF10_0218), translation elongation factor 1 alpha 1 (PF13_0305), proteasome 26S subunit (MAL13P1.343), dihydrolipoamide dehydrogenase (PFL1550w), translation elongation factor 2 (PF14_0486), adaptor-related protein complex 1 (PF13_0062), polymerase RNA I (PF11_0358) - <t>DNA</t> repair: DNA primase (PF14_0366 and PFI0530c), rpa1 (PFI0235w) - Protein folding: ferredoxin reductase (PF11_0407), Hsp10 (PFL0740c), Hsp60 (PF10_0153), Hsp70 (PF11_0351 and PF08_0054), Hsp90 (PFL1070c and PF07_0029), prohibitin (PF08_0006), DnaJ (PFF1415c). (B) Representation of ATP-dependent gene sub-networks altered in hyperoxic conditions. V-type ATPase: V-type ATPase putative (MAL13P1.271), vacuolar ATP synthase subunit h putative (PF13_0034), vacuolar ATP synthetase putative (PFE0965c), vacuolar ATP synthase subunit F putative (PF11_0412), vacuolar ATP synthase subunit D putative (PF13_0227), vacuolar ATP synthase catalytic subunit a (PF13_0065) - Mitochondrial ATP synthase F1: ATP synthase subunit putative (PF14_0615), mitochondrial ATP synthase F1 epsilon subunit (MAL7P1.75), mitochondrial ATP synthase F1 alpha subunit putative (PFB0795w). Red and blue colors correspond respectively to up- and down-regulated genes compared between hyperoxic to normoxic conditions.
    G2505b Dna Microarray Scanner, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 91/100, based on 23 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/g2505b dna microarray scanner/product/Agilent technologies
    Average 91 stars, based on 23 article reviews
    Price from $9.99 to $1999.99
    g2505b dna microarray scanner - by Bioz Stars, 2020-04
    91/100 stars
      Buy from Supplier

    Image Search Results


    Design of the cassava oligo-DNA microarray.

    Journal: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes

    Article Title: Transcriptome Analysis Using a High-Density Oligomicroarray under Drought Stress in Various Genotypes of Cassava: An Important Tropical Crop

    doi: 10.1093/dnares/dss016

    Figure Lengend Snippet: Design of the cassava oligo-DNA microarray.

    Article Snippet: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4 × 44 K array slides.

    Techniques: Microarray

    Characterization of green algal DUO1 orthologs. a Expression profiles of DUO1 orthologs from three Chara species, C. braunii (Cbr), C. australis (Cau), and C. leptospora (Cle) representing two distant clades (subgenera) 41 . Ribosomal protein L6 ( RPL6 ) was used as the internal control. The expression of two flagella component genes ( RSP11 and PACRG ) was also analyzed in C. braunii . Cbr DUO1 gene structure and amplified probed regions are shown in Supplementary Figure 7a . The whole untrimmed images are shown in Supplementary Figure 7b . Oogonia contain the egg. Antheridia contain developing sperm. Thalli are somatic vegetative tissue. b Position weight matrix representations of the top-scoring 8-mer DNA sequences bound by different MYB domains on a protein-binding DNA microarray. CpeDUO1 is DUO1 from Closterium peracerosum-strigosum-littorale complex (conjugating green alga). Numbers denoted on the right side of each motif represent the motif E- and Z-scores 19 . c In vivo transcriptional activation potentials of green algal DUO1 chimeras. DUO1 transcriptional activation potentials were measured by relative luciferase activity (right) ( n = 4; ** p

