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  • 99
    Zymo Research chip dna clean
    Binding of Bcl11b to regulatory regions in the Thpok gene. a <t>DNA</t> pull-down assay showing in vitro Bcl11b binding to wild-type (Wt) Thpok silencer ( Sth ) core sequences, but not efficiently to mutant (Mut.) sequences. One representative of two experiments. b Co-immune precipitation assay showing interaction of Bcl11b with Runx1. One representative of two experiments. c Flow cytometry showing an increase of CD8 + T cells de-repressing Thpok-GFP upon reduction of Bcl11b dosage in Runx mutant mice. One representative of two independent experiments. d Bcl11b ChIP-seq tracks at the Thpok , Thpok gfp:ΔTESPE , and Sfpi1 genes in total thymocytes along with Runx ChIP-seq (GSE90794) tracks at the Thpok gene ( top ) for reference. Gene structure, transcriptional orientation and conservations in mammals (Cons.) in the Thpok gene are indicated. Positions of Thpok silencer ( Sth ), two enhancers ( TE and PE ), distal P1-promoter ( P1 ) and proximal enhancer ( PE ) in the Thpok gene, and upstream regulatory element ( URE ) in the Sfpi1 gene are indicated as arrowheads . e Co-occupancy by Runx at Bcl11b-bound genome regions. Runx recognition site (5′-ACCPuCA-3′) was listed among the top two common sequences for Bcl11b-bound regions. f ChIP-PCR assay for binding of Runx, Bcl11b, and ThPOK to Wt and Runx site mutated (RSM) Sth regions in CD4 + T cells from Thpok +/gfp:241-401RM mice. Lanes 1, 2, and 3 are input, control IgG and antibody-against the indicated transcription factor, respectively. One representative of two independent experiments. g <t>ChIP-qPCR</t> analyses showing binding of Runx and Bcl11b to the Sth and PE in CD4 + (white bars) and CD8 + (gray bars) T cells. Combined data from three independent ChIP experiments is shown. ** P
    Chip Dna Clean, supplied by Zymo Research, used in various techniques. Bioz Stars score: 99/100, based on 450 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    91
    Agilent technologies dna chips
    Amplification results using the proposed <t>DNA</t> extraction method (on-chip- electrophoresis results). The size of PCR products are 79–115 bp ( <t>CSRM60</t> ), 100–124 bp ( INRA035 ). Left to right: L, ladder; 1, sample washing water control ( CSRM60 ); 2, extraction solution (without hair shaft) control ( CSRM60 ); 3, ddH 2 O control ( CSRM60 ); 4, DNA from hair shafts of pure bred Luxi cattle ( CSRM60 ); 5, DNA from liver of beef cattle ( CSRM60 ); 6, sample washing water control ( INRA035 ); 7, extraction solution (without hair shaft) control ( INRA035 ); 8, ddH 2 O control ( INRA035 ); 9, DNA from hair shafts of pure bred Luxi cattle ( INRA035 ); 10, DNA from liver of beef cattle ( INRA035 ).
    Dna Chips, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 91/100, based on 154 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    91
    BioMed Diagnostics Inc dna chip
    The human papillomavirus <t>(HPV)</t> oligonucleotide microarray detected single infections using HPV probes (16/18/31/33/35/39/45/51/52/56/58/59/66/68/69). Hybridised signals were visualised using a <t>DNA</t> chip scanner
    Dna Chip, supplied by BioMed Diagnostics Inc, used in various techniques. Bioz Stars score: 91/100, based on 9 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    91
    Thermo Fisher oligonucleotide microarray
    a). A portion of a scanned cDNA <t>microarray</t> showing the differential expression of perforin in the cDNA microarray. Arrow indicates the position of spots corresponding to perforin (D2). Differential expression is only 3.8 b). Shows the differential expression of perforin in oligonucleotide array. Calculated fold change is 103. (I). Hybridization pattern for the perforin probe set (with RNA isolated from normal PBMC), PM = Perfect match, MM = Mismatch. (II). Hybridization pattern for the perforin probe set (with RNA isolated from leukemic LGL), PM = Perfect match, MM = Mismatch Note: Even though the gene is present in trace amounts in PBMC, it is calculated as absent because of the high background caused by MM hybridization. c). Northern blot showing the expression of perforin. Lane LGL = total RNA obtained from leukemic LGL. Lane N = total RNA isolated from normal healthy individuals. Sample from LGL leukemia patients showed over-expression of perforin.
    Oligonucleotide Microarray, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 91/100, based on 328 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    94
    Zymo Research chip dna
    a). A portion of a scanned cDNA <t>microarray</t> showing the differential expression of perforin in the cDNA microarray. Arrow indicates the position of spots corresponding to perforin (D2). Differential expression is only 3.8 b). Shows the differential expression of perforin in oligonucleotide array. Calculated fold change is 103. (I). Hybridization pattern for the perforin probe set (with RNA isolated from normal PBMC), PM = Perfect match, MM = Mismatch. (II). Hybridization pattern for the perforin probe set (with RNA isolated from leukemic LGL), PM = Perfect match, MM = Mismatch Note: Even though the gene is present in trace amounts in PBMC, it is calculated as absent because of the high background caused by MM hybridization. c). Northern blot showing the expression of perforin. Lane LGL = total RNA obtained from leukemic LGL. Lane N = total RNA isolated from normal healthy individuals. Sample from LGL leukemia patients showed over-expression of perforin.
    Chip Dna, supplied by Zymo Research, used in various techniques. Bioz Stars score: 94/100, based on 294 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    91
    Bio-Rad dna chips
    a). A portion of a scanned cDNA <t>microarray</t> showing the differential expression of perforin in the cDNA microarray. Arrow indicates the position of spots corresponding to perforin (D2). Differential expression is only 3.8 b). Shows the differential expression of perforin in oligonucleotide array. Calculated fold change is 103. (I). Hybridization pattern for the perforin probe set (with RNA isolated from normal PBMC), PM = Perfect match, MM = Mismatch. (II). Hybridization pattern for the perforin probe set (with RNA isolated from leukemic LGL), PM = Perfect match, MM = Mismatch Note: Even though the gene is present in trace amounts in PBMC, it is calculated as absent because of the high background caused by MM hybridization. c). Northern blot showing the expression of perforin. Lane LGL = total RNA obtained from leukemic LGL. Lane N = total RNA isolated from normal healthy individuals. Sample from LGL leukemia patients showed over-expression of perforin.
    Dna Chips, supplied by Bio-Rad, used in various techniques. Bioz Stars score: 91/100, based on 184 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    ATUM chip dna
    Dominant negative Lsr2 variant (Lsr2*) inhibits <t>DNA</t> binding by wild type Lsr2 and promotes antibiotic production in S. venezuelae . ( A ) Electrophoretic mobility shift assay illustrating DNA binding by wild type Lsr2, no DNA binding by the R82A mutant allele (mutant Lsr2*), and effective inhibition of Lsr2 binding by the mutant variant, based on the increasing abundance of ‘free probe’ as mutant concentrations rise. Probe: 1.5 kb region corresponding to the Lsr2 binding site in the chloramphenicol biosynthetic cluster. Reactions were separated on a 1% agarose gel stained with ethidium bromide. ( B ) Bioactivity of S. venezuelae extracts against Micrococcus luteus . Wild type S. venezuelae carrying either a control (empty) plasmid (left), or one overexpressing the mutant 9R82A) Lsr2 variant (right; Lsr2*) were cultured for 18 hr prior to extraction in methanol and reconstitution in DMSO. Extracts were applied to Whatman filter discs, and cultures were grown overnight. ( C ) Quantitative PCR analysis of Lsr2-3xFLAG-binding to the validated target site sven_0926 , following ChIP, for a strain carrying an empty plasmid (control) or overexpressing Lsr2* (O/E Lsr2*). Overexpressing Lsr2* led to a 40% drop in binding by Lsr2. ChIP experiments were conducted in duplicate, and <t>qPCR</t> was done for each replicate in technical triplicate.
    Chip Dna, supplied by ATUM, used in various techniques. Bioz Stars score: 92/100, based on 34 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    88
    Zymo Research chip dna clean and concentrator columns
    Dominant negative Lsr2 variant (Lsr2*) inhibits <t>DNA</t> binding by wild type Lsr2 and promotes antibiotic production in S. venezuelae . ( A ) Electrophoretic mobility shift assay illustrating DNA binding by wild type Lsr2, no DNA binding by the R82A mutant allele (mutant Lsr2*), and effective inhibition of Lsr2 binding by the mutant variant, based on the increasing abundance of ‘free probe’ as mutant concentrations rise. Probe: 1.5 kb region corresponding to the Lsr2 binding site in the chloramphenicol biosynthetic cluster. Reactions were separated on a 1% agarose gel stained with ethidium bromide. ( B ) Bioactivity of S. venezuelae extracts against Micrococcus luteus . Wild type S. venezuelae carrying either a control (empty) plasmid (left), or one overexpressing the mutant 9R82A) Lsr2 variant (right; Lsr2*) were cultured for 18 hr prior to extraction in methanol and reconstitution in DMSO. Extracts were applied to Whatman filter discs, and cultures were grown overnight. ( C ) Quantitative PCR analysis of Lsr2-3xFLAG-binding to the validated target site sven_0926 , following ChIP, for a strain carrying an empty plasmid (control) or overexpressing Lsr2* (O/E Lsr2*). Overexpressing Lsr2* led to a 40% drop in binding by Lsr2. ChIP experiments were conducted in duplicate, and <t>qPCR</t> was done for each replicate in technical triplicate.
    Chip Dna Clean And Concentrator Columns, supplied by Zymo Research, used in various techniques. Bioz Stars score: 88/100, based on 113 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    90
    Zymo Research chip dna clean concentrator kit
    Dominant negative Lsr2 variant (Lsr2*) inhibits <t>DNA</t> binding by wild type Lsr2 and promotes antibiotic production in S. venezuelae . ( A ) Electrophoretic mobility shift assay illustrating DNA binding by wild type Lsr2, no DNA binding by the R82A mutant allele (mutant Lsr2*), and effective inhibition of Lsr2 binding by the mutant variant, based on the increasing abundance of ‘free probe’ as mutant concentrations rise. Probe: 1.5 kb region corresponding to the Lsr2 binding site in the chloramphenicol biosynthetic cluster. Reactions were separated on a 1% agarose gel stained with ethidium bromide. ( B ) Bioactivity of S. venezuelae extracts against Micrococcus luteus . Wild type S. venezuelae carrying either a control (empty) plasmid (left), or one overexpressing the mutant 9R82A) Lsr2 variant (right; Lsr2*) were cultured for 18 hr prior to extraction in methanol and reconstitution in DMSO. Extracts were applied to Whatman filter discs, and cultures were grown overnight. ( C ) Quantitative PCR analysis of Lsr2-3xFLAG-binding to the validated target site sven_0926 , following ChIP, for a strain carrying an empty plasmid (control) or overexpressing Lsr2* (O/E Lsr2*). Overexpressing Lsr2* led to a 40% drop in binding by Lsr2. ChIP experiments were conducted in duplicate, and <t>qPCR</t> was done for each replicate in technical triplicate.
    Chip Dna Clean Concentrator Kit, supplied by Zymo Research, used in various techniques. Bioz Stars score: 90/100, based on 643 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    88
    CapitalBio Corporation dna chips e coli dna chips
    Dominant negative Lsr2 variant (Lsr2*) inhibits <t>DNA</t> binding by wild type Lsr2 and promotes antibiotic production in S. venezuelae . ( A ) Electrophoretic mobility shift assay illustrating DNA binding by wild type Lsr2, no DNA binding by the R82A mutant allele (mutant Lsr2*), and effective inhibition of Lsr2 binding by the mutant variant, based on the increasing abundance of ‘free probe’ as mutant concentrations rise. Probe: 1.5 kb region corresponding to the Lsr2 binding site in the chloramphenicol biosynthetic cluster. Reactions were separated on a 1% agarose gel stained with ethidium bromide. ( B ) Bioactivity of S. venezuelae extracts against Micrococcus luteus . Wild type S. venezuelae carrying either a control (empty) plasmid (left), or one overexpressing the mutant 9R82A) Lsr2 variant (right; Lsr2*) were cultured for 18 hr prior to extraction in methanol and reconstitution in DMSO. Extracts were applied to Whatman filter discs, and cultures were grown overnight. ( C ) Quantitative PCR analysis of Lsr2-3xFLAG-binding to the validated target site sven_0926 , following ChIP, for a strain carrying an empty plasmid (control) or overexpressing Lsr2* (O/E Lsr2*). Overexpressing Lsr2* led to a 40% drop in binding by Lsr2. ChIP experiments were conducted in duplicate, and <t>qPCR</t> was done for each replicate in technical triplicate.
    Dna Chips E Coli Dna Chips, supplied by CapitalBio Corporation, used in various techniques. Bioz Stars score: 88/100, based on 6 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    91
    Bio-Rad 1k dna chip
    Dominant negative Lsr2 variant (Lsr2*) inhibits <t>DNA</t> binding by wild type Lsr2 and promotes antibiotic production in S. venezuelae . ( A ) Electrophoretic mobility shift assay illustrating DNA binding by wild type Lsr2, no DNA binding by the R82A mutant allele (mutant Lsr2*), and effective inhibition of Lsr2 binding by the mutant variant, based on the increasing abundance of ‘free probe’ as mutant concentrations rise. Probe: 1.5 kb region corresponding to the Lsr2 binding site in the chloramphenicol biosynthetic cluster. Reactions were separated on a 1% agarose gel stained with ethidium bromide. ( B ) Bioactivity of S. venezuelae extracts against Micrococcus luteus . Wild type S. venezuelae carrying either a control (empty) plasmid (left), or one overexpressing the mutant 9R82A) Lsr2 variant (right; Lsr2*) were cultured for 18 hr prior to extraction in methanol and reconstitution in DMSO. Extracts were applied to Whatman filter discs, and cultures were grown overnight. ( C ) Quantitative PCR analysis of Lsr2-3xFLAG-binding to the validated target site sven_0926 , following ChIP, for a strain carrying an empty plasmid (control) or overexpressing Lsr2* (O/E Lsr2*). Overexpressing Lsr2* led to a 40% drop in binding by Lsr2. ChIP experiments were conducted in duplicate, and <t>qPCR</t> was done for each replicate in technical triplicate.
    1k Dna Chip, supplied by Bio-Rad, used in various techniques. Bioz Stars score: 91/100, based on 8 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    90
    Agilent technologies hs dna chip
    FES expression is regulated by promoter methylation in human melanomas. ( A ) Analysis of FES expression in 474 melanoma clinical samples from the TCGA cohort. The left panel shows FES mRNA levels ordered from the highest (red) to the lowest (green). The middle panel shows <t>DNA</t> methylation profile obtained from 19 array probes located in the CpG sites of FES . The schematic above shows a representation of the FES locus, with UTR regions in white and exons in black. CpG positions are shown as red stripes. The right panel depicts the copy number status of the FES locus split into cases that show loss (in blue) and gain (in red) and samples in which the CNA status of FES was not assessed (in gray). ( B ) FES expression in short-term melanoma cultures (MM) and 3 normal melanocyte cultures (NM). Upper graph shows expression of FES mRNA levels as determined by RT-qPCR. Values are normalized to the mean <t>RNA</t> level of normal melanocytes, which was set to 1. Error bars show mean ± SD ( n = 2). The middle panel shows Western blot analysis of FES. Actin served as a loading control. The bottom panel shows methylation profile of short-term melanoma cultures and normal melanocytes as determined by bisulfite sequencing of 20 CpG sites located at positions ranging from –72 to +115 from the FES ′ TSS. BRAF V600E (B) and NRAS Q61K,L,R (N) mutational status is indicated on top of the sample name. ( C ) Expression of FES in MM031 cell culture after treatment with demethylating agent decitabine or its vehicle. The upper panel shows FES mRNA levels assessed by qRT-PCR. Western blot analysis in the 2 lower panels shows FES protein levels. GAPDH served as a loading control.
    Hs Dna Chip, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 90/100, based on 263 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Image Search Results


