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    Rabbit IgG polyclonal antibody for mouse Dnmt2 DNA methyltransferase 2 tested for WB in Mouse
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    99
    Zymo Research chip dna clean concentrator kit
    Chip Dna Clean Concentrator Kit, supplied by Zymo Research, used in various techniques. Bioz Stars score: 99/100, based on 734 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Agilent technologies dna microarray scanner
    <t>DNA</t> methylation and H3K4me3 in the normal livers of A/J and WSB/EiJ mice. a MeDIP <t>microarray</t> 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
    Dna Microarray Scanner, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 95/100, based on 11093 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher affymetrix dna microarrays
    Gene expression profile of syndecan 1 and CD9 Gene expression profiles of syndecan 1 (A) and CD9 (B) were determined with <t>Affymetrix</t> U133 A+B <t>microarrays</t> in seven normal BMPC samples, purified malignant plasma cells of seven patients with MGUS and 65 patients with MM, and 20 HMCLs. C. Surface expression of CD9 was determined using FACS with an anti-CD9-PE antibody (solid line) and a PE-isotype control (dotted line).
    Affymetrix Dna Microarrays, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 90/100, based on 427 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Agilent technologies high sensitivity dna chip
    ORF37’s DNase activity is required for efficient packaging of viral <t>DNA</t> and nuclear egress. (A) <t>qPCR</t> analysis of BamHI-digested total and encapsidated (DNase I-resistant) DNAs from 72-hpi 293L/wt and 293L/Q129H cells. When normalized to the total viral DNA, DNA encapsidation in 293L/Q129H cells was significantly reduced compared to the wt control; ***, P
    High Sensitivity Dna Chip, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 94/100, based on 5086 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Agilent technologies oligonucleotide microarrays
    Modulation of mRNAs as evaluated by <t>microarrays</t> during collagen induced arthritis (CIA). Hierarchical clustering and color heat-map of the transcriptome (mRNAs) of CD3+ T cells from the spleen and lymph nodes of 12-week-old mice from the resistant DBA-2/J strain and the susceptible DBA-1/J strain immunized with chicken type II collagen, based on microarray expression profiling. The control mice were immunized just with complete Freund’s adjuvant (CFA) without any collagen. The dendrogram and heat-map were obtained using cluster and tree-view algorithms through Agilent GeneSpring platform. This figure shows the expression of genes related to immune system function based on Gene Ontology (GO terms). Heat map legend: Red = up regulation, green = down regulation, black = unmodulated (Pearson correlation metrics). Sample dendrogram legend: red-line = DBA-1/J control; blue-line = DBA-1/J CIA; brown-line = DBA-2/J control; gray-line = DBA-2/J CIA.
    Oligonucleotide Microarrays, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 93/100, based on 491 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher cdna microarrays
    Modulation of mRNAs as evaluated by <t>microarrays</t> during collagen induced arthritis (CIA). Hierarchical clustering and color heat-map of the transcriptome (mRNAs) of CD3+ T cells from the spleen and lymph nodes of 12-week-old mice from the resistant DBA-2/J strain and the susceptible DBA-1/J strain immunized with chicken type II collagen, based on microarray expression profiling. The control mice were immunized just with complete Freund’s adjuvant (CFA) without any collagen. The dendrogram and heat-map were obtained using cluster and tree-view algorithms through Agilent GeneSpring platform. This figure shows the expression of genes related to immune system function based on Gene Ontology (GO terms). Heat map legend: Red = up regulation, green = down regulation, black = unmodulated (Pearson correlation metrics). Sample dendrogram legend: red-line = DBA-1/J control; blue-line = DBA-1/J CIA; brown-line = DBA-2/J control; gray-line = DBA-2/J CIA.
    Cdna Microarrays, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 387 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Agilent technologies dna 1000 chip
    Electrophoretogram of sequencing libraries. The graph shows the length distribution curves of sequencing libraries obtained with Illumina TruSeqTM RNA sample preparation kit (Low-Throughput protocol) according to manufacturer’s protocol. The length of DNA fragments was between 200 and 700 pb. Curves were generated on a 2100 bioanalyzer using <t>DNA</t> 1000 chip (Agilent Technologies). For each sample three biological replicates were performed
    Dna 1000 Chip, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 94/100, based on 2795 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Agilent technologies bioanalyzer high sensitivity dna chip
    The workflow of L1Hs-targeted enrichment library preparation (A) Double-strand genomic <t>DNA</t> (blue) is extracted from a Korean individual genome (KPGP9). Red boxes indicate the regions where the probe binds to the 3′ UTR of L1Hs elements. (B) Genomic DNA is fragmented by aquatic ultrasonic wave of the Covaris S2 system. Sheared DNAs have an average size of 550 bp, which is suitable for HiSeq sequencing. (C) The Illumina’s adaptor (green) is ligated at both ends of the fragmented DNAs. (D) The adaptor-ligated DNAs is hybridized with the L1Hs-targeted probe (red and orange). Only the presence of the L1Hs 3′ UTR allows the sequence-specific binding of the probe. (E) Targeted DNA fragments are selectively elongated from the probe-binding strands. (F) Because the probe sequence attached to the L1Hs 3′ UTR and the Illumina’s adaptor sequences at both ends are known, targeted DNAs are enriched by PCR with the primer set. After library construction, the final product is confirmed using the Agilent <t>Bioanalyzer</t> High Sensitivity chip assay.
    Bioanalyzer High Sensitivity Dna Chip, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 91/100, based on 1850 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Agilent technologies bioanalyzer dna 1000 chip
    CRISPR/Cas9 deletion of MTA1 in breast cancer cells. a . T7 endonuclease assay PCR results. Electropherogram of the T7 endonuclease digestion of MTA1 genomic PCR products visualized on an Agilent <t>Bioanalyzer</t> <t>DNA</t> 1000 Chip. Due to location of sgRNA target site, digestion of PCR products was predicted to generate the following fragments: wildtype 800 bp, sgRNA #1: 500 and 310 bp, sgRNA#3: 700 and 100 bp, and sgRNA #5: 760 and 40 bp. b . Western blot of MTA1 in MCF7 and MDA-MB-231 MTA1 knockout cells. GAPDH is included as an equal loading control. c . Cell proliferation assay of MCF7 and MDA-MB-231 knockout cells, compared to cells expressing an empty vector, n = 4 **** p
    Bioanalyzer Dna 1000 Chip, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 94/100, based on 2363 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Illumina Inc truseq dna sample preparation kit
    CRISPR/Cas9 deletion of MTA1 in breast cancer cells. a . T7 endonuclease assay PCR results. Electropherogram of the T7 endonuclease digestion of MTA1 genomic PCR products visualized on an Agilent <t>Bioanalyzer</t> <t>DNA</t> 1000 Chip. Due to location of sgRNA target site, digestion of PCR products was predicted to generate the following fragments: wildtype 800 bp, sgRNA #1: 500 and 310 bp, sgRNA#3: 700 and 100 bp, and sgRNA #5: 760 and 40 bp. b . Western blot of MTA1 in MCF7 and MDA-MB-231 MTA1 knockout cells. GAPDH is included as an equal loading control. c . Cell proliferation assay of MCF7 and MDA-MB-231 knockout cells, compared to cells expressing an empty vector, n = 4 **** p
    Truseq Dna Sample Preparation Kit, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 99/100, based on 2301 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher high density oligonucleotide arrays
    CRISPR/Cas9 deletion of MTA1 in breast cancer cells. a . T7 endonuclease assay PCR results. Electropherogram of the T7 endonuclease digestion of MTA1 genomic PCR products visualized on an Agilent <t>Bioanalyzer</t> <t>DNA</t> 1000 Chip. Due to location of sgRNA target site, digestion of PCR products was predicted to generate the following fragments: wildtype 800 bp, sgRNA #1: 500 and 310 bp, sgRNA#3: 700 and 100 bp, and sgRNA #5: 760 and 40 bp. b . Western blot of MTA1 in MCF7 and MDA-MB-231 MTA1 knockout cells. GAPDH is included as an equal loading control. c . Cell proliferation assay of MCF7 and MDA-MB-231 knockout cells, compared to cells expressing an empty vector, n = 4 **** p
    High Density Oligonucleotide Arrays, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 397 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher gene chip scanner 3000
    CRISPR/Cas9 deletion of MTA1 in breast cancer cells. a . T7 endonuclease assay PCR results. Electropherogram of the T7 endonuclease digestion of MTA1 genomic PCR products visualized on an Agilent <t>Bioanalyzer</t> <t>DNA</t> 1000 Chip. Due to location of sgRNA target site, digestion of PCR products was predicted to generate the following fragments: wildtype 800 bp, sgRNA #1: 500 and 310 bp, sgRNA#3: 700 and 100 bp, and sgRNA #5: 760 and 40 bp. b . Western blot of MTA1 in MCF7 and MDA-MB-231 MTA1 knockout cells. GAPDH is included as an equal loading control. c . Cell proliferation assay of MCF7 and MDA-MB-231 knockout cells, compared to cells expressing an empty vector, n = 4 **** p
    Gene Chip Scanner 3000, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 1460 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Agilent technologies oligonucleotide array based cgh
    CRISPR/Cas9 deletion of MTA1 in breast cancer cells. a . T7 endonuclease assay PCR results. Electropherogram of the T7 endonuclease digestion of MTA1 genomic PCR products visualized on an Agilent <t>Bioanalyzer</t> <t>DNA</t> 1000 Chip. Due to location of sgRNA target site, digestion of PCR products was predicted to generate the following fragments: wildtype 800 bp, sgRNA #1: 500 and 310 bp, sgRNA#3: 700 and 100 bp, and sgRNA #5: 760 and 40 bp. b . Western blot of MTA1 in MCF7 and MDA-MB-231 MTA1 knockout cells. GAPDH is included as an equal loading control. c . Cell proliferation assay of MCF7 and MDA-MB-231 knockout cells, compared to cells expressing an empty vector, n = 4 **** p
    Oligonucleotide Array Based Cgh, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 91/100, based on 672 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher arabidopsis thaliana affymetrix gene chips
    CRISPR/Cas9 deletion of MTA1 in breast cancer cells. a . T7 endonuclease assay PCR results. Electropherogram of the T7 endonuclease digestion of MTA1 genomic PCR products visualized on an Agilent <t>Bioanalyzer</t> <t>DNA</t> 1000 Chip. Due to location of sgRNA target site, digestion of PCR products was predicted to generate the following fragments: wildtype 800 bp, sgRNA #1: 500 and 310 bp, sgRNA#3: 700 and 100 bp, and sgRNA #5: 760 and 40 bp. b . Western blot of MTA1 in MCF7 and MDA-MB-231 MTA1 knockout cells. GAPDH is included as an equal loading control. c . Cell proliferation assay of MCF7 and MDA-MB-231 knockout cells, compared to cells expressing an empty vector, n = 4 **** p
    Arabidopsis Thaliana Affymetrix Gene Chips, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 90/100, based on 332 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Illumina Inc microarray oligonucleotide
    Results of singleplex amplification and <t>microarray</t> hybridization of select, biotin-labelled amplified purified pathogen DNA targets and hybridization to the Alere ArrayTube TM printed meningitis microarray. ( A ) No template control singleplex amplification, ( B ) Streptococcus pneumoniae singleplex amplification (Primers SPne1_2, 2.5 ng/mL target DNA), ( C ) Listeria monocytogenes singleplex amplification (Primers LiMo4_6, 2.5 ng/mL target DNA), ( D ) Staphyl aureus singleplex amplification (Primers StAUB_3, 2.5 ng/mL DNA). ( E ) N. meningitidis Serogroup B singleplex amplification (Primers NsMB4, 2.5 ng/mL DNA), ( F ) No template control multiplex amplification, ( G ) S. pneumoniae multiplex amplification, ( H ) L. monocytogenes multiplex amplification, ( I ) S. aureus multiplex amplification, ( J ) N. meningitidis serogroup B multiplex amplification.
    Microarray Oligonucleotide, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 92/100, based on 2 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Millipore cdna microarray
    Results of singleplex amplification and <t>microarray</t> hybridization of select, biotin-labelled amplified purified pathogen DNA targets and hybridization to the Alere ArrayTube TM printed meningitis microarray. ( A ) No template control singleplex amplification, ( B ) Streptococcus pneumoniae singleplex amplification (Primers SPne1_2, 2.5 ng/mL target DNA), ( C ) Listeria monocytogenes singleplex amplification (Primers LiMo4_6, 2.5 ng/mL target DNA), ( D ) Staphyl aureus singleplex amplification (Primers StAUB_3, 2.5 ng/mL DNA). ( E ) N. meningitidis Serogroup B singleplex amplification (Primers NsMB4, 2.5 ng/mL DNA), ( F ) No template control multiplex amplification, ( G ) S. pneumoniae multiplex amplification, ( H ) L. monocytogenes multiplex amplification, ( I ) S. aureus multiplex amplification, ( J ) N. meningitidis serogroup B multiplex amplification.
    Cdna Microarray, supplied by Millipore, used in various techniques. Bioz Stars score: 92/100, based on 32 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Agilent technologies 2100 bioanalyzer high sensitivity dna chip
    Results of singleplex amplification and <t>microarray</t> hybridization of select, biotin-labelled amplified purified pathogen DNA targets and hybridization to the Alere ArrayTube TM printed meningitis microarray. ( A ) No template control singleplex amplification, ( B ) Streptococcus pneumoniae singleplex amplification (Primers SPne1_2, 2.5 ng/mL target DNA), ( C ) Listeria monocytogenes singleplex amplification (Primers LiMo4_6, 2.5 ng/mL target DNA), ( D ) Staphyl aureus singleplex amplification (Primers StAUB_3, 2.5 ng/mL DNA). ( E ) N. meningitidis Serogroup B singleplex amplification (Primers NsMB4, 2.5 ng/mL DNA), ( F ) No template control multiplex amplification, ( G ) S. pneumoniae multiplex amplification, ( H ) L. monocytogenes multiplex amplification, ( I ) S. aureus multiplex amplification, ( J ) N. meningitidis serogroup B multiplex amplification.
    2100 Bioanalyzer High Sensitivity Dna Chip, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 89/100, based on 359 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Agilent technologies dna 1000 chips
    gRNA mediated cleavage reveals mir-29b-1 as the main source of mature miR-29b. ( a ) Surveyor assay detecting the mutations on miR-29b gene locus. mmu-mir-29b-1 was shown to have mutations in cas1-1, cas1-2, cas2-1 and cas2-2; mmu-mir-29b-2 displayed mutations in cas2-1, cas2-2, cas3-1, cas3-2 and cas3-3. ( b ) Surveyor assay showed mutations on hsa-mir-29b-1 and hsa-mir-29b-2 sequences in clone cas1-1, cas1-2, cas1-3 and cas1-4. Surveyor assay products were visualized on Bioanalyser equipment using <t>DNA</t> 1000 chip. Full-length Bioanalyser images for ( a , b ) are presented in Supplementary Fig. 5 .
    Dna 1000 Chips, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 89/100, based on 486 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher u133a oligonucleotide microarray
    Heat map presentation of correlations between CK19 and various cadherins expressions after Affymetrix <t>U133A</t> oligonucleotide <t>microarray</t> analysis. Red colors represented positive correlation and blue colors represented negative correlation. The significance of correlation was determined by Pearson correlation coefficient R 2 . For CDH17, the R 2 was 0.867, P
    U133a Oligonucleotide Microarray, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 88/100, based on 35 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher genechip oligonucleotide array
    Heat map presentation of correlations between CK19 and various cadherins expressions after Affymetrix <t>U133A</t> oligonucleotide <t>microarray</t> analysis. Red colors represented positive correlation and blue colors represented negative correlation. The significance of correlation was determined by Pearson correlation coefficient R 2 . For CDH17, the R 2 was 0.867, P
    Genechip Oligonucleotide Array, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 25 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Rabbit IgG polyclonal antibody for mouse DNMT3 DNA methyltransferase 3A tested for WB in Human Mouse
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    SimpleChIP Human DNAJB9 Exon 1 Primers contain a mix of forward and reverse PCR primers that are specific to exon 1 of the human DnaJ homolog subfamily B member 9
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    The ChIP Elute Kit uses a fast and simple method to reverse cross link elute and purify DNA captured by chromatin immunoprecipitation ChIP This kit replaces long and tedious protocols
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    Image Search Results


