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Illumina Inc multiplex oligonucleotide
Multiplex Oligonucleotide, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 88/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/result/multiplex oligonucleotide/product/Illumina Inc
Average 88 stars, based on 1 article reviews
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Polymerase Chain Reaction:

Article Title: De Novo Assembly and Characterization of Four Anthozoan (Phylum Cnidaria) Transcriptomes
Article Snippet: .. PCR included template cDNA, Phusion Taq polymerase buffer (Thermo Scientific, MA), dNTPs, 5′ Illumina “i5” barcoding oligo, 3′ Illumina “i7” multiplex oligonucleotide, and Phusion High Fidelity Taq polymerase (Thermo Scientific, MA). ..

Multiplex Assay:

Article Title: De Novo Assembly and Characterization of Four Anthozoan (Phylum Cnidaria) Transcriptomes
Article Snippet: .. PCR included template cDNA, Phusion Taq polymerase buffer (Thermo Scientific, MA), dNTPs, 5′ Illumina “i5” barcoding oligo, 3′ Illumina “i7” multiplex oligonucleotide, and Phusion High Fidelity Taq polymerase (Thermo Scientific, MA). ..

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  • 85
    Illumina Inc multiplexed illumina oligonucleotide assays
    (A) Genotyping of parental lines and 576 Ae. tauschii F 2 plants in the AL8/78 × AS75 mapping population with <t>Illumina</t> GoldenGate oligonucleotide assay querying an A/G SNP at EST locus BE499478 (nucleotide position 403 in the Ae. tauschii reference sequence, ) . The graph is a normalized polar coordinate ( R , θ ) plot. Theta ( x -axis) is an angle of deviation of Cy3 and Cy5 fluorescence from pure Cy3 and pure Cy5 signal (0 and 1). The closer a point is to 0 or 1, the greater the proportion of Cy3 or Cy5 fluorescent signal, respectively, is present. R ( y -axis) is the Manhattan distance of observed Cy3 and Cy5 fluorescence to the origin (pole), which is 0 fluorescence. The closer a point is to 0 on the y -axis, the weaker the total fluorescence. The red, blue and purple ovals have the diameter of 2 standard deviations computed from the dispersal of the red, blue and purple dots, respectively. The darker colored regions define genotype call areas for homozygous (red and blue dots) and heterozygous (purple dots) plants. The numbers of plants in each cluster are indicated below the x -axis. (B) Clustering of 57 BAC and BiBAC super-pools assayed with the same oligonucleotides as in (A). Genotype call areas derived from the mapping population shown in 1A were directly exported for analysis of the BAC pools. The green and orange spots represent the parental genotypes of the mapping population; the red spots are the BAC and BiBAC pools scored by us as positive and black spots BAC and BiBAC pools scored as negative. Note that all red spots have the same normalized angular deviation (normalized theta) as DNA of Ae. tauschii AL8/78 and large distance from origin ( R value) indicating high fluorescence. In contrast, the black spots have a low R value indicating only residual Cy3 and Cy5 fluorescence and variable values of normalized theta ranging from 0 all the way to 1. (C) Clustering of the same 57 BAC and BiBAC super-pools without defining call areas on the basis of clustering segregating Ae. tauschii SNP genotypes. Note failure of separation of the positive and negative clusters from each other.
    Multiplexed Illumina Oligonucleotide Assays, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 85/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/multiplexed illumina oligonucleotide assays/product/Illumina Inc
    Average 85 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
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    94
    Illumina Inc illumina adapters
    Schematic representation of different strategies for viral genome resequencing. A) Total RNA library: all the RNA species present in the sample are sequenced, no assumption on which genome is present, B) Hybridisation capture of a mRNA library: a good reference genome is needed to design the probes for capture, C) PCR enrichment: the desired genome is amplified from cDNA, a reference genome is needed to design specific oligos. Red lines, genomes of interest; Blue segments, <t>Illumina</t> adapters; Black lines, other RNA species.
    Illumina Adapters, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 94/100, based on 781 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/illumina adapters/product/Illumina Inc
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    92
    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 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    86
    Illumina Inc multiple chip dna
    <t>BCL6</t> and STAT5 occupy Socs2 <t>DNA</t> reciprocally in response to GH. (A) 3T3-F442A preadipocytes were treated with GH for 0, 0.5 or 48 h and ChIP was carried out using antibodies against BCL6, STAT5, STAT5a or STAT5b. ChIP DNA was probed with primers specific to the STAT5 occupancy sequence on the Socs2 promoter. IgG served as a negative control and 1% input was used as an internal control, in this and subsequent figures. Data are representative of at least two experiments. (B) 3T3-F442A preadipocytes and adipocytes were treated with GH for 0 and 24 h and ChIP was carried out using antibodies against BCL6, STAT5, and phosphorylated STAT5 (P-STAT5). ChIP DNA was probed with primers specific to the STAT5 occupancy sequence on the Socs2 promoter. (C) Male littermate mice were treated ip with GH (1.5 mg/kg in 48 h) (+) or vehicle (−). Liver was used for ChIP analysis using antibodies against BCL6, STAT5 or P-STAT5 and probed for Socs2 as above.
    Multiple Chip Dna, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    (A) Genotyping of parental lines and 576 Ae. tauschii F 2 plants in the AL8/78 × AS75 mapping population with Illumina GoldenGate oligonucleotide assay querying an A/G SNP at EST locus BE499478 (nucleotide position 403 in the Ae. tauschii reference sequence, ) . The graph is a normalized polar coordinate ( R , θ ) plot. Theta ( x -axis) is an angle of deviation of Cy3 and Cy5 fluorescence from pure Cy3 and pure Cy5 signal (0 and 1). The closer a point is to 0 or 1, the greater the proportion of Cy3 or Cy5 fluorescent signal, respectively, is present. R ( y -axis) is the Manhattan distance of observed Cy3 and Cy5 fluorescence to the origin (pole), which is 0 fluorescence. The closer a point is to 0 on the y -axis, the weaker the total fluorescence. The red, blue and purple ovals have the diameter of 2 standard deviations computed from the dispersal of the red, blue and purple dots, respectively. The darker colored regions define genotype call areas for homozygous (red and blue dots) and heterozygous (purple dots) plants. The numbers of plants in each cluster are indicated below the x -axis. (B) Clustering of 57 BAC and BiBAC super-pools assayed with the same oligonucleotides as in (A). Genotype call areas derived from the mapping population shown in 1A were directly exported for analysis of the BAC pools. The green and orange spots represent the parental genotypes of the mapping population; the red spots are the BAC and BiBAC pools scored by us as positive and black spots BAC and BiBAC pools scored as negative. Note that all red spots have the same normalized angular deviation (normalized theta) as DNA of Ae. tauschii AL8/78 and large distance from origin ( R value) indicating high fluorescence. In contrast, the black spots have a low R value indicating only residual Cy3 and Cy5 fluorescence and variable values of normalized theta ranging from 0 all the way to 1. (C) Clustering of the same 57 BAC and BiBAC super-pools without defining call areas on the basis of clustering segregating Ae. tauschii SNP genotypes. Note failure of separation of the positive and negative clusters from each other.