    Binding of Bcl11b to regulatory regions in the Thpok gene. a DNA pull-down assay showing in vitro Bcl11b binding to wild-type (Wt) Thpok silencer ( Sth ) core sequences, but not efficiently to mutant (Mut.) sequences. One representative of two experiments. b Co-immune precipitation assay showing interaction of Bcl11b with Runx1. One representative of two experiments. c Flow cytometry showing an increase of CD8 + T cells de-repressing Thpok-GFP upon reduction of Bcl11b dosage in Runx mutant mice. One representative of two independent experiments. d Bcl11b ChIP-seq tracks at the Thpok , Thpok gfp:ΔTESPE , and Sfpi1 genes in total thymocytes along with Runx ChIP-seq (GSE90794) tracks at the Thpok gene ( top ) for reference. Gene structure, transcriptional orientation and conservations in mammals (Cons.) in the Thpok gene are indicated. Positions of Thpok silencer ( Sth ), two enhancers ( TE and PE ), distal P1-promoter ( P1 ) and proximal enhancer ( PE ) in the Thpok gene, and upstream regulatory element ( URE ) in the Sfpi1 gene are indicated as arrowheads . e Co-occupancy by Runx at Bcl11b-bound genome regions. Runx recognition site (5′-ACCPuCA-3′) was listed among the top two common sequences for Bcl11b-bound regions. f ChIP-PCR assay for binding of Runx, Bcl11b, and ThPOK to Wt and Runx site mutated (RSM) Sth regions in CD4 + T cells from Thpok +/gfp:241-401RM mice. Lanes 1, 2, and 3 are input, control IgG and antibody-against the indicated transcription factor, respectively. One representative of two independent experiments. g ChIP-qPCR analyses showing binding of Runx and Bcl11b to the Sth and PE in CD4 + (white bars) and CD8 + (gray bars) T cells. Combined data from three independent ChIP experiments is shown. ** P