    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

    Journal: BMC Genomics

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

    doi: 10.1186/s12864-016-2617-2

    Figure Lengend 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

    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).

    Techniques: 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

    Journal: BMC Genomics

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

    doi: 10.1186/s12864-016-2617-2

    Figure Lengend 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

    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).

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

    Gene expression profile of syndecan 1 and CD9 Gene expression profiles of syndecan 1 (A) and CD9 (B) were determined with Affymetrix U133 A+B microarrays in seven normal BMPC samples, purified malignant plasma cells of seven patients with MGUS and 65 patients with MM, and 20 HMCLs. C. Surface expression of CD9 was determined using FACS with an anti-CD9-PE antibody (solid line) and a PE-isotype control (dotted line).

    Journal: Oncogene

    Article Title: Expression of EGF-family receptors and amphiregulin in multiple myeloma. Amphiregulin is a growth factor for myeloma cells

    doi: 10.1038/sj.onc.1208536

    Figure Lengend Snippet: Gene expression profile of syndecan 1 and CD9 Gene expression profiles of syndecan 1 (A) and CD9 (B) were determined with Affymetrix U133 A+B microarrays in seven normal BMPC samples, purified malignant plasma cells of seven patients with MGUS and 65 patients with MM, and 20 HMCLs. C. Surface expression of CD9 was determined using FACS with an anti-CD9-PE antibody (solid line) and a PE-isotype control (dotted line).