    Journal: BMC Genomics

    Article Title: A high-throughput strategy for screening of bacterial artificial chromosome libraries and anchoring of clones on a genetic map constructed with single nucleotide polymorphisms

    doi: 10.1186/1471-2164-10-28

    Figure Lengend Snippet: (A) Genotyping of parental lines and 576 Ae. tauschii F 2 plants in the AL8/78 × AS75 mapping population with Illumina GoldenGate oligonucleotide assay querying an A/G SNP at EST locus BE499478 (nucleotide position 403 in the Ae. tauschii reference sequence, ) . The graph is a normalized polar coordinate ( R , θ ) plot. Theta ( x -axis) is an angle of deviation of Cy3 and Cy5 fluorescence from pure Cy3 and pure Cy5 signal (0 and 1). The closer a point is to 0 or 1, the greater the proportion of Cy3 or Cy5 fluorescent signal, respectively, is present. R ( y -axis) is the Manhattan distance of observed Cy3 and Cy5 fluorescence to the origin (pole), which is 0 fluorescence. The closer a point is to 0 on the y -axis, the weaker the total fluorescence. The red, blue and purple ovals have the diameter of 2 standard deviations computed from the dispersal of the red, blue and purple dots, respectively. The darker colored regions define genotype call areas for homozygous (red and blue dots) and heterozygous (purple dots) plants. The numbers of plants in each cluster are indicated below the x -axis. (B) Clustering of 57 BAC and BiBAC super-pools assayed with the same oligonucleotides as in (A). Genotype call areas derived from the mapping population shown in 1A were directly exported for analysis of the BAC pools. The green and orange spots represent the parental genotypes of the mapping population; the red spots are the BAC and BiBAC pools scored by us as positive and black spots BAC and BiBAC pools scored as negative. Note that all red spots have the same normalized angular deviation (normalized theta) as DNA of Ae. tauschii AL8/78 and large distance from origin ( R value) indicating high fluorescence. In contrast, the black spots have a low R value indicating only residual Cy3 and Cy5 fluorescence and variable values of normalized theta ranging from 0 all the way to 1. (C) Clustering of the same 57 BAC and BiBAC super-pools without defining call areas on the basis of clustering segregating Ae. tauschii SNP genotypes. Note failure of separation of the positive and negative clusters from each other.