    Journal: Nature Communications

    Article Title: Priming of lineage-specifying genes by Bcl11b is required for lineage choice in post-selection thymocytes

    doi: 10.1038/s41467-017-00768-1

    Figure Lengend Snippet: Binding of Bcl11b to regulatory regions in the Thpok gene. a DNA pull-down assay showing in vitro Bcl11b binding to wild-type (Wt) Thpok silencer ( Sth ) core sequences, but not efficiently to mutant (Mut.) sequences. One representative of two experiments. b Co-immune precipitation assay showing interaction of Bcl11b with Runx1. One representative of two experiments. c Flow cytometry showing an increase of CD8 + T cells de-repressing Thpok-GFP upon reduction of Bcl11b dosage in Runx mutant mice. One representative of two independent experiments. d Bcl11b ChIP-seq tracks at the Thpok , Thpok gfp:ΔTESPE , and Sfpi1 genes in total thymocytes along with Runx ChIP-seq (GSE90794) tracks at the Thpok gene ( top ) for reference. Gene structure, transcriptional orientation and conservations in mammals (Cons.) in the Thpok gene are indicated. Positions of Thpok silencer ( Sth ), two enhancers ( TE and PE ), distal P1-promoter ( P1 ) and proximal enhancer ( PE ) in the Thpok gene, and upstream regulatory element ( URE ) in the Sfpi1 gene are indicated as arrowheads . e Co-occupancy by Runx at Bcl11b-bound genome regions. Runx recognition site (5′-ACCPuCA-3′) was listed among the top two common sequences for Bcl11b-bound regions. f ChIP-PCR assay for binding of Runx, Bcl11b, and ThPOK to Wt and Runx site mutated (RSM) Sth regions in CD4 + T cells from Thpok +/gfp:241-401RM mice. Lanes 1, 2, and 3 are input, control IgG and antibody-against the indicated transcription factor, respectively. One representative of two independent experiments. g ChIP-qPCR analyses showing binding of Runx and Bcl11b to the Sth and PE in CD4 + (white bars) and CD8 + (gray bars) T cells. Combined data from three independent ChIP experiments is shown. ** P

    Article Snippet: DNA was purified by Phenol/Chloroform extraction for ChIP-seq or ChIP DNA Clean and Concentrator kit (ZYMO RESEARCH) for ChIP-qPCR.