    Article Snippet: Using Affymetrix DNA microarrays, we show here that the AREG gene was expressed by purified primary myeloma cells from 65 patients and that the expression was higher than in normal bone marrow plasma cells or plasmablastic cells.

    Techniques: Expressing, Purification, FACS

    Gene expression profile of amphiregulin and HB-EGF Gene expression profiles of amphiregulin (A) and HB-EGF (B) were determined with Affymetrix U133 A+B DNA microarrays in seven polyclonal plasmablastic cell (PPC) samples, seven normal bone marrow plasma cell (BMPC) samples, purified malignant plasma cells of seven patients with MGUS and 65 patients with MM, and 20 myeloma cell lines (HMCLs). MMI, MMII and MMIII indicate data from myeloma cells of patients with stage I, II or III MM. Statistical comparisons were made with a Mann-Whitney test.

    Journal: Oncogene

    Article Title: Expression of EGF-family receptors and amphiregulin in multiple myeloma. Amphiregulin is a growth factor for myeloma cells

    doi: 10.1038/sj.onc.1208536

    Figure Lengend Snippet: Gene expression profile of amphiregulin and HB-EGF Gene expression profiles of amphiregulin (A) and HB-EGF (B) were determined with Affymetrix U133 A+B DNA microarrays in seven polyclonal plasmablastic cell (PPC) samples, seven normal bone marrow plasma cell (BMPC) samples, purified malignant plasma cells of seven patients with MGUS and 65 patients with MM, and 20 myeloma cell lines (HMCLs). MMI, MMII and MMIII indicate data from myeloma cells of patients with stage I, II or III MM. Statistical comparisons were made with a Mann-Whitney test.

    Article Snippet: Using Affymetrix DNA microarrays, we show here that the AREG gene was expressed by purified primary myeloma cells from 65 patients and that the expression was higher than in normal bone marrow plasma cells or plasmablastic cells.

    Techniques: Expressing, Purification, MANN-WHITNEY

    ORF37’s DNase activity is required for efficient packaging of viral DNA and nuclear egress. (A) qPCR analysis of BamHI-digested total and encapsidated (DNase I-resistant) DNAs from 72-hpi 293L/wt and 293L/Q129H cells. When normalized to the total viral DNA, DNA encapsidation in 293L/Q129H cells was significantly reduced compared to the wt control; ***, P

    Journal: Journal of Virology

    Article Title: The DNase Activity of Kaposi’s Sarcoma-Associated Herpesvirus SOX Protein Serves an Important Role in Viral Genome Processing during Lytic Replication

    doi: 10.1128/JVI.01983-18

    Figure Lengend Snippet: ORF37’s DNase activity is required for efficient packaging of viral DNA and nuclear egress. (A) qPCR analysis of BamHI-digested total and encapsidated (DNase I-resistant) DNAs from 72-hpi 293L/wt and 293L/Q129H cells. When normalized to the total viral DNA, DNA encapsidation in 293L/Q129H cells was significantly reduced compared to the wt control; ***, P

    Article Snippet: The ChIP-Seq libraries were validated using a Bioanalyzer 2100 with a high-sensitivity DNA ChIP (Agilent) and quantified by qPCR (Kappa kit).

    Techniques: Activity Assay, Real-time Polymerase Chain Reaction

    Generation of ORF37-DNase-inactivated (Q129H) recombinant KSHV (the Q129H mutant) via homologous recombination. (A) Schematic diagram showing generation of the Q129H mutant, where amino acid residue 129 of ORF37 was point mutated to histidine by homologous recombination and GalK-Kan r counterselection. Insertion of the galK -Kan r cassette was confirmed by BamHI restriction fragment analysis and Southern hybridization with a GalK-specific probe, indicated in red (Probe). (B) EtBr-stained gel and Southern blot of BamHI-digested BAC16-wt (lane 2), an intermediate containing a galK -Kan r cassette (lane 3), and the Q129H mutant (lane 4). The Southern blot with a 32 P-labeled GalK probe showed the expected 2.6-kb band in the intermediate (lane 3). (C, a ) DNA sequencing of BAC Q129H confirmed the desired mutation in the ORF37 gene. ( b ) High-throughput sequencing reads of BAC Q129H confirmed mutation in the ORF37 gene. (D) GFP expression levels from HEK293L cells stably transfected with BAC16-wt or the Q129H DNAs post-hygromycin selection were imaged directly from the fixed cells by fluorescence microscopy. The green images show the expression of GFP, confirming the presence of BAC16-wt or the Q129H mutant, and the gray images are the corresponding bright-field images. (E) Comparison of expression levels of LANA, RTA, and ORF37 via Western blot analysis of uninduced and 48-hpi 293L/wt and 293L/Q129H cells confirmed the persistence and reactivation of both viruses. Staining of the same blot with GAPDH-specific antibody served as a loading control. (F, a ) Analysis of the host shutoff activity of the Q129H mutant using RNAs extracted from uninduced and 48-hpi 293L/wt and 293L/Q129H cells. RNA was resolved and subjected to Northern blotting and hybridization with a 32 P-labeled GFP probe, which confirmed that the Q129H mutant retained its ability to degrade the host mRNA. ( b ) Immunofluorescence analysis for RTA expression in 293L/wt and 293L/Q129H cells indicated almost all the cells underwent lytic reaction at 48 hpi. DIC, differential interference contrast. (G) Relative quantification of the viral mRNA levels from 48-hpi 293L/Q129H cells compared to the 293L/wt control using a custom real-time qPCR analysis of the KSHV genes in a 96-well format showed almost identical levels of all viral transcripts. The fold changes for the individual KSHV genes were calculated using the ΔΔ C T method normalized to GAPDH and relative to BAC16-wt, defined as 1.

    Journal: Journal of Virology

    Article Title: The DNase Activity of Kaposi’s Sarcoma-Associated Herpesvirus SOX Protein Serves an Important Role in Viral Genome Processing during Lytic Replication

    doi: 10.1128/JVI.01983-18

    Figure Lengend Snippet: Generation of ORF37-DNase-inactivated (Q129H) recombinant KSHV (the Q129H mutant) via homologous recombination. (A) Schematic diagram showing generation of the Q129H mutant, where amino acid residue 129 of ORF37 was point mutated to histidine by homologous recombination and GalK-Kan r counterselection. Insertion of the galK -Kan r cassette was confirmed by BamHI restriction fragment analysis and Southern hybridization with a GalK-specific probe, indicated in red (Probe). (B) EtBr-stained gel and Southern blot of BamHI-digested BAC16-wt (lane 2), an intermediate containing a galK -Kan r cassette (lane 3), and the Q129H mutant (lane 4). The Southern blot with a 32 P-labeled GalK probe showed the expected 2.6-kb band in the intermediate (lane 3). (C, a ) DNA sequencing of BAC Q129H confirmed the desired mutation in the ORF37 gene. ( b ) High-throughput sequencing reads of BAC Q129H confirmed mutation in the ORF37 gene. (D) GFP expression levels from HEK293L cells stably transfected with BAC16-wt or the Q129H DNAs post-hygromycin selection were imaged directly from the fixed cells by fluorescence microscopy. The green images show the expression of GFP, confirming the presence of BAC16-wt or the Q129H mutant, and the gray images are the corresponding bright-field images. (E) Comparison of expression levels of LANA, RTA, and ORF37 via Western blot analysis of uninduced and 48-hpi 293L/wt and 293L/Q129H cells confirmed the persistence and reactivation of both viruses. Staining of the same blot with GAPDH-specific antibody served as a loading control. (F, a ) Analysis of the host shutoff activity of the Q129H mutant using RNAs extracted from uninduced and 48-hpi 293L/wt and 293L/Q129H cells. RNA was resolved and subjected to Northern blotting and hybridization with a 32 P-labeled GFP probe, which confirmed that the Q129H mutant retained its ability to degrade the host mRNA. ( b ) Immunofluorescence analysis for RTA expression in 293L/wt and 293L/Q129H cells indicated almost all the cells underwent lytic reaction at 48 hpi. DIC, differential interference contrast. (G) Relative quantification of the viral mRNA levels from 48-hpi 293L/Q129H cells compared to the 293L/wt control using a custom real-time qPCR analysis of the KSHV genes in a 96-well format showed almost identical levels of all viral transcripts. The fold changes for the individual KSHV genes were calculated using the ΔΔ C T method normalized to GAPDH and relative to BAC16-wt, defined as 1.

    Article Snippet: The ChIP-Seq libraries were validated using a Bioanalyzer 2100 with a high-sensitivity DNA ChIP (Agilent) and quantified by qPCR (Kappa kit).