    Journal: Nature Communications

    Article Title: Transcription factor DUO1 generated by neo-functionalization is associated with evolution of sperm differentiation in plants

    doi: 10.1038/s41467-018-07728-3

    Figure Lengend Snippet: Characterization of green algal DUO1 orthologs. a Expression profiles of DUO1 orthologs from three Chara species, C. braunii (Cbr), C. australis (Cau), and C. leptospora (Cle) representing two distant clades (subgenera) 41 . Ribosomal protein L6 ( RPL6 ) was used as the internal control. The expression of two flagella component genes ( RSP11 and PACRG ) was also analyzed in C. braunii . Cbr DUO1 gene structure and amplified probed regions are shown in Supplementary Figure 7a . The whole untrimmed images are shown in Supplementary Figure 7b . Oogonia contain the egg. Antheridia contain developing sperm. Thalli are somatic vegetative tissue. b Position weight matrix representations of the top-scoring 8-mer DNA sequences bound by different MYB domains on a protein-binding DNA microarray. CpeDUO1 is DUO1 from Closterium peracerosum-strigosum-littorale complex (conjugating green alga). Numbers denoted on the right side of each motif represent the motif E- and Z-scores 19 . c In vivo transcriptional activation potentials of green algal DUO1 chimeras. DUO1 transcriptional activation potentials were measured by relative luciferase activity (right) ( n = 4; ** p

    Article Snippet: The slide was spun dry by centrifugation (1 min at 500 rpm) and scanned at 2 μm resolution in a Agilent’s DNA Microarray Scanner for monitoring the amount of dsDNA.

    Techniques: Expressing, Amplification, Protein Binding, Microarray, In Vivo, Activation Assay, Luciferase, Activity Assay

    Effects of CNT-1 and CNT-2 on gene expression in NR8383 cells. Venn diagram showing the number of upregulated and downregulated genes in NR8383 cells exposed to CNT-1 or CNT-2 for 24 h (A). Heat map generated from DNA microarray data reflecting differential expression of genes involved in the response to stimulus (GO: 0050896) in NR8383 cells exposed to CNT-1 or CNT-2 for 24 h. Expression levels are colored blue for low intensity and red for high intensity (see scale at the bottom right corner) (B).

    Journal: Inhalation Toxicology

    Article Title: Size effects of single-walled carbon nanotubes on in vivo and in vitro pulmonary toxicity

    doi: 10.3109/08958378.2015.1026620

    Figure Lengend Snippet: Effects of CNT-1 and CNT-2 on gene expression in NR8383 cells. Venn diagram showing the number of upregulated and downregulated genes in NR8383 cells exposed to CNT-1 or CNT-2 for 24 h (A). Heat map generated from DNA microarray data reflecting differential expression of genes involved in the response to stimulus (GO: 0050896) in NR8383 cells exposed to CNT-1 or CNT-2 for 24 h. Expression levels are colored blue for low intensity and red for high intensity (see scale at the bottom right corner) (B).

    Article Snippet: Each labeled cRNA probe was used separately for hybridization to a 4 × 44 K Whole Rat Genome Microarray Kit (G4131F; Agilent Technologies, Santa Clara, CA), and hybridization was performed at 65 °C for 17 h. Hybridized microarray slides were washed according to the instructions of the manufacturer and were scanned with an Agilent DNA Microarray Scanner (G2565BA; Agilent Technologies, Santa Clara, CA) at 5-μm resolution.