    Techniques: Binding Assay, Pull Down Assay, In Vitro, Mutagenesis, Flow Cytometry, Cytometry, Mouse Assay, Chromatin Immunoprecipitation, Polymerase Chain Reaction, Real-time Polymerase Chain Reaction

    Biological replicates for ChIP experiments in Figure 5 . ChIP assays were performed with FAMAp:FAMA-MYC in Col ( A ), FAMAp:RBR-MYC in Col ( B ), and FAMAp:RBR-MYC in FAMA LGK plants ( C ) using an anti-Myc antibody as in ( Lau et al., 2014 ). ChIPed DNA was quantified by qPCR with primers specific to the indicated gene promoters or the negative control region, IR1 or RB45 ( Cruz-Ramirez et al., 2012 ) and ( Weimer et al., 2012 ). Input-adjusted signals were normalized to Col. Values are means ± SEM. DOI: http://dx.doi.org/10.7554/eLife.03271.015

    Journal: eLife

    Article Title: Irreversible fate commitment in the Arabidopsis stomatal lineage requires a FAMA and RETINOBLASTOMA-RELATED module

    doi: 10.7554/eLife.03271

    Figure Lengend Snippet: Biological replicates for ChIP experiments in Figure 5 . ChIP assays were performed with FAMAp:FAMA-MYC in Col ( A ), FAMAp:RBR-MYC in Col ( B ), and FAMAp:RBR-MYC in FAMA LGK plants ( C ) using an anti-Myc antibody as in ( Lau et al., 2014 ). ChIPed DNA was quantified by qPCR with primers specific to the indicated gene promoters or the negative control region, IR1 or RB45 ( Cruz-Ramirez et al., 2012 ) and ( Weimer et al., 2012 ). Input-adjusted signals were normalized to Col. Values are means ± SEM. DOI: http://dx.doi.org/10.7554/eLife.03271.015

    Article Snippet: ChIPed DNA was purified by the ChIP DNA Clean & Concentrator (Zymo).

    Techniques: Chromatin Immunoprecipitation, Real-time Polymerase Chain Reaction, Negative Control

    Dissection of FAMA and RBR binding on stomatal target genes. ( A and D ) Map of the SPCH ( A ) and EPF1 ( D ) loci. Arrow indicates orientation of the gene and the transcription start site. Genome coordinate is indicated above the gene structure. Black bars indicate genomic region probed by ChIP-qPCR assays. Key: U, upstream; P, promoter; D, downstream. ( B , C , E and F ) ChIP assays were performed with FAMAp:FAMA-MYC in fama ( B and E ) and FAMAp:RBR-MYC in Col ( C and F ), using an anti-Myc antibody as in ( Lau et al., 2014 ). ChIPed DNA was quantified by qPCR with primers specific to the indicated genomic regions relative to SPCH ( B and C ) and EPF1 ( E and F ) or the negative control region, RB45 ( Weimer et al., 2012 ). Input-adjusted signals were normalized to Col. Values are means ± SEM. DOI: http://dx.doi.org/10.7554/eLife.03271.016

    Journal: eLife

    Article Title: Irreversible fate commitment in the Arabidopsis stomatal lineage requires a FAMA and RETINOBLASTOMA-RELATED module

    doi: 10.7554/eLife.03271

    Figure Lengend Snippet: Dissection of FAMA and RBR binding on stomatal target genes. ( A and D ) Map of the SPCH ( A ) and EPF1 ( D ) loci. Arrow indicates orientation of the gene and the transcription start site. Genome coordinate is indicated above the gene structure. Black bars indicate genomic region probed by ChIP-qPCR assays. Key: U, upstream; P, promoter; D, downstream. ( B , C , E and F ) ChIP assays were performed with FAMAp:FAMA-MYC in fama ( B and E ) and FAMAp:RBR-MYC in Col ( C and F ), using an anti-Myc antibody as in ( Lau et al., 2014 ). ChIPed DNA was quantified by qPCR with primers specific to the indicated genomic regions relative to SPCH ( B and C ) and EPF1 ( E and F ) or the negative control region, RB45 ( Weimer et al., 2012 ). Input-adjusted signals were normalized to Col. Values are means ± SEM. DOI: http://dx.doi.org/10.7554/eLife.03271.016

    Article Snippet: ChIPed DNA was purified by the ChIP DNA Clean & Concentrator (Zymo).

    Techniques: Dissection, Binding Assay, Chromatin Immunoprecipitation, Real-time Polymerase Chain Reaction, Negative Control

    Acidosis-driven MondoA transcriptional activity depends on electron transport. ( A and B ) TXNIP protein levels were determine by immunoblotting following a 4 hr HBSS treatment of MEFs in the presence of the indicated inhibitors. Cont; control, Chlor; Chloroquine (25 μM), Mon; monensin (5 μM), Met; metformin (1 mM), FCCP; carbonilcyanide p -triflouromethoxyphenylhydrazone (1 µM), Oligo; oligomycin (1 μM). ( C–E ), TXNIP mRNA levels were determine using RT-qPCR following 4 hr treatments with DMEM Acidic : ( C ) 143B osteosarcoma cells, ( D ) 143Bρ 0 cells, and ( E ) 143Bρ 0 :WT-Cybrid cells complemented with wild type mitochondria. ( F ) Schematic depicting nuclear- and mitochondrial-DNA encoded components of the ETC. ( G ) TXNIP mRNA levels following 4 hr DMEM Acidic treatments of 143Bρ 0 :ΔATP6/ATP8-Cybrid cells expressing empty vector or nuclear encoded, mitochondrial-targeted ATP6 and ATP8. *p

    Journal: eLife

    Article Title: Cellular acidosis triggers human MondoA transcriptional activity by driving mitochondrial ATP production

    doi: 10.7554/eLife.40199

    Figure Lengend Snippet: Acidosis-driven MondoA transcriptional activity depends on electron transport. ( A and B ) TXNIP protein levels were determine by immunoblotting following a 4 hr HBSS treatment of MEFs in the presence of the indicated inhibitors. Cont; control, Chlor; Chloroquine (25 μM), Mon; monensin (5 μM), Met; metformin (1 mM), FCCP; carbonilcyanide p -triflouromethoxyphenylhydrazone (1 µM), Oligo; oligomycin (1 μM). ( C–E ), TXNIP mRNA levels were determine using RT-qPCR following 4 hr treatments with DMEM Acidic : ( C ) 143B osteosarcoma cells, ( D ) 143Bρ 0 cells, and ( E ) 143Bρ 0 :WT-Cybrid cells complemented with wild type mitochondria. ( F ) Schematic depicting nuclear- and mitochondrial-DNA encoded components of the ETC. ( G ) TXNIP mRNA levels following 4 hr DMEM Acidic treatments of 143Bρ 0 :ΔATP6/ATP8-Cybrid cells expressing empty vector or nuclear encoded, mitochondrial-targeted ATP6 and ATP8. *p

    Article Snippet: After reversal of crosslinks and ChIP DNA purification (Zymo Research, D5201), MondoA binding on TXNIP, ARRDC4, KLF10 and TMEM97 were determined by normalizing to input.