    Techniques: Recombinant, Mutagenesis, Homologous Recombination, Hybridization, Staining, Southern Blot, Labeling, DNA Sequencing, BAC Assay, Next-Generation Sequencing, Expressing, Stable Transfection, Transfection, Selection, Fluorescence, Microscopy, Western Blot, Activity Assay, Northern Blot, Immunofluorescence, Real-time Polymerase Chain Reaction

    DNase activity of ORF37 did not affect latent/lytic KSHV DNA synthesis but rather virion production. (A and B) Comparison of intracellular KSHV genome copies in latent/uninduced and 48-hpi 293L/wt and 293L/Q129H cells, as analyzed by qPCR. The values were normalized to GAPDH and calculated relative to BAC16-wt, defined as 1. Equal numbers of KSHV genome copies were maintained during the latent phase; however, only a slight decrease in KSHV genome copies was observed during the lytic phase of virus replication. (C) Detection of extracellular KSHV progeny virion production in the supernatants of 5-dpi 293L/wt and 293L/Q129H cells revealed a 10-fold decrease in virus production in 293L/Q129H supernatants compared to wt supernatants. (D and E) HEK293L cells infected with 293L/wt and 293L/Q129H virus supernatants were assayed by flow cytometry 2 days postinfection. The side scatter (SSC) versus forward scatter (FSC) plot was used to identify GFP-positive cells/signals. (F) Mean value of at least three independent experiments from the values determined in panel E. The error bars represent standard deviations of the mean from the results of three different experiments; ***, P

    Journal: Journal of Virology

    Article Title: The DNase Activity of Kaposi’s Sarcoma-Associated Herpesvirus SOX Protein Serves an Important Role in Viral Genome Processing during Lytic Replication

    doi: 10.1128/JVI.01983-18

    Figure Lengend Snippet: DNase activity of ORF37 did not affect latent/lytic KSHV DNA synthesis but rather virion production. (A and B) Comparison of intracellular KSHV genome copies in latent/uninduced and 48-hpi 293L/wt and 293L/Q129H cells, as analyzed by qPCR. The values were normalized to GAPDH and calculated relative to BAC16-wt, defined as 1. Equal numbers of KSHV genome copies were maintained during the latent phase; however, only a slight decrease in KSHV genome copies was observed during the lytic phase of virus replication. (C) Detection of extracellular KSHV progeny virion production in the supernatants of 5-dpi 293L/wt and 293L/Q129H cells revealed a 10-fold decrease in virus production in 293L/Q129H supernatants compared to wt supernatants. (D and E) HEK293L cells infected with 293L/wt and 293L/Q129H virus supernatants were assayed by flow cytometry 2 days postinfection. The side scatter (SSC) versus forward scatter (FSC) plot was used to identify GFP-positive cells/signals. (F) Mean value of at least three independent experiments from the values determined in panel E. The error bars represent standard deviations of the mean from the results of three different experiments; ***, P

    Article Snippet: The ChIP-Seq libraries were validated using a Bioanalyzer 2100 with a high-sensitivity DNA ChIP (Agilent) and quantified by qPCR (Kappa kit).

    Techniques: Activity Assay, DNA Synthesis, Real-time Polymerase Chain Reaction, Infection, Flow Cytometry, Cytometry

    Effect of sequencing depth and sample size on the data set properties. Using our main data set on MD regulatory activity, we randomly removed samples and reads to create new data sets with different properties. Data sets with a total of n = 6 and n = 10 samples include n = 3 and 5 replicates in each experimental condition, respectively, each with a fixed numbers of reads sampled for each mRNA-seq library (x-axis in A-C). As a function of RNA-seq reads generated (subsampled), we show: ( A ) the number of analyzable 200 bp regions based on the criteria reported in the main text (regions must be covered in > 50% of both DNA and RNA samples in the data set); this has the effect of imposing a stricter threshold on larger data sets; ( B ) the median coverage in mRNA libraries for each CpG site included in analyzed regions; and ( C ) the total number of CpG sites included in analyzed regions. Each point shows the mean value across five random read subsets of the depth shown on the x-axis. As expected, more regions and CpGs are retained for analysis with increasing sequencing depth, but more regions are analyzed in a smaller data set (n = 6 versus 10 replicates), because of our requirement for a region to be covered in > 50% of samples. However, smaller data sets suffer from reduced power. ( D ) The number of enhancers identified from a linear model (FDR

    Journal: eLife

    Article Title: Genome-wide quantification of the effects of DNA methylation on human gene regulation

    doi: 10.7554/eLife.37513

    Figure Lengend Snippet: Effect of sequencing depth and sample size on the data set properties. Using our main data set on MD regulatory activity, we randomly removed samples and reads to create new data sets with different properties. Data sets with a total of n = 6 and n = 10 samples include n = 3 and 5 replicates in each experimental condition, respectively, each with a fixed numbers of reads sampled for each mRNA-seq library (x-axis in A-C). As a function of RNA-seq reads generated (subsampled), we show: ( A ) the number of analyzable 200 bp regions based on the criteria reported in the main text (regions must be covered in > 50% of both DNA and RNA samples in the data set); this has the effect of imposing a stricter threshold on larger data sets; ( B ) the median coverage in mRNA libraries for each CpG site included in analyzed regions; and ( C ) the total number of CpG sites included in analyzed regions. Each point shows the mean value across five random read subsets of the depth shown on the x-axis. As expected, more regions and CpGs are retained for analysis with increasing sequencing depth, but more regions are analyzed in a smaller data set (n = 6 versus 10 replicates), because of our requirement for a region to be covered in > 50% of samples. However, smaller data sets suffer from reduced power. ( D ) The number of enhancers identified from a linear model (FDR

    Article Snippet: All final DNA-seq and mRNA-seq libraries were quantified on an Agilent DNA High Sensitivity Chip and sequenced on the Illumina 4000 platform using 100 bp PE reads (see for sample-specific read depths).

    Techniques: Sequencing, Activity Assay, RNA Sequencing Assay, Generated

    Plasmid transfection does not induce a strong type I interferon (IFN-I) response. qPCR-based assessment (following ( Muerdter et al., 2018 )) of mRNA induction of six IFN-I response genes after transient transfection. These genes were chosen because they were initially used to identify a type I interferon response in STARR-seq data by Muerdter et al. (2018) , and because each is a key player in cGAS/STING signaling, the primary avenue through which mammalian cells sense cytoplasmic DNA. Results are shown for experiments conducted using total RNA derived from K562 cells transfected with methylated or unmethylated pmSTARRseq1 plasmid pools (containing human DNA inserts). The y-axis represents the fold change in mRNA expression levels (on a log 2 scale) between cells transfected with plasmid DNA (+DNA) relative to the mean levels observed for the same gene in untransfected cells (-DNA). Whiskers on boxplots represent the values for the third and first quartiles, plus or minus 1.5 × the interquartile range, respectively. Log2-fold changes did not significantly differ from 0 (one-sided Wilcoxon-signed rank test, p > 0.05) except for OAS3 (p = 0.047), and none of the genes was significantly affected after multiple hypothesis test correction. This result agrees with ENCODE RNA-seq data for K562s indicating inactivity of the cGAS/STING pathway.

    Journal: eLife

    Article Title: Genome-wide quantification of the effects of DNA methylation on human gene regulation

    doi: 10.7554/eLife.37513

    Figure Lengend Snippet: Plasmid transfection does not induce a strong type I interferon (IFN-I) response. qPCR-based assessment (following ( Muerdter et al., 2018 )) of mRNA induction of six IFN-I response genes after transient transfection. These genes were chosen because they were initially used to identify a type I interferon response in STARR-seq data by Muerdter et al. (2018) , and because each is a key player in cGAS/STING signaling, the primary avenue through which mammalian cells sense cytoplasmic DNA. Results are shown for experiments conducted using total RNA derived from K562 cells transfected with methylated or unmethylated pmSTARRseq1 plasmid pools (containing human DNA inserts). The y-axis represents the fold change in mRNA expression levels (on a log 2 scale) between cells transfected with plasmid DNA (+DNA) relative to the mean levels observed for the same gene in untransfected cells (-DNA). Whiskers on boxplots represent the values for the third and first quartiles, plus or minus 1.5 × the interquartile range, respectively. Log2-fold changes did not significantly differ from 0 (one-sided Wilcoxon-signed rank test, p > 0.05) except for OAS3 (p = 0.047), and none of the genes was significantly affected after multiple hypothesis test correction. This result agrees with ENCODE RNA-seq data for K562s indicating inactivity of the cGAS/STING pathway.

    Article Snippet: All final DNA-seq and mRNA-seq libraries were quantified on an Agilent DNA High Sensitivity Chip and sequenced on the Illumina 4000 platform using 100 bp PE reads (see for sample-specific read depths).