    Article Snippet: The multiplexed Illumina oligonucleotide assays are most time and cost effective if large numbers of markers in large numbers of DNAs are genotyped and if no additional work is needed to identify positive BAC clones.

    Techniques: Oligonucleotide Assay, Sequencing, Fluorescence, BAC Assay, Derivative Assay

    Schematic representation of different strategies for viral genome resequencing. A) Total RNA library: all the RNA species present in the sample are sequenced, no assumption on which genome is present, B) Hybridisation capture of a mRNA library: a good reference genome is needed to design the probes for capture, C) PCR enrichment: the desired genome is amplified from cDNA, a reference genome is needed to design specific oligos. Red lines, genomes of interest; Blue segments, Illumina adapters; Black lines, other RNA species.

    Journal: PLoS ONE

    Article Title: A Modified RNA-Seq Approach for Whole Genome Sequencing of RNA Viruses from Faecal and Blood Samples

    doi: 10.1371/journal.pone.0066129

    Figure Lengend Snippet: Schematic representation of different strategies for viral genome resequencing. A) Total RNA library: all the RNA species present in the sample are sequenced, no assumption on which genome is present, B) Hybridisation capture of a mRNA library: a good reference genome is needed to design the probes for capture, C) PCR enrichment: the desired genome is amplified from cDNA, a reference genome is needed to design specific oligos. Red lines, genomes of interest; Blue segments, Illumina adapters; Black lines, other RNA species.

    Article Snippet: Additionally, upon ligation of Illumina Adapters (Multiplexing Sample Preparation Oligonucleotide Kit) each library was size selected with two Ampure Bead steps (firstly, 1∶0.7× volume and secondly, the supernatant from the first bind was taken for a 1∶1.7× volume clean-up), selecting 200–600 bp fragments in 30 µl 10 mM Tris-Cl, pH 8.5.

    Techniques: Hybridization, Capture-C, Polymerase Chain Reaction, Amplification

    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

    BCL6 and STAT5 occupy Socs2 DNA reciprocally in response to GH. (A) 3T3-F442A preadipocytes were treated with GH for 0, 0.5 or 48 h and ChIP was carried out using antibodies against BCL6, STAT5, STAT5a or STAT5b. ChIP DNA was probed with primers specific to the STAT5 occupancy sequence on the Socs2 promoter. IgG served as a negative control and 1% input was used as an internal control, in this and subsequent figures. Data are representative of at least two experiments. (B) 3T3-F442A preadipocytes and adipocytes were treated with GH for 0 and 24 h and ChIP was carried out using antibodies against BCL6, STAT5, and phosphorylated STAT5 (P-STAT5). ChIP DNA was probed with primers specific to the STAT5 occupancy sequence on the Socs2 promoter. (C) Male littermate mice were treated ip with GH (1.5 mg/kg in 48 h) (+) or vehicle (−). Liver was used for ChIP analysis using antibodies against BCL6, STAT5 or P-STAT5 and probed for Socs2 as above.

    Journal: Molecular and cellular endocrinology

    Article Title: Reciprocal occupancy of BCL6 and STAT5 on Growth Hormone target genes: contrasting transcriptional outcomes and promoter-specific roles of p300 and HDAC3