    Techniques: Activity Assay, Quantitative RT-PCR, Expressing, Plasmid Preparation

    ITGA6 is a direct HIF transcriptional target gene. a A schematic representation of putative HREs identified in the proximal promoter of ITGA6 that were assessed for HIF-1α and/or HIF-2α recruitment by ChIP assays. b MDA-MB-231 shControl and shHIF1A cells were cultured at hypoxia (0.5 % O 2 ) for 6 h, and chromatin fragments were immunoprecipitated using HIF-1α or HIF-2α antibodies or anti-rabbit IgG (as the non-specific binding control). SYBR Green-based qRT-PCR was conducted on the purified, isolated DNA fragments to determine the site fold enrichment of HIFα recruitment relative to signal detected in the anti-rabbit IgG control per genotype (qRT-PCR values observed for the IgG control were set to 1.0 per genotype). As the positive control, qRT-PCR was also performed using primers flanking a previously validated, functional HRE site in the 3’ EPO enhancer. Each panel shows the mean site fold enrichment ± SEM of technical replicates; data presented are representative of three replicate experiments. c Luciferase reporter assays were used to compare relative luciferase activity between MDA-MB-231 shControl or shHIF1A/shHIF2A cells transiently transfected with a wild type ITGA6 promoter linked to luciferase (ITGA6-Luc; white bars) or a HRE mutant promoter construct [ITGA6 (mutant)-Luc; grey bars] and then cultured at normoxia (Nor) or hypoxia (Hyp). In some cases, a stabilized version of murine HIF-1α was also co-transfected (+HIF1A). The mean ± standard deviation are shown; p

    Journal: Molecular Cancer

    Article Title: ITGA6 is directly regulated by hypoxia-inducible factors and enriches for cancer stem cell activity and invasion in metastatic breast cancer models

    doi: 10.1186/s12943-016-0510-x

    Figure Lengend Snippet: ITGA6 is a direct HIF transcriptional target gene. a A schematic representation of putative HREs identified in the proximal promoter of ITGA6 that were assessed for HIF-1α and/or HIF-2α recruitment by ChIP assays. b MDA-MB-231 shControl and shHIF1A cells were cultured at hypoxia (0.5 % O 2 ) for 6 h, and chromatin fragments were immunoprecipitated using HIF-1α or HIF-2α antibodies or anti-rabbit IgG (as the non-specific binding control). SYBR Green-based qRT-PCR was conducted on the purified, isolated DNA fragments to determine the site fold enrichment of HIFα recruitment relative to signal detected in the anti-rabbit IgG control per genotype (qRT-PCR values observed for the IgG control were set to 1.0 per genotype). As the positive control, qRT-PCR was also performed using primers flanking a previously validated, functional HRE site in the 3’ EPO enhancer. Each panel shows the mean site fold enrichment ± SEM of technical replicates; data presented are representative of three replicate experiments. c Luciferase reporter assays were used to compare relative luciferase activity between MDA-MB-231 shControl or shHIF1A/shHIF2A cells transiently transfected with a wild type ITGA6 promoter linked to luciferase (ITGA6-Luc; white bars) or a HRE mutant promoter construct [ITGA6 (mutant)-Luc; grey bars] and then cultured at normoxia (Nor) or hypoxia (Hyp). In some cases, a stabilized version of murine HIF-1α was also co-transfected (+HIF1A). The mean ± standard deviation are shown; p

    Article Snippet: Reverse crosslinking was accomplished by adding 1 μl of 10 mg/ml RNase and 5 M NaCl to a final concentration of 0.2 M and incubation at 65 °C for 5 h, followed by digestion with Proteinase K at 37 °C for 1 h. Immunoprecipitated DNA was recovered using the ChIP DNA Clean and Concentrator kit (Zymo Research, Irvine, CA). qRT-PCR was performed on all samples using LightCycler 480 SYBR Green master mix.

    Techniques: Chromatin Immunoprecipitation, Multiple Displacement Amplification, Cell Culture, Immunoprecipitation, Binding Assay, SYBR Green Assay, Quantitative RT-PCR, Purification, Isolation, Positive Control, Functional Assay, Luciferase, Activity Assay, Transfection, Mutagenesis, Construct, Standard Deviation

    SUMOylation facilitates HDAC2-to-ROR-γt binding and inhibits IL-17 expression. a Lysates from cLPLs of WT mice were immunoprecipitated with anti-ROR-γt, anti-HDAC2 antibody, or control IgG antibody and immunoblotted with antibody against ROR-γt or HDAC2. b Transduced ROR-γt –/– CD4 + T cells expressing either WT-ROR-γt or the K187R-ROR-γt were immunoprecipitated with anti-V5 antibody and immunoblot with antibody against V5 or HDAC2. c Binding of HDAC2 to the IL-17 promoter was assessed by ChIP analysis using a DNA-protein complex from cLPLs of WT mice that was immunoprecipitated with anti-ROR-γt, anti-HDAC2, or control IgG antibody. d SUMOylation of ROR-γt facilitates HDAC2 recruitment to the IL-17 promoter. ChIP analysis was conducted using DNA-protein complex from transduced ROR-γt –/– CD4 + T cells expressing either WT-ROR-γt or the K187R-ROR-γt and immunoprecipitated with anti–ROR-γt, anti-HDAC2, or control IgG antibody. e A luciferase assay was performed of lysates from Jurkat T cells transfected with various combinations (below plot) of IL - 17-promoter-driven luciferase plasmid (pGL4-mIL17p), plasmid encoding WT-ROR-γt or K187R-ROR-γt along with either HDAC2-WT or HDAC2-H141A. Results are presented in relative luciferase units (RLU). Data are from one experiment representative of three or more independent experiments with similar results. * p

    Journal: Nature Communications

    Article Title: SUMOylation of ROR-γt inhibits IL-17 expression and inflammation via HDAC2

    doi: 10.1038/s41467-018-06924-5

    Figure Lengend Snippet: SUMOylation facilitates HDAC2-to-ROR-γt binding and inhibits IL-17 expression. a Lysates from cLPLs of WT mice were immunoprecipitated with anti-ROR-γt, anti-HDAC2 antibody, or control IgG antibody and immunoblotted with antibody against ROR-γt or HDAC2. b Transduced ROR-γt –/– CD4 + T cells expressing either WT-ROR-γt or the K187R-ROR-γt were immunoprecipitated with anti-V5 antibody and immunoblot with antibody against V5 or HDAC2. c Binding of HDAC2 to the IL-17 promoter was assessed by ChIP analysis using a DNA-protein complex from cLPLs of WT mice that was immunoprecipitated with anti-ROR-γt, anti-HDAC2, or control IgG antibody. d SUMOylation of ROR-γt facilitates HDAC2 recruitment to the IL-17 promoter. ChIP analysis was conducted using DNA-protein complex from transduced ROR-γt –/– CD4 + T cells expressing either WT-ROR-γt or the K187R-ROR-γt and immunoprecipitated with anti–ROR-γt, anti-HDAC2, or control IgG antibody. e A luciferase assay was performed of lysates from Jurkat T cells transfected with various combinations (below plot) of IL - 17-promoter-driven luciferase plasmid (pGL4-mIL17p), plasmid encoding WT-ROR-γt or K187R-ROR-γt along with either HDAC2-WT or HDAC2-H141A. Results are presented in relative luciferase units (RLU). Data are from one experiment representative of three or more independent experiments with similar results. * p

    Article Snippet: After cross-link reversal and proteinase K treatment, immunoprecipitated DNA was purified using the ChIP DNA Clean kit (Zymo Research, Irvine, CA, USA).