    Techniques: Plasmid Preparation, Transfection, Real-time Polymerase Chain Reaction, Derivative Assay, Methylation, Expressing, RNA Sequencing Assay

    Diversity in plasmid DNA-seq libraries versus mRNA-seq libraries. ( A ) As previously observed in STARR-seq experiments ( Arnold et al., 2013 ), plasmid DNA libraries extracted from transfected K562 cells are more diverse than mRNA-derived libraries (y-axis: proportion of all sequenced fragments that had a unique start and end coordinate within a given replicate, for methylated and unmethylated DNA-seq and mRNA-seq libraries). Whiskers on boxplots represent the values for the third and first quartiles, plus or minus 1.5 × the interquartile range, respectively. ( B ) Most fragments that appear in DNA-seq libraries but not RNA-seq libraries were at low abundance in the plasmid DNA pool. Y-axis: the proportion of 200 bp regions with zero counts from all mRNA-seq libraries, binned by quantile of normalized mean DNA-seq coverage across all input libraries (x-axis). ( C–D ) For fragments that had zero counts from all mRNA-seq libraries, the proportion of regions that overlap chromatin states ( C ) lacking H3K4me1 and H3K27ac (indicating inactive regions) and ( D ) marked by H3K4me1 and H3K27ac (indicating active regions). Proportions are binned by quantile of normalized mean DNA-seq coverage across all input libraries (x-axis). DNA fragments that were input into the experiment at high abundance, but for which no mRNAs were observed, were more likely to come from endogenously inactive regions and less likely to come from endogenously active regions. This pattern suggests that lower fragment diversity in mRNA-seq libraries relative to DNA-seq libraries is not purely technical, but also influenced by the fragment’s regulatory potential. In B-D, results are shown for the unmethylated condition for simplicity (parallel analyses for the methylated condition yielded similar results).

    Journal: eLife

    Article Title: Genome-wide quantification of the effects of DNA methylation on human gene regulation

    doi: 10.7554/eLife.37513

    Figure Lengend Snippet: Diversity in plasmid DNA-seq libraries versus mRNA-seq libraries. ( A ) As previously observed in STARR-seq experiments ( Arnold et al., 2013 ), plasmid DNA libraries extracted from transfected K562 cells are more diverse than mRNA-derived libraries (y-axis: proportion of all sequenced fragments that had a unique start and end coordinate within a given replicate, for methylated and unmethylated DNA-seq and mRNA-seq libraries). Whiskers on boxplots represent the values for the third and first quartiles, plus or minus 1.5 × the interquartile range, respectively. ( B ) Most fragments that appear in DNA-seq libraries but not RNA-seq libraries were at low abundance in the plasmid DNA pool. Y-axis: the proportion of 200 bp regions with zero counts from all mRNA-seq libraries, binned by quantile of normalized mean DNA-seq coverage across all input libraries (x-axis). ( C–D ) For fragments that had zero counts from all mRNA-seq libraries, the proportion of regions that overlap chromatin states ( C ) lacking H3K4me1 and H3K27ac (indicating inactive regions) and ( D ) marked by H3K4me1 and H3K27ac (indicating active regions). Proportions are binned by quantile of normalized mean DNA-seq coverage across all input libraries (x-axis). DNA fragments that were input into the experiment at high abundance, but for which no mRNAs were observed, were more likely to come from endogenously inactive regions and less likely to come from endogenously active regions. This pattern suggests that lower fragment diversity in mRNA-seq libraries relative to DNA-seq libraries is not purely technical, but also influenced by the fragment’s regulatory potential. In B-D, results are shown for the unmethylated condition for simplicity (parallel analyses for the methylated condition yielded similar results).

    Article Snippet: All final DNA-seq and mRNA-seq libraries were quantified on an Agilent DNA High Sensitivity Chip and sequenced on the Illumina 4000 platform using 100 bp PE reads (see for sample-specific read depths).

    Techniques: Plasmid Preparation, DNA Sequencing, Transfection, Derivative Assay, Methylation, RNA Sequencing Assay

    Modulation of mRNAs as evaluated by microarrays during collagen induced arthritis (CIA). Hierarchical clustering and color heat-map of the transcriptome (mRNAs) of CD3+ T cells from the spleen and lymph nodes of 12-week-old mice from the resistant DBA-2/J strain and the susceptible DBA-1/J strain immunized with chicken type II collagen, based on microarray expression profiling. The control mice were immunized just with complete Freund’s adjuvant (CFA) without any collagen. The dendrogram and heat-map were obtained using cluster and tree-view algorithms through Agilent GeneSpring platform. This figure shows the expression of genes related to immune system function based on Gene Ontology (GO terms). Heat map legend: Red = up regulation, green = down regulation, black = unmodulated (Pearson correlation metrics). Sample dendrogram legend: red-line = DBA-1/J control; blue-line = DBA-1/J CIA; brown-line = DBA-2/J control; gray-line = DBA-2/J CIA.

    Journal: PLoS ONE

    Article Title: T Cell Post-Transcriptional miRNA-mRNA Interaction Networks Identify Targets Associated with Susceptibility/Resistance to Collagen-induced Arthritis

    doi: 10.1371/journal.pone.0054803

    Figure Lengend Snippet: Modulation of mRNAs as evaluated by microarrays during collagen induced arthritis (CIA). Hierarchical clustering and color heat-map of the transcriptome (mRNAs) of CD3+ T cells from the spleen and lymph nodes of 12-week-old mice from the resistant DBA-2/J strain and the susceptible DBA-1/J strain immunized with chicken type II collagen, based on microarray expression profiling. The control mice were immunized just with complete Freund’s adjuvant (CFA) without any collagen. The dendrogram and heat-map were obtained using cluster and tree-view algorithms through Agilent GeneSpring platform. This figure shows the expression of genes related to immune system function based on Gene Ontology (GO terms). Heat map legend: Red = up regulation, green = down regulation, black = unmodulated (Pearson correlation metrics). Sample dendrogram legend: red-line = DBA-1/J control; blue-line = DBA-1/J CIA; brown-line = DBA-2/J control; gray-line = DBA-2/J CIA.

    Article Snippet: Cyanine-labeled complementary RNA was hybridized to microarrays in SureHyb chambers (Agilent) in a rotator oven using Agilent mouse 4×44 K oligonucleotide microarrays (Agilent Technologies) for 18 h at 60°C.

    Techniques: Mouse Assay, Microarray, Expressing

    Modulation of miRNAs as evaluated by microarrays during collagen induced arthritis (CIA). Hierarchical clustering and color heat-map of miRNome (miRNAs) of CD3 + T cells from the spleen and lymph nodes of 12-week-old mice from the resistant DBA-2/J and the susceptible DBA-1/J strain, both immunized with chicken type II collagen, based on microarray expression profiling. The control mice were immunized just with complete Freund’s adjuvant (CFA) without any collagen. The dendrogram and heat-map were obtained using cluster and tree-view algorithms through Agilent GeneSpring platform. Heat map legend: Red = up regulation, green = down regulation, black = unmodulated (Pearson correlation metrics).

    Journal: PLoS ONE

    Article Title: T Cell Post-Transcriptional miRNA-mRNA Interaction Networks Identify Targets Associated with Susceptibility/Resistance to Collagen-induced Arthritis

    doi: 10.1371/journal.pone.0054803

    Figure Lengend Snippet: Modulation of miRNAs as evaluated by microarrays during collagen induced arthritis (CIA). Hierarchical clustering and color heat-map of miRNome (miRNAs) of CD3 + T cells from the spleen and lymph nodes of 12-week-old mice from the resistant DBA-2/J and the susceptible DBA-1/J strain, both immunized with chicken type II collagen, based on microarray expression profiling. The control mice were immunized just with complete Freund’s adjuvant (CFA) without any collagen. The dendrogram and heat-map were obtained using cluster and tree-view algorithms through Agilent GeneSpring platform. Heat map legend: Red = up regulation, green = down regulation, black = unmodulated (Pearson correlation metrics).

    Article Snippet: Cyanine-labeled complementary RNA was hybridized to microarrays in SureHyb chambers (Agilent) in a rotator oven using Agilent mouse 4×44 K oligonucleotide microarrays (Agilent Technologies) for 18 h at 60°C.

    Techniques: Mouse Assay, Microarray, Expressing

    Modulation of mRNAs as evaluated by microarrays. Hierarchical clustering and color heat-map of the transcriptome (mRNAs) of thymocytes isolated from 28-day-old DBA-1/J and DBA-2/J mice and CD3 + T cells from the spleen and lymph nodes of 4-week-old mice from both strains based on microarray expression profiling. The dendrogram and heat-map were obtained using cluster and tree-view algorithms through Agilent GeneSpring platform. This figure shows the modulation of genes related to immune system based on Gene Ontology (GO terms). Heat map legend: Red = up regulation, green = down regulation, black = unmodulated (Pearson correlation metrics). Sample dendrogram legend: red-line = Naïve T cell DBA-1/J; blue-line = Naïve T cell DBA-2/J; brown-line = Thymocytes DBA-1/J; gray-line = Thymocytes DBA-2/J.