    doi: 10.1016/j.mce.2014.07.020

    Figure Lengend Snippet: BCL6 and STAT5 occupy Socs2 DNA reciprocally in response to GH. (A) 3T3-F442A preadipocytes were treated with GH for 0, 0.5 or 48 h and ChIP was carried out using antibodies against BCL6, STAT5, STAT5a or STAT5b. ChIP DNA was probed with primers specific to the STAT5 occupancy sequence on the Socs2 promoter. IgG served as a negative control and 1% input was used as an internal control, in this and subsequent figures. Data are representative of at least two experiments. (B) 3T3-F442A preadipocytes and adipocytes were treated with GH for 0 and 24 h and ChIP was carried out using antibodies against BCL6, STAT5, and phosphorylated STAT5 (P-STAT5). ChIP DNA was probed with primers specific to the STAT5 occupancy sequence on the Socs2 promoter. (C) Male littermate mice were treated ip with GH (1.5 mg/kg in 48 h) (+) or vehicle (−). Liver was used for ChIP analysis using antibodies against BCL6, STAT5 or P-STAT5 and probed for Socs2 as above.

    Article Snippet: ChIP DNA samples were pre-tested for quality by PCR using primers specific for the BCL6/STAT5 binding site in murine Socs2 , and multiple ChIP DNA samples immunoprecipitated (IP) with the same antibody under the same GH treatment conditions were pooled to obtain a sufficient amount of DNA ( > 10 ng) for generating ChIP-Seq libraries as recommended by the Illumina ChIP-Seq Library Preparation Protocol.

    Techniques: Chromatin Immunoprecipitation, Sequencing, Negative Control, Mouse Assay

    BCL6 and STAT5 show reciprocal occupancy at transcription start sites of Socs2 , Cish , and Bcl6 . (A) Peaks of BCL6 occupancy determined by ChIP-Seq were identified by HPeak at the transcription start sites (TSS) of Socs2 , Cish and Bcl6 . Shown are the UCSC Genome Browser profiles for BCL6 occupancy in 3T3-F442A adipocytes treated with GH for 0 or 48 h. Y axis scales were set at 60 for Socs2 , 35 for Cish , and 20 for Bcl6 as determined by maximum peak height in the absence of GH as calculated by HPeak. Top panel: Socs2. TSS: mouse chromosome (chr) 10: 94879491. Peak location 0 h GH: chr10: 94879276-94880050; 48 h GH: chr10: 94879326-94879975. Predicted BCL6/STAT consensus sites: chr10: 94879539-94879547 and chr10: 94879550-94879558. Second panel: Cish. TSS: chr9: 107199020. Peak location 0 h GH: chr9: 107198726-107199400; 48 h GH: chr9: 107198751-107199150. Predicted BCL6/STAT consensus sites: chr9: 107198991-107198999 and chr9: 107199002-107199010. Third panel: Bcl6 . TSS: chr16: 23988698. Peak location 0 h GH: chr16: 23988401-23988850; 48 h GH: chr16: 23988776-23988900. Predicted BCL6/STAT consensus sites: chr16: 23988676-23988684 and chr16: 23988717-23988725. Bottom panel: Peak profile at Bcl6 promoter region with expanded scale to visualize peaks in detail. Arrows to the left of gene names indicate direction of transcription, from 5′ to 3′. Gene structure diagrammed at bottom of each profile. (B) 3T3-F442A adipocytes were treated with GH for 0 or 48 h and ChIP was carried out using antibodies against BCL6 and STAT5. ChIP DNA was probed with primers specific to the BCL6 occupancy sites corresponding to ChIP-Seq (peaks) on the Socs2 (lanes 1 and 2), Cish (lanes 3 and 4) and Bcl6 (lanes 5 and 6) genes. (C) 3T3-F442A adipocytes were treated with GH for 0, 4 or 48 h. RNA was prepared and analyzed by qPCR using primers for Socs2, Cish and Bcl6. Bars show mean + SE of triplicates in an experiment which was repeated at least 3 times.

    Journal: Molecular and cellular endocrinology

    Article Title: Reciprocal occupancy of BCL6 and STAT5 on Growth Hormone target genes: contrasting transcriptional outcomes and promoter-specific roles of p300 and HDAC3