    Techniques: Binding Assay, Expressing, Mouse Assay, Immunoprecipitation, Chromatin Immunoprecipitation, Luciferase, Transfection, Plasmid Preparation

    p53 interacts with the let-7a3 and let-7b gene enhancer. (A) PCR primers were designed to potential p53 binding sites upstream of let-7a3 and let-7b gene overlapping transcripts OTTHUMG00000030111 and OTTHUMG00000150446. HCT 116 cells were irradiated, fixed and p53 was immunoprecipitated using anti-p53 antibody. Real-time RT-PCR was then performed which revealed binding in the p53 +/+ cells after radiation but not in the p53 −/− cells (B). All results were normalized to input DNA. (C) Human genomic DNA upstream of let-7a3 and let-7b containing the p53 binding site was cloned upstream of luciferase in the vectors pGL3 basic or pGL4.23[ luc2 /minP]. Each of these constructs was transfected into HCT116 p53 +/+ cells. Twenty-four hours after transfection, lysates were collected and assayed for luciferase activity (D). The active pGL4.23[luc2/minP] clone was transfected into HCT116 p53 +/+ and p53 −/− cells that were irradiated to 2 Gy and assayed for luciferase expression. Although no change in luciferase expression was noted with transfection of the minimal promoter alone, the addition of the enhancer element resulted in suppression of luciferase expression in the HCT116 p53 +/+ cells but not the p53 −/− cells (E). * denotes p

    Journal: PLoS ONE

    Article Title: Cellular Stress Induced Alterations in MicroRNA let-7a and let-7b Expression Are Dependent on p53

    doi: 10.1371/journal.pone.0024429

    Figure Lengend Snippet: p53 interacts with the let-7a3 and let-7b gene enhancer. (A) PCR primers were designed to potential p53 binding sites upstream of let-7a3 and let-7b gene overlapping transcripts OTTHUMG00000030111 and OTTHUMG00000150446. HCT 116 cells were irradiated, fixed and p53 was immunoprecipitated using anti-p53 antibody. Real-time RT-PCR was then performed which revealed binding in the p53 +/+ cells after radiation but not in the p53 −/− cells (B). All results were normalized to input DNA. (C) Human genomic DNA upstream of let-7a3 and let-7b containing the p53 binding site was cloned upstream of luciferase in the vectors pGL3 basic or pGL4.23[ luc2 /minP]. Each of these constructs was transfected into HCT116 p53 +/+ cells. Twenty-four hours after transfection, lysates were collected and assayed for luciferase activity (D). The active pGL4.23[luc2/minP] clone was transfected into HCT116 p53 +/+ and p53 −/− cells that were irradiated to 2 Gy and assayed for luciferase expression. Although no change in luciferase expression was noted with transfection of the minimal promoter alone, the addition of the enhancer element resulted in suppression of luciferase expression in the HCT116 p53 +/+ cells but not the p53 −/− cells (E). * denotes p

    Article Snippet: Input and immunoprecipitated DNA samples were purified with a ChIP DNA cleanup kit (Zymo Research).

    Techniques: Polymerase Chain Reaction, Binding Assay, Irradiation, Immunoprecipitation, Quantitative RT-PCR, Clone Assay, Luciferase, Construct, Transfection, Activity Assay, Expressing

    Amplification results using the proposed DNA extraction method (on-chip- electrophoresis results). The size of PCR products are 79–115 bp ( CSRM60 ), 100–124 bp ( INRA035 ). Left to right: L, ladder; 1, sample washing water control ( CSRM60 ); 2, extraction solution (without hair shaft) control ( CSRM60 ); 3, ddH 2 O control ( CSRM60 ); 4, DNA from hair shafts of pure bred Luxi cattle ( CSRM60 ); 5, DNA from liver of beef cattle ( CSRM60 ); 6, sample washing water control ( INRA035 ); 7, extraction solution (without hair shaft) control ( INRA035 ); 8, ddH 2 O control ( INRA035 ); 9, DNA from hair shafts of pure bred Luxi cattle ( INRA035 ); 10, DNA from liver of beef cattle ( INRA035 ).

    Journal: PLoS ONE

    Article Title: A Simple Method to Extract DNA from Hair Shafts Using Enzymatic Laundry Powder

    doi: 10.1371/journal.pone.0069588

    Figure Lengend Snippet: Amplification results using the proposed DNA extraction method (on-chip- electrophoresis results). The size of PCR products are 79–115 bp ( CSRM60 ), 100–124 bp ( INRA035 ). Left to right: L, ladder; 1, sample washing water control ( CSRM60 ); 2, extraction solution (without hair shaft) control ( CSRM60 ); 3, ddH 2 O control ( CSRM60 ); 4, DNA from hair shafts of pure bred Luxi cattle ( CSRM60 ); 5, DNA from liver of beef cattle ( CSRM60 ); 6, sample washing water control ( INRA035 ); 7, extraction solution (without hair shaft) control ( INRA035 ); 8, ddH 2 O control ( INRA035 ); 9, DNA from hair shafts of pure bred Luxi cattle ( INRA035 ); 10, DNA from liver of beef cattle ( INRA035 ).

    Article Snippet: Then, amplification products (locus CSRM60 and INRA035 ) were pipette onto DNA Chips (on-chip-electrophoresis, Agilent DNA 1000 Kit, for use with the Agilent 2100 bioanalyzer) and operated as its Guide described, while the others were visualized under UV light on 1.2% agarose gels by staining with GeneGreen (Tiangen Biotech (Beijing) Co., Ltd.).

    Techniques: Amplification, DNA Extraction, Chromatin Immunoprecipitation, Electrophoresis, Polymerase Chain Reaction

    Comparison of amplification results of DNA extracted from hair shafts using the proposed method and that extracted from liver using commercial Genomic DNA Purification Kit (on-chip-electrophoresis results). The above panel is INRA035 comparison result, sample 6 is amplification result of hair shaft DNA from pure bred Luxi cattle and sample 3 is amplification result of liver DNA from beef cattle; The below panel is CSRM60 comparison result, sample 2 is amplification result of hair shaft DNA from pure bred Luxi cattle and sample 11 is amplification result of liver DNA from beef cattle.

    Journal: PLoS ONE

    Article Title: A Simple Method to Extract DNA from Hair Shafts Using Enzymatic Laundry Powder

    doi: 10.1371/journal.pone.0069588

    Figure Lengend Snippet: Comparison of amplification results of DNA extracted from hair shafts using the proposed method and that extracted from liver using commercial Genomic DNA Purification Kit (on-chip-electrophoresis results). The above panel is INRA035 comparison result, sample 6 is amplification result of hair shaft DNA from pure bred Luxi cattle and sample 3 is amplification result of liver DNA from beef cattle; The below panel is CSRM60 comparison result, sample 2 is amplification result of hair shaft DNA from pure bred Luxi cattle and sample 11 is amplification result of liver DNA from beef cattle.

    Article Snippet: Then, amplification products (locus CSRM60 and INRA035 ) were pipette onto DNA Chips (on-chip-electrophoresis, Agilent DNA 1000 Kit, for use with the Agilent 2100 bioanalyzer) and operated as its Guide described, while the others were visualized under UV light on 1.2% agarose gels by staining with GeneGreen (Tiangen Biotech (Beijing) Co., Ltd.).