    Journal: PLoS ONE

    Article Title: T Cell Post-Transcriptional miRNA-mRNA Interaction Networks Identify Targets Associated with Susceptibility/Resistance to Collagen-induced Arthritis

    doi: 10.1371/journal.pone.0054803

    Figure Lengend Snippet: Modulation of mRNAs as evaluated by microarrays. Hierarchical clustering and color heat-map of the transcriptome (mRNAs) of thymocytes isolated from 28-day-old DBA-1/J and DBA-2/J mice and CD3 + T cells from the spleen and lymph nodes of 4-week-old mice from both strains based on microarray expression profiling. The dendrogram and heat-map were obtained using cluster and tree-view algorithms through Agilent GeneSpring platform. This figure shows the modulation of genes related to immune system based on Gene Ontology (GO terms). Heat map legend: Red = up regulation, green = down regulation, black = unmodulated (Pearson correlation metrics). Sample dendrogram legend: red-line = Naïve T cell DBA-1/J; blue-line = Naïve T cell DBA-2/J; brown-line = Thymocytes DBA-1/J; gray-line = Thymocytes DBA-2/J.

    Article Snippet: Cyanine-labeled complementary RNA was hybridized to microarrays in SureHyb chambers (Agilent) in a rotator oven using Agilent mouse 4×44 K oligonucleotide microarrays (Agilent Technologies) for 18 h at 60°C.

    Techniques: Isolation, Mouse Assay, Microarray, Expressing

    Modulation of miRNAs as evaluated by microarrays. Hierarchical clustering and color heat-map of miRNome (miRNAs) of thymocytes isolated from 4-week-old DBA-1/J and DBA-2/J mice and CD3 + T cells from the spleen and lymph nodes of 4-week-old mice from both strains based on microarray expression profiling. The dendrogram and heat-map were obtained using cluster and tree-view algorithms through Agilent GeneSpring platform. Heat map legend: Red = up regulation, green = down regulation, black = unmodulated (Pearson correlation metrics).

    Journal: PLoS ONE

    Article Title: T Cell Post-Transcriptional miRNA-mRNA Interaction Networks Identify Targets Associated with Susceptibility/Resistance to Collagen-induced Arthritis

    doi: 10.1371/journal.pone.0054803

    Figure Lengend Snippet: Modulation of miRNAs as evaluated by microarrays. Hierarchical clustering and color heat-map of miRNome (miRNAs) of thymocytes isolated from 4-week-old DBA-1/J and DBA-2/J mice and CD3 + T cells from the spleen and lymph nodes of 4-week-old mice from both strains based on microarray expression profiling. The dendrogram and heat-map were obtained using cluster and tree-view algorithms through Agilent GeneSpring platform. Heat map legend: Red = up regulation, green = down regulation, black = unmodulated (Pearson correlation metrics).

    Article Snippet: Cyanine-labeled complementary RNA was hybridized to microarrays in SureHyb chambers (Agilent) in a rotator oven using Agilent mouse 4×44 K oligonucleotide microarrays (Agilent Technologies) for 18 h at 60°C.

    Techniques: Isolation, Mouse Assay, Microarray, Expressing

    Size distribution of genetic variants . (a) A non-redundant size spectrum of SNP and CNV (including indels) and a breakdown of the proportion of gain to loss. The indel/CNV dataset consists of variants detected by assembly comparison, mate-pair, split-read, NimbleGen 42 M comparative genomic hybridization (CGH) and Agilent 24 M. The results show that the number and the size of variants are negatively correlated. Although the proportions of gains and losses are quite equal across the size spectrum, there are some deviations. Losses are more abundant in the 1 to 10 kb range, and this is mainly due to the inability of the 2-kb and 10-kb library mate-pair clones to detect insertions larger than their clone size. The opposite is seen for large events, where duplications are more common than deletions, which may be due to both biological and methodological biases. The increase in the number of events near 300 bp and 6 kb can be explained by short interspersed nuclear element (SINE) and long interspersed nuclear element (LINE) indels, respectively. The general peak around 10 kb corresponds to the interval with the highest clone coverage. (b) Size distribution of gains (insertions and duplications) highlighting the detection range of each methodology. The split-read method is designed to capture insertions from 11 bp to the size of a Sanger-based sequence read (approximately 1 kb). There is no insertion detected in the size range between the 2 kb and 10 kb library using the mate-pair approach. Furthermore, due to technical limitations, large gains (≥ 100,000 bp) cannot be identified with the sequencing-based approaches, while these are readily identified by microarrays. (c) Size distribution of deletions.

    Journal: Genome Biology

    Article Title: Towards a comprehensive structural variation map of an individual human genome

    doi: 10.1186/gb-2010-11-5-r52

    Figure Lengend Snippet: Size distribution of genetic variants . (a) A non-redundant size spectrum of SNP and CNV (including indels) and a breakdown of the proportion of gain to loss. The indel/CNV dataset consists of variants detected by assembly comparison, mate-pair, split-read, NimbleGen 42 M comparative genomic hybridization (CGH) and Agilent 24 M. The results show that the number and the size of variants are negatively correlated. Although the proportions of gains and losses are quite equal across the size spectrum, there are some deviations. Losses are more abundant in the 1 to 10 kb range, and this is mainly due to the inability of the 2-kb and 10-kb library mate-pair clones to detect insertions larger than their clone size. The opposite is seen for large events, where duplications are more common than deletions, which may be due to both biological and methodological biases. The increase in the number of events near 300 bp and 6 kb can be explained by short interspersed nuclear element (SINE) and long interspersed nuclear element (LINE) indels, respectively. The general peak around 10 kb corresponds to the interval with the highest clone coverage. (b) Size distribution of gains (insertions and duplications) highlighting the detection range of each methodology. The split-read method is designed to capture insertions from 11 bp to the size of a Sanger-based sequence read (approximately 1 kb). There is no insertion detected in the size range between the 2 kb and 10 kb library using the mate-pair approach. Furthermore, due to technical limitations, large gains (≥ 100,000 bp) cannot be identified with the sequencing-based approaches, while these are readily identified by microarrays. (c) Size distribution of deletions.

    Article Snippet: A significant amount of variation was detected from the two custom CGH arrays: an Agilent oligonucleotide array set with 24 million features (Agilent 24 M) [ ], and a NimbleGen oligonucleotide array set containing 42 million features (NimbleGen 42 M) [ ].

    Techniques: Hybridization, Clone Assay, Sequencing

    Overall workflow of the current study . Two distinct technologies were used to identify SV in the Venter genome: whole genome sequencing and genomic microarrays. The sequencing experiments, the construction of the Venter genome assembly, and the assembly comparison with NCBI build 36 (B36) reference had been completed in previous studies [ 1 , 16 , 39 ]. Hence, these experiments are shown as blue boxes. The scope of the current study is denoted in orange boxes. We re-analyzed the initial sequencing data, and searched for SVs in sequence alignments by the mate-pair and split-read approaches. We also used three distinct comparative genomic hybridization (CGH) array platforms: Agilent 24 M, NimbleGen 42 M and Agilent 244 K. Unlike the other array platforms, which were designed based on the B36 assembly, the Agilent 244 K targeted scaffold segments unique to the Celera/Venter assembly. To denote this, Figure 1 shows a dotted line connecting between the assembly comparison outcome and the Agilent 244 K box. Finally, the Affymetrix 6.0 and Illumina 1 M SNP arrays were also used in the present study.

    Journal: Genome Biology

    Article Title: Towards a comprehensive structural variation map of an individual human genome

    doi: 10.1186/gb-2010-11-5-r52

    Figure Lengend Snippet: Overall workflow of the current study . Two distinct technologies were used to identify SV in the Venter genome: whole genome sequencing and genomic microarrays. The sequencing experiments, the construction of the Venter genome assembly, and the assembly comparison with NCBI build 36 (B36) reference had been completed in previous studies [ 1 , 16 , 39 ]. Hence, these experiments are shown as blue boxes. The scope of the current study is denoted in orange boxes. We re-analyzed the initial sequencing data, and searched for SVs in sequence alignments by the mate-pair and split-read approaches. We also used three distinct comparative genomic hybridization (CGH) array platforms: Agilent 24 M, NimbleGen 42 M and Agilent 244 K. Unlike the other array platforms, which were designed based on the B36 assembly, the Agilent 244 K targeted scaffold segments unique to the Celera/Venter assembly. To denote this, Figure 1 shows a dotted line connecting between the assembly comparison outcome and the Agilent 244 K box. Finally, the Affymetrix 6.0 and Illumina 1 M SNP arrays were also used in the present study.

    Article Snippet: A significant amount of variation was detected from the two custom CGH arrays: an Agilent oligonucleotide array set with 24 million features (Agilent 24 M) [ ], and a NimbleGen oligonucleotide array set containing 42 million features (NimbleGen 42 M) [ ].

    Techniques: Sequencing, Hybridization

    Difference in the size distributions of reported indels/CNVs in published personal genome sequencing studies . The graphs show variation found in a few personal genome sequencing studies [ 1 - 4 , 6 - 8 ]. These diagrams indicate that multiple approaches are needed for better detection of CNVs. Here, the total variant set in the Venter genome found in both the Levy et al. [ 1 ] and the current study is displayed. Unlike the current study where the size of mate-pair indels is equal to the difference between the mapping distance and the expected insert size, the SVs in the Ahn et al. [ 6 ] study are only based on the mapping distance. Besides the NGS data, we have also included the variants detected by the high density Agilent 24 M data in the Kim et al. [ 7 ] study. In Wheeler et al. [ 2 ], insertions identified by intra-read alignment would be limited by the size of the sequencing read; hence, large insertions beyond the read length were not detected. Wang et al. [ 4 ], Kim et al. , and McKernan et al. [ 8 ] detected small variants based on split-reads and large ones based on mate-pairs and microarrays, but failed to detect variation between these size ranges. Also, see Additional file 1 . (a) Insertion and duplication size distribution. (b) Deletion size distribution.