    Techniques: Expressing, Generated, Microarray

    Gene networks involved in the metabolic adaptation to hyperoxia in tightly synchronized P. falciparum cultures . Using PS 6.0™ software and microarray expression data, gene networks were built and genes modulated in response to hyperoxia are represented. (A) Representation of metabolic interrelations related to adaptative hyperoxia exposure. Energetic metabolism: aspartate carbamoyltransferase (P13_0240), carbamoyl-phosphate synthetase (PF13_0044), glutamine-fructose-6-phosphate transaminase (PF10_0245), glucose-6-phosphate dehydrogenase (PF14_0511), acetyl-CoA synthetase (PFF1350c), gapdh (PF14_0598) - Signal transduction: regulatory sub-unit of cAMP-dependent protein kinase (PFL1110c), catalytic sub-unit of cAMP-dependent protein kinase (PFI1685w), ser thr protein kinase (PF13_0085) - Translation: citrate synthase (PF10_0218), translation elongation factor 1 alpha 1 (PF13_0305), proteasome 26S subunit (MAL13P1.343), dihydrolipoamide dehydrogenase (PFL1550w), translation elongation factor 2 (PF14_0486), adaptor-related protein complex 1 (PF13_0062), polymerase RNA I (PF11_0358) - DNA repair: DNA primase (PF14_0366 and PFI0530c), rpa1 (PFI0235w) - Protein folding: ferredoxin reductase (PF11_0407), Hsp10 (PFL0740c), Hsp60 (PF10_0153), Hsp70 (PF11_0351 and PF08_0054), Hsp90 (PFL1070c and PF07_0029), prohibitin (PF08_0006), DnaJ (PFF1415c). (B) Representation of ATP-dependent gene sub-networks altered in hyperoxic conditions. V-type ATPase: V-type ATPase putative (MAL13P1.271), vacuolar ATP synthase subunit h putative (PF13_0034), vacuolar ATP synthetase putative (PFE0965c), vacuolar ATP synthase subunit F putative (PF11_0412), vacuolar ATP synthase subunit D putative (PF13_0227), vacuolar ATP synthase catalytic subunit a (PF13_0065) - Mitochondrial ATP synthase F1: ATP synthase subunit putative (PF14_0615), mitochondrial ATP synthase F1 epsilon subunit (MAL7P1.75), mitochondrial ATP synthase F1 alpha subunit putative (PFB0795w). Red and blue colors correspond respectively to up- and down-regulated genes compared between hyperoxic to normoxic conditions.

    Journal: Malaria Journal

    Article Title: Global response of Plasmodium falciparum to hyperoxia: a combined transcriptomic and proteomic approach

    doi: 10.1186/1475-2875-10-4

    Figure Lengend Snippet: Gene networks involved in the metabolic adaptation to hyperoxia in tightly synchronized P. falciparum cultures . Using PS 6.0™ software and microarray expression data, gene networks were built and genes modulated in response to hyperoxia are represented. (A) Representation of metabolic interrelations related to adaptative hyperoxia exposure. Energetic metabolism: aspartate carbamoyltransferase (P13_0240), carbamoyl-phosphate synthetase (PF13_0044), glutamine-fructose-6-phosphate transaminase (PF10_0245), glucose-6-phosphate dehydrogenase (PF14_0511), acetyl-CoA synthetase (PFF1350c), gapdh (PF14_0598) - Signal transduction: regulatory sub-unit of cAMP-dependent protein kinase (PFL1110c), catalytic sub-unit of cAMP-dependent protein kinase (PFI1685w), ser thr protein kinase (PF13_0085) - Translation: citrate synthase (PF10_0218), translation elongation factor 1 alpha 1 (PF13_0305), proteasome 26S subunit (MAL13P1.343), dihydrolipoamide dehydrogenase (PFL1550w), translation elongation factor 2 (PF14_0486), adaptor-related protein complex 1 (PF13_0062), polymerase RNA I (PF11_0358) - DNA repair: DNA primase (PF14_0366 and PFI0530c), rpa1 (PFI0235w) - Protein folding: ferredoxin reductase (PF11_0407), Hsp10 (PFL0740c), Hsp60 (PF10_0153), Hsp70 (PF11_0351 and PF08_0054), Hsp90 (PFL1070c and PF07_0029), prohibitin (PF08_0006), DnaJ (PFF1415c). (B) Representation of ATP-dependent gene sub-networks altered in hyperoxic conditions. V-type ATPase: V-type ATPase putative (MAL13P1.271), vacuolar ATP synthase subunit h putative (PF13_0034), vacuolar ATP synthetase putative (PFE0965c), vacuolar ATP synthase subunit F putative (PF11_0412), vacuolar ATP synthase subunit D putative (PF13_0227), vacuolar ATP synthase catalytic subunit a (PF13_0065) - Mitochondrial ATP synthase F1: ATP synthase subunit putative (PF14_0615), mitochondrial ATP synthase F1 epsilon subunit (MAL7P1.75), mitochondrial ATP synthase F1 alpha subunit putative (PFB0795w). Red and blue colors correspond respectively to up- and down-regulated genes compared between hyperoxic to normoxic conditions.

    Article Snippet: Slides were scanned at 5 μm resolution with a G2505B DNA microarray scanner (Agilent Technologies).

    Techniques: Software, Microarray, Expressing, Transduction