    Techniques: Amplification, DNA Purification, Chromatin Immunoprecipitation, Electrophoresis

    The human papillomavirus (HPV) oligonucleotide microarray detected single infections using HPV probes (16/18/31/33/35/39/45/51/52/56/58/59/66/68/69). Hybridised signals were visualised using a DNA chip scanner

    Journal:

    Article Title: Multinucleation of koilocytes is in fact multilobation and is related to aberration of the G2 checkpoint

    doi: 10.1136/jcp.2004.022152

    Figure Lengend Snippet: The human papillomavirus (HPV) oligonucleotide microarray detected single infections using HPV probes (16/18/31/33/35/39/45/51/52/56/58/59/66/68/69). Hybridised signals were visualised using a DNA chip scanner

    Article Snippet: After confirmation of 22 HPV genotypes by DNA chip (Biomed Lab Co, Seoul, Korea), we looked at koilocytes from the cervical swab and tissue specimens by three dimensional confocal restoration—we reconstructed stacks of two dimensional images of koilocytes to produce three dimensional images by confocal microscopy.

    Techniques: Microarray, Chromatin Immunoprecipitation

    a). A portion of a scanned cDNA microarray showing the differential expression of perforin in the cDNA microarray. Arrow indicates the position of spots corresponding to perforin (D2). Differential expression is only 3.8 b). Shows the differential expression of perforin in oligonucleotide array. Calculated fold change is 103. (I). Hybridization pattern for the perforin probe set (with RNA isolated from normal PBMC), PM = Perfect match, MM = Mismatch. (II). Hybridization pattern for the perforin probe set (with RNA isolated from leukemic LGL), PM = Perfect match, MM = Mismatch Note: Even though the gene is present in trace amounts in PBMC, it is calculated as absent because of the high background caused by MM hybridization. c). Northern blot showing the expression of perforin. Lane LGL = total RNA obtained from leukemic LGL. Lane N = total RNA isolated from normal healthy individuals. Sample from LGL leukemia patients showed over-expression of perforin.

    Journal: BMC Bioinformatics

    Article Title: Microarray results: how accurate are they?

    doi: 10.1186/1471-2105-3-22

    Figure Lengend Snippet: a). A portion of a scanned cDNA microarray showing the differential expression of perforin in the cDNA microarray. Arrow indicates the position of spots corresponding to perforin (D2). Differential expression is only 3.8 b). Shows the differential expression of perforin in oligonucleotide array. Calculated fold change is 103. (I). Hybridization pattern for the perforin probe set (with RNA isolated from normal PBMC), PM = Perfect match, MM = Mismatch. (II). Hybridization pattern for the perforin probe set (with RNA isolated from leukemic LGL), PM = Perfect match, MM = Mismatch Note: Even though the gene is present in trace amounts in PBMC, it is calculated as absent because of the high background caused by MM hybridization. c). Northern blot showing the expression of perforin. Lane LGL = total RNA obtained from leukemic LGL. Lane N = total RNA isolated from normal healthy individuals. Sample from LGL leukemia patients showed over-expression of perforin.

    Article Snippet: Kuo et al (2002) compared the data from two high-throughput DNA microarray technologies, cDNA microarray (Stanford type) and oligonucleotide microarray (from Affymetrix) and found very little correlation between these two platforms [ ].

    Techniques: Microarray, Expressing, Hybridization, Isolation, Northern Blot, Over Expression

    a). A portion of a scanned cDNA microarray showing the differential expression of granzyme H. The cDNA fragment spotted on position F12 corresponds to granzyme H (indicated by arrow). (I). Hybridization profile for LGL leukemia cells. (II). Hybridization profile for control. Balanced differential expression, 6.3. b). Shows the differential expression of Granzyme B in oligonucleotide array . Calculated fold change is 20.5 (I). Hybridization pattern for the granzyme B probe set (with RNA isolated from normal PBMC), PM = Perfect match, MM = Mismatch. (II). Hybridization pattern for the granzyme B probe set (with RNA isolated from leukemic LGL), PM = Perfect match, MM = Mismatch c). Northern blot showing expression of granzyme B/H. The probe used was the same as the probes spotted on the microarray. Lane LGL = total RNA samples isolated from LGL leukemia patient Lane N = total RNA isolated from normal healthy control. NA = Total RNA isolated from PBMC of a normal healthy individual activated with IL2 and PHA. d). RNase protection assay for granzyme B. Probe set hAPO-4 obtained from PharMingen contains a specific probe for granzyme B. Note: Leukemic LGL cells over-expressed granzyme B (Lane LGL), whereas very low levels of granzyme B were observed in PBMC from normal healthy control (Lane N). Normal activated PBMC showed strong expression of granzyme B (Lane NA). e). RNase protection assay for granzyme H. Probe set hAPO-4 obtained from PharMingen contains a specific probe for granzyme H. Leukemic LGL cells showed over-expression (Lane LGL). PBMC obtained from a normal healthy individual (Lane N) and activated PBMC showed trace expression.

    Journal: BMC Bioinformatics

    Article Title: Microarray results: how accurate are they?

    doi: 10.1186/1471-2105-3-22

    Figure Lengend Snippet: a). A portion of a scanned cDNA microarray showing the differential expression of granzyme H. The cDNA fragment spotted on position F12 corresponds to granzyme H (indicated by arrow). (I). Hybridization profile for LGL leukemia cells. (II). Hybridization profile for control. Balanced differential expression, 6.3. b). Shows the differential expression of Granzyme B in oligonucleotide array . Calculated fold change is 20.5 (I). Hybridization pattern for the granzyme B probe set (with RNA isolated from normal PBMC), PM = Perfect match, MM = Mismatch. (II). Hybridization pattern for the granzyme B probe set (with RNA isolated from leukemic LGL), PM = Perfect match, MM = Mismatch c). Northern blot showing expression of granzyme B/H. The probe used was the same as the probes spotted on the microarray. Lane LGL = total RNA samples isolated from LGL leukemia patient Lane N = total RNA isolated from normal healthy control. NA = Total RNA isolated from PBMC of a normal healthy individual activated with IL2 and PHA. d). RNase protection assay for granzyme B. Probe set hAPO-4 obtained from PharMingen contains a specific probe for granzyme B. Note: Leukemic LGL cells over-expressed granzyme B (Lane LGL), whereas very low levels of granzyme B were observed in PBMC from normal healthy control (Lane N). Normal activated PBMC showed strong expression of granzyme B (Lane NA). e). RNase protection assay for granzyme H. Probe set hAPO-4 obtained from PharMingen contains a specific probe for granzyme H. Leukemic LGL cells showed over-expression (Lane LGL). PBMC obtained from a normal healthy individual (Lane N) and activated PBMC showed trace expression.

    Article Snippet: Kuo et al (2002) compared the data from two high-throughput DNA microarray technologies, cDNA microarray (Stanford type) and oligonucleotide microarray (from Affymetrix) and found very little correlation between these two platforms [ ].