    Journal: Genome Biology

    Article Title: Towards a comprehensive structural variation map of an individual human genome

    doi: 10.1186/gb-2010-11-5-r52

    Figure Lengend Snippet: Difference in the size distributions of reported indels/CNVs in published personal genome sequencing studies . The graphs show variation found in a few personal genome sequencing studies [ 1 - 4 , 6 - 8 ]. These diagrams indicate that multiple approaches are needed for better detection of CNVs. Here, the total variant set in the Venter genome found in both the Levy et al. [ 1 ] and the current study is displayed. Unlike the current study where the size of mate-pair indels is equal to the difference between the mapping distance and the expected insert size, the SVs in the Ahn et al. [ 6 ] study are only based on the mapping distance. Besides the NGS data, we have also included the variants detected by the high density Agilent 24 M data in the Kim et al. [ 7 ] study. In Wheeler et al. [ 2 ], insertions identified by intra-read alignment would be limited by the size of the sequencing read; hence, large insertions beyond the read length were not detected. Wang et al. [ 4 ], Kim et al. , and McKernan et al. [ 8 ] detected small variants based on split-reads and large ones based on mate-pairs and microarrays, but failed to detect variation between these size ranges. Also, see Additional file 1 . (a) Insertion and duplication size distribution. (b) Deletion size distribution.

    Article Snippet: A significant amount of variation was detected from the two custom CGH arrays: an Agilent oligonucleotide array set with 24 million features (Agilent 24 M) [ ], and a NimbleGen oligonucleotide array set containing 42 million features (NimbleGen 42 M) [ ].

    Techniques: Sequencing, Variant Assay, Next-Generation Sequencing

    Electrophoretogram of sequencing libraries. The graph shows the length distribution curves of sequencing libraries obtained with Illumina TruSeqTM RNA sample preparation kit (Low-Throughput protocol) according to manufacturer’s protocol. The length of DNA fragments was between 200 and 700 pb. Curves were generated on a 2100 bioanalyzer using DNA 1000 chip (Agilent Technologies). For each sample three biological replicates were performed

    Journal: SpringerPlus

    Article Title: High quality RNA extraction from Maqui berry for its application in next-generation sequencing

    doi: 10.1186/s40064-016-2906-x

    Figure Lengend Snippet: Electrophoretogram of sequencing libraries. The graph shows the length distribution curves of sequencing libraries obtained with Illumina TruSeqTM RNA sample preparation kit (Low-Throughput protocol) according to manufacturer’s protocol. The length of DNA fragments was between 200 and 700 pb. Curves were generated on a 2100 bioanalyzer using DNA 1000 chip (Agilent Technologies). For each sample three biological replicates were performed

    Article Snippet: Subsequently, the libraries were validated using DNA 1000 chip (on Agilent Technologies 2100 bioanalyzer).

    Techniques: Sequencing, Sample Prep, Generated, Chromatin Immunoprecipitation

    The workflow of L1Hs-targeted enrichment library preparation (A) Double-strand genomic DNA (blue) is extracted from a Korean individual genome (KPGP9). Red boxes indicate the regions where the probe binds to the 3′ UTR of L1Hs elements. (B) Genomic DNA is fragmented by aquatic ultrasonic wave of the Covaris S2 system. Sheared DNAs have an average size of 550 bp, which is suitable for HiSeq sequencing. (C) The Illumina’s adaptor (green) is ligated at both ends of the fragmented DNAs. (D) The adaptor-ligated DNAs is hybridized with the L1Hs-targeted probe (red and orange). Only the presence of the L1Hs 3′ UTR allows the sequence-specific binding of the probe. (E) Targeted DNA fragments are selectively elongated from the probe-binding strands. (F) Because the probe sequence attached to the L1Hs 3′ UTR and the Illumina’s adaptor sequences at both ends are known, targeted DNAs are enriched by PCR with the primer set. After library construction, the final product is confirmed using the Agilent Bioanalyzer High Sensitivity chip assay.

    Journal: Molecules and Cells

    Article Title: Novel Discovery of LINE-1 in a Korean Individual by a Target Enrichment Method

    doi: 10.14348/molcells.2018.0351

    Figure Lengend Snippet: The workflow of L1Hs-targeted enrichment library preparation (A) Double-strand genomic DNA (blue) is extracted from a Korean individual genome (KPGP9). Red boxes indicate the regions where the probe binds to the 3′ UTR of L1Hs elements. (B) Genomic DNA is fragmented by aquatic ultrasonic wave of the Covaris S2 system. Sheared DNAs have an average size of 550 bp, which is suitable for HiSeq sequencing. (C) The Illumina’s adaptor (green) is ligated at both ends of the fragmented DNAs. (D) The adaptor-ligated DNAs is hybridized with the L1Hs-targeted probe (red and orange). Only the presence of the L1Hs 3′ UTR allows the sequence-specific binding of the probe. (E) Targeted DNA fragments are selectively elongated from the probe-binding strands. (F) Because the probe sequence attached to the L1Hs 3′ UTR and the Illumina’s adaptor sequences at both ends are known, targeted DNAs are enriched by PCR with the primer set. After library construction, the final product is confirmed using the Agilent Bioanalyzer High Sensitivity chip assay.

    Article Snippet: After ligation purification, the quality of each library was assessed by using a Bioanalyzer high Sensitivity DNA chip (Agilent Technologies, USA) ( ).

    Techniques: Sequencing, Binding Assay, Polymerase Chain Reaction, Chromatin Immunoprecipitation

    CRISPR/Cas9 deletion of MTA1 in breast cancer cells. a . T7 endonuclease assay PCR results. Electropherogram of the T7 endonuclease digestion of MTA1 genomic PCR products visualized on an Agilent Bioanalyzer DNA 1000 Chip. Due to location of sgRNA target site, digestion of PCR products was predicted to generate the following fragments: wildtype 800 bp, sgRNA #1: 500 and 310 bp, sgRNA#3: 700 and 100 bp, and sgRNA #5: 760 and 40 bp. b . Western blot of MTA1 in MCF7 and MDA-MB-231 MTA1 knockout cells. GAPDH is included as an equal loading control. c . Cell proliferation assay of MCF7 and MDA-MB-231 knockout cells, compared to cells expressing an empty vector, n = 4 **** p

    Journal: Cell Communication and Signaling : CCS

    Article Title: Metastasis-associated protein 1 (MTA1) is transferred by exosomes and contributes to the regulation of hypoxia and estrogen signaling in breast cancer cells

    doi: 10.1186/s12964-019-0325-7

    Figure Lengend Snippet: CRISPR/Cas9 deletion of MTA1 in breast cancer cells. a . T7 endonuclease assay PCR results. Electropherogram of the T7 endonuclease digestion of MTA1 genomic PCR products visualized on an Agilent Bioanalyzer DNA 1000 Chip. Due to location of sgRNA target site, digestion of PCR products was predicted to generate the following fragments: wildtype 800 bp, sgRNA #1: 500 and 310 bp, sgRNA#3: 700 and 100 bp, and sgRNA #5: 760 and 40 bp. b . Western blot of MTA1 in MCF7 and MDA-MB-231 MTA1 knockout cells. GAPDH is included as an equal loading control. c . Cell proliferation assay of MCF7 and MDA-MB-231 knockout cells, compared to cells expressing an empty vector, n = 4 **** p

    Article Snippet: The T7EI digestion products were visualized by running on an Agilent Bioanalyzer DNA 1000 Chip (Agilent Technologies).

    Techniques: CRISPR, Polymerase Chain Reaction, Chromatin Immunoprecipitation, Western Blot, Multiple Displacement Amplification, Knock-Out, Proliferation Assay, Expressing, Plasmid Preparation

    Results of singleplex amplification and microarray hybridization of select, biotin-labelled amplified purified pathogen DNA targets and hybridization to the Alere ArrayTube TM printed meningitis microarray. ( A ) No template control singleplex amplification, ( B ) Streptococcus pneumoniae singleplex amplification (Primers SPne1_2, 2.5 ng/mL target DNA), ( C ) Listeria monocytogenes singleplex amplification (Primers LiMo4_6, 2.5 ng/mL target DNA), ( D ) Staphyl aureus singleplex amplification (Primers StAUB_3, 2.5 ng/mL DNA). ( E ) N. meningitidis Serogroup B singleplex amplification (Primers NsMB4, 2.5 ng/mL DNA), ( F ) No template control multiplex amplification, ( G ) S. pneumoniae multiplex amplification, ( H ) L. monocytogenes multiplex amplification, ( I ) S. aureus multiplex amplification, ( J ) N. meningitidis serogroup B multiplex amplification.

    Journal: High-Throughput

    Article Title: Development and Assessment of a Diagnostic DNA Oligonucleotide Microarray for Detection and Typing of Meningitis-Associated Bacterial Species

    doi: 10.3390/ht7040032

    Figure Lengend Snippet: Results of singleplex amplification and microarray hybridization of select, biotin-labelled amplified purified pathogen DNA targets and hybridization to the Alere ArrayTube TM printed meningitis microarray. ( A ) No template control singleplex amplification, ( B ) Streptococcus pneumoniae singleplex amplification (Primers SPne1_2, 2.5 ng/mL target DNA), ( C ) Listeria monocytogenes singleplex amplification (Primers LiMo4_6, 2.5 ng/mL target DNA), ( D ) Staphyl aureus singleplex amplification (Primers StAUB_3, 2.5 ng/mL DNA). ( E ) N. meningitidis Serogroup B singleplex amplification (Primers NsMB4, 2.5 ng/mL DNA), ( F ) No template control multiplex amplification, ( G ) S. pneumoniae multiplex amplification, ( H ) L. monocytogenes multiplex amplification, ( I ) S. aureus multiplex amplification, ( J ) N. meningitidis serogroup B multiplex amplification.

    Article Snippet: Printing of Microarray Oligonucleotide Probes in Glass Slide Format All 50- and 70-mer bacterial species and strain oligonucleotide probes for the glass slide format microarray were synthesised by Illumina (Illumina, Cambridge, UK) and printed in quadruplicate onto epoxy-coated Nexterion E slides (Schott Ltd., Stafford, UK) using a BioRobotics Microgrid II gridder (Digilab Inc., Hopkinton, MA, USA).

    Techniques: Amplification, Microarray, Hybridization, Purification, Multiplex Assay

    Fluorescence intensity heat-map of probe hybridization using amplified targets from patient cerebral spinal fluid (CSF) nucleic acids, hybridized to the glass slide-printed meningitis microarray using the manual hybridization method and formamide-free hybridization buffer.

    Journal: High-Throughput

    Article Title: Development and Assessment of a Diagnostic DNA Oligonucleotide Microarray for Detection and Typing of Meningitis-Associated Bacterial Species

    doi: 10.3390/ht7040032

    Figure Lengend Snippet: Fluorescence intensity heat-map of probe hybridization using amplified targets from patient cerebral spinal fluid (CSF) nucleic acids, hybridized to the glass slide-printed meningitis microarray using the manual hybridization method and formamide-free hybridization buffer.

    Article Snippet: Printing of Microarray Oligonucleotide Probes in Glass Slide Format All 50- and 70-mer bacterial species and strain oligonucleotide probes for the glass slide format microarray were synthesised by Illumina (Illumina, Cambridge, UK) and printed in quadruplicate onto epoxy-coated Nexterion E slides (Schott Ltd., Stafford, UK) using a BioRobotics Microgrid II gridder (Digilab Inc., Hopkinton, MA, USA).

    Techniques: Fluorescence, Hybridization, Amplification, Microarray

    Fluorescence intensity of probe hybridization with amplified Cy3-labelled bacterial DNA targets using purified pathogen nucleic acids to the glass slide-printed meningitis microarray, depicted in heatmap format ( A ) nonmeningococcal pathogens, ( B ) typed meningococcal pathogens, ( C ) untyped meningococcal pathogens, and ( D ) nonmeningococcal Neisseria spp.

    Journal: High-Throughput

    Article Title: Development and Assessment of a Diagnostic DNA Oligonucleotide Microarray for Detection and Typing of Meningitis-Associated Bacterial Species

    doi: 10.3390/ht7040032

    Figure Lengend Snippet: Fluorescence intensity of probe hybridization with amplified Cy3-labelled bacterial DNA targets using purified pathogen nucleic acids to the glass slide-printed meningitis microarray, depicted in heatmap format ( A ) nonmeningococcal pathogens, ( B ) typed meningococcal pathogens, ( C ) untyped meningococcal pathogens, and ( D ) nonmeningococcal Neisseria spp.

    Article Snippet: Printing of Microarray Oligonucleotide Probes in Glass Slide Format All 50- and 70-mer bacterial species and strain oligonucleotide probes for the glass slide format microarray were synthesised by Illumina (Illumina, Cambridge, UK) and printed in quadruplicate onto epoxy-coated Nexterion E slides (Schott Ltd., Stafford, UK) using a BioRobotics Microgrid II gridder (Digilab Inc., Hopkinton, MA, USA).

    Techniques: Fluorescence, Hybridization, Amplification, Purification, Microarray

    Fluorescence intensity of probe hybridization with amplified targets using patient CSF nucleic acids, depicted in heat-map format. From the glass slide-printed meningitis microarray, hybridizations using the Advalytix hybridization platform and formamide-containing hybridization buffer.

    Journal: High-Throughput

    Article Title: Development and Assessment of a Diagnostic DNA Oligonucleotide Microarray for Detection and Typing of Meningitis-Associated Bacterial Species

    doi: 10.3390/ht7040032

    Figure Lengend Snippet: Fluorescence intensity of probe hybridization with amplified targets using patient CSF nucleic acids, depicted in heat-map format. From the glass slide-printed meningitis microarray, hybridizations using the Advalytix hybridization platform and formamide-containing hybridization buffer.

    Article Snippet: Printing of Microarray Oligonucleotide Probes in Glass Slide Format All 50- and 70-mer bacterial species and strain oligonucleotide probes for the glass slide format microarray were synthesised by Illumina (Illumina, Cambridge, UK) and printed in quadruplicate onto epoxy-coated Nexterion E slides (Schott Ltd., Stafford, UK) using a BioRobotics Microgrid II gridder (Digilab Inc., Hopkinton, MA, USA).

    Techniques: Fluorescence, Hybridization, Amplification, Microarray

    gRNA mediated cleavage reveals mir-29b-1 as the main source of mature miR-29b. ( a ) Surveyor assay detecting the mutations on miR-29b gene locus. mmu-mir-29b-1 was shown to have mutations in cas1-1, cas1-2, cas2-1 and cas2-2; mmu-mir-29b-2 displayed mutations in cas2-1, cas2-2, cas3-1, cas3-2 and cas3-3. ( b ) Surveyor assay showed mutations on hsa-mir-29b-1 and hsa-mir-29b-2 sequences in clone cas1-1, cas1-2, cas1-3 and cas1-4. Surveyor assay products were visualized on Bioanalyser equipment using DNA 1000 chip. Full-length Bioanalyser images for ( a , b ) are presented in Supplementary Fig. 5 .

    Journal: Scientific Reports

    Article Title: Novel miR-29b target regulation patterns are revealed in two different cell lines

    doi: 10.1038/s41598-019-53868-x

    Figure Lengend Snippet: gRNA mediated cleavage reveals mir-29b-1 as the main source of mature miR-29b. ( a ) Surveyor assay detecting the mutations on miR-29b gene locus. mmu-mir-29b-1 was shown to have mutations in cas1-1, cas1-2, cas2-1 and cas2-2; mmu-mir-29b-2 displayed mutations in cas2-1, cas2-2, cas3-1, cas3-2 and cas3-3. ( b ) Surveyor assay showed mutations on hsa-mir-29b-1 and hsa-mir-29b-2 sequences in clone cas1-1, cas1-2, cas1-3 and cas1-4. Surveyor assay products were visualized on Bioanalyser equipment using DNA 1000 chip. Full-length Bioanalyser images for ( a , b ) are presented in Supplementary Fig. 5 .

    Article Snippet: Surveyor nuclease digestion products were visualized on Bioanalyser equipment using DNA 1000 chips (Agilent Technologies) containing interconnected microchannels for separation of nucleic acid fragment based on their sizes.

    Techniques: Chromatin Immunoprecipitation

    Heat map presentation of correlations between CK19 and various cadherins expressions after Affymetrix U133A oligonucleotide microarray analysis. Red colors represented positive correlation and blue colors represented negative correlation. The significance of correlation was determined by Pearson correlation coefficient R 2 . For CDH17, the R 2 was 0.867, P

    Journal: Oncology Letters

    Article Title: Cadherin 17 is related to recurrence and poor prognosis of cytokeratin 19-positive hepatocellular carcinoma

    doi: 10.3892/ol.2017.7320

    Figure Lengend Snippet: Heat map presentation of correlations between CK19 and various cadherins expressions after Affymetrix U133A oligonucleotide microarray analysis. Red colors represented positive correlation and blue colors represented negative correlation. The significance of correlation was determined by Pearson correlation coefficient R 2 . For CDH17, the R 2 was 0.867, P

    Article Snippet: Through the use of an Affymetrix U133A oligonucleotide microarray [20 patients with hepatitis B virus (HBV)-HCC], it was demonstrated that cadherin 17 (CDH17) significantly correlated with CK19 expression (R2 , 0.867; P < 0.001) in HBV-HCC.

    Techniques: Microarray