    doi: 10.1016/j.mce.2014.07.020

    Figure Lengend Snippet: BCL6 and STAT5 show reciprocal occupancy at transcription start sites of Socs2 , Cish , and Bcl6 . (A) Peaks of BCL6 occupancy determined by ChIP-Seq were identified by HPeak at the transcription start sites (TSS) of Socs2 , Cish and Bcl6 . Shown are the UCSC Genome Browser profiles for BCL6 occupancy in 3T3-F442A adipocytes treated with GH for 0 or 48 h. Y axis scales were set at 60 for Socs2 , 35 for Cish , and 20 for Bcl6 as determined by maximum peak height in the absence of GH as calculated by HPeak. Top panel: Socs2. TSS: mouse chromosome (chr) 10: 94879491. Peak location 0 h GH: chr10: 94879276-94880050; 48 h GH: chr10: 94879326-94879975. Predicted BCL6/STAT consensus sites: chr10: 94879539-94879547 and chr10: 94879550-94879558. Second panel: Cish. TSS: chr9: 107199020. Peak location 0 h GH: chr9: 107198726-107199400; 48 h GH: chr9: 107198751-107199150. Predicted BCL6/STAT consensus sites: chr9: 107198991-107198999 and chr9: 107199002-107199010. Third panel: Bcl6 . TSS: chr16: 23988698. Peak location 0 h GH: chr16: 23988401-23988850; 48 h GH: chr16: 23988776-23988900. Predicted BCL6/STAT consensus sites: chr16: 23988676-23988684 and chr16: 23988717-23988725. Bottom panel: Peak profile at Bcl6 promoter region with expanded scale to visualize peaks in detail. Arrows to the left of gene names indicate direction of transcription, from 5′ to 3′. Gene structure diagrammed at bottom of each profile. (B) 3T3-F442A adipocytes were treated with GH for 0 or 48 h and ChIP was carried out using antibodies against BCL6 and STAT5. ChIP DNA was probed with primers specific to the BCL6 occupancy sites corresponding to ChIP-Seq (peaks) on the Socs2 (lanes 1 and 2), Cish (lanes 3 and 4) and Bcl6 (lanes 5 and 6) genes. (C) 3T3-F442A adipocytes were treated with GH for 0, 4 or 48 h. RNA was prepared and analyzed by qPCR using primers for Socs2, Cish and Bcl6. Bars show mean + SE of triplicates in an experiment which was repeated at least 3 times.

    Article Snippet: ChIP DNA samples were pre-tested for quality by PCR using primers specific for the BCL6/STAT5 binding site in murine Socs2 , and multiple ChIP DNA samples immunoprecipitated (IP) with the same antibody under the same GH treatment conditions were pooled to obtain a sufficient amount of DNA ( > 10 ng) for generating ChIP-Seq libraries as recommended by the Illumina ChIP-Seq Library Preparation Protocol.

    Techniques: Chromogenic In Situ Hybridization, Chromatin Immunoprecipitation, Real-time Polymerase Chain Reaction

    Enrichment of AcH3 and AcH4 increases in response to GH on Socs2 and Cish , but not Bcl6 . 3T3-F442A adipocytes were treated without (open bars) or with GH (gray bars) for (A) 24 h or (B) 30 min. ChIP was performed using antibodies against AcH3, AcH4, or H3K4me3. QPCR was used to analyze enrichment of these activating histone marks at the BCL6/STAT5 sites on Socs2 , Cish , and Bcl6 promoter sequences. Signal from ChIP DNA was normalized to input samples for respective treatment conditions. IgG was used as negative control. Each bar shows the mean ± SE from 4 independent experiments. Asterisks (*) indicate responses to GH that are statistically significant ( P

    Journal: Molecular and cellular endocrinology

    Article Title: Reciprocal occupancy of BCL6 and STAT5 on Growth Hormone target genes: contrasting transcriptional outcomes and promoter-specific roles of p300 and HDAC3

    doi: 10.1016/j.mce.2014.07.020

    Figure Lengend Snippet: Enrichment of AcH3 and AcH4 increases in response to GH on Socs2 and Cish , but not Bcl6 . 3T3-F442A adipocytes were treated without (open bars) or with GH (gray bars) for (A) 24 h or (B) 30 min. ChIP was performed using antibodies against AcH3, AcH4, or H3K4me3. QPCR was used to analyze enrichment of these activating histone marks at the BCL6/STAT5 sites on Socs2 , Cish , and Bcl6 promoter sequences. Signal from ChIP DNA was normalized to input samples for respective treatment conditions. IgG was used as negative control. Each bar shows the mean ± SE from 4 independent experiments. Asterisks (*) indicate responses to GH that are statistically significant ( P

    Article Snippet: ChIP DNA samples were pre-tested for quality by PCR using primers specific for the BCL6/STAT5 binding site in murine Socs2 , and multiple ChIP DNA samples immunoprecipitated (IP) with the same antibody under the same GH treatment conditions were pooled to obtain a sufficient amount