    Techniques: Microarray, Expressing, Hybridization, Isolation, Northern Blot, Rnase Protection Assay, Over Expression

    a). A portion of a scanned cDNA microarray showing the differential expression of PAC-1. The cDNA fragment spotted on position E6 corresponds to PAC-1. (I) Hybridization pattern for LGL patient. (II). Hybridization pattern for control. b). Shows the differential expression of PAC-1 in oligonucleotide array. Calculated fold change is 1.6 (I) Hybridization pattern for the PAC-1 probe set (RNA isolated from normal PBMC. PM = Perfect Match, MM = Mismatch. (II) Hybridization pattern for the PAC-1 probe set (RNA isolated from leukemic LGL cells. PM = Perfect Match, MM = Mismatch. c). Northern blot showing the expression of PAC-1 like genes. The probe used was the same as the one spotted on the microarray. Lane LGL = total RNA isolated from LGL leukemia patients (LGL). Lane N = total RNA isolated from normal healthy controls.

    Journal: BMC Bioinformatics

    Article Title: Microarray results: how accurate are they?

    doi: 10.1186/1471-2105-3-22

    Figure Lengend Snippet: a). A portion of a scanned cDNA microarray showing the differential expression of PAC-1. The cDNA fragment spotted on position E6 corresponds to PAC-1. (I) Hybridization pattern for LGL patient. (II). Hybridization pattern for control. b). Shows the differential expression of PAC-1 in oligonucleotide array. Calculated fold change is 1.6 (I) Hybridization pattern for the PAC-1 probe set (RNA isolated from normal PBMC. PM = Perfect Match, MM = Mismatch. (II) Hybridization pattern for the PAC-1 probe set (RNA isolated from leukemic LGL cells. PM = Perfect Match, MM = Mismatch. c). Northern blot showing the expression of PAC-1 like genes. The probe used was the same as the one spotted on the microarray. Lane LGL = total RNA isolated from LGL leukemia patients (LGL). Lane N = total RNA isolated from normal healthy controls.

    Article Snippet: Kuo et al (2002) compared the data from two high-throughput DNA microarray technologies, cDNA microarray (Stanford type) and oligonucleotide microarray (from Affymetrix) and found very little correlation between these two platforms [ ].

    Techniques: Microarray, Expressing, Hybridization, Isolation, Northern Blot

    a). A portion of a scanned cDNA microarray showing the differential expression of NKG2 C. The cDNA fragment spotted on position H11 correspond to NKG2 C. (I) Hybridization pattern for LGL patient. (II). Hybridization pattern for control. b). Northern Blot showing the expression of NKG2 family members. The probe used was the same as the one spotted on the microarray. Lane LGL = total RNA isolated from LGL leukemia patients (LGL). Lanes N = total RNA isolated from normal healthy controls.

    Journal: BMC Bioinformatics

    Article Title: Microarray results: how accurate are they?

    doi: 10.1186/1471-2105-3-22

    Figure Lengend Snippet: a). A portion of a scanned cDNA microarray showing the differential expression of NKG2 C. The cDNA fragment spotted on position H11 correspond to NKG2 C. (I) Hybridization pattern for LGL patient. (II). Hybridization pattern for control. b). Northern Blot showing the expression of NKG2 family members. The probe used was the same as the one spotted on the microarray. Lane LGL = total RNA isolated from LGL leukemia patients (LGL). Lanes N = total RNA isolated from normal healthy controls.

    Article Snippet: Kuo et al (2002) compared the data from two high-throughput DNA microarray technologies, cDNA microarray (Stanford type) and oligonucleotide microarray (from Affymetrix) and found very little correlation between these two platforms [ ].

    Techniques: Microarray, Expressing, Hybridization, Northern Blot, Isolation

    Dominant negative Lsr2 variant (Lsr2*) inhibits DNA binding by wild type Lsr2 and promotes antibiotic production in S. venezuelae . ( A ) Electrophoretic mobility shift assay illustrating DNA binding by wild type Lsr2, no DNA binding by the R82A mutant allele (mutant Lsr2*), and effective inhibition of Lsr2 binding by the mutant variant, based on the increasing abundance of ‘free probe’ as mutant concentrations rise. Probe: 1.5 kb region corresponding to the Lsr2 binding site in the chloramphenicol biosynthetic cluster. Reactions were separated on a 1% agarose gel stained with ethidium bromide. ( B ) Bioactivity of S. venezuelae extracts against Micrococcus luteus . Wild type S. venezuelae carrying either a control (empty) plasmid (left), or one overexpressing the mutant 9R82A) Lsr2 variant (right; Lsr2*) were cultured for 18 hr prior to extraction in methanol and reconstitution in DMSO. Extracts were applied to Whatman filter discs, and cultures were grown overnight. ( C ) Quantitative PCR analysis of Lsr2-3xFLAG-binding to the validated target site sven_0926 , following ChIP, for a strain carrying an empty plasmid (control) or overexpressing Lsr2* (O/E Lsr2*). Overexpressing Lsr2* led to a 40% drop in binding by Lsr2. ChIP experiments were conducted in duplicate, and qPCR was done for each replicate in technical triplicate.

    Journal: eLife

    Article Title: Silencing cryptic specialized metabolism in Streptomyces by the nucleoid-associated protein Lsr2

    doi: 10.7554/eLife.47691

    Figure Lengend Snippet: Dominant negative Lsr2 variant (Lsr2*) inhibits DNA binding by wild type Lsr2 and promotes antibiotic production in S. venezuelae . ( A ) Electrophoretic mobility shift assay illustrating DNA binding by wild type Lsr2, no DNA binding by the R82A mutant allele (mutant Lsr2*), and effective inhibition of Lsr2 binding by the mutant variant, based on the increasing abundance of ‘free probe’ as mutant concentrations rise. Probe: 1.5 kb region corresponding to the Lsr2 binding site in the chloramphenicol biosynthetic cluster. Reactions were separated on a 1% agarose gel stained with ethidium bromide. ( B ) Bioactivity of S. venezuelae extracts against Micrococcus luteus . Wild type S. venezuelae carrying either a control (empty) plasmid (left), or one overexpressing the mutant 9R82A) Lsr2 variant (right; Lsr2*) were cultured for 18 hr prior to extraction in methanol and reconstitution in DMSO. Extracts were applied to Whatman filter discs, and cultures were grown overnight. ( C ) Quantitative PCR analysis of Lsr2-3xFLAG-binding to the validated target site sven_0926 , following ChIP, for a strain carrying an empty plasmid (control) or overexpressing Lsr2* (O/E Lsr2*). Overexpressing Lsr2* led to a 40% drop in binding by Lsr2. ChIP experiments were conducted in duplicate, and qPCR was done for each replicate in technical triplicate.

    Article Snippet: To quantify the abundance of target genes of interest in the ChIP DNA, 20 μL qPCR reactions were prepared using Luna Universal qPCR Master Mix (New England Biolabs) and 2.5 μL of ChIP DNA (1:10) as template.

    Techniques: Dominant Negative Mutation, Variant Assay, Binding Assay, Electrophoretic Mobility Shift Assay, Mutagenesis, Inhibition, Agarose Gel Electrophoresis, Staining, Plasmid Preparation, Cell Culture, Real-time Polymerase Chain Reaction, Chromatin Immunoprecipitation

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

    Journal: The Journal of Clinical Investigation

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

    doi: 10.1172/JCI91291

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

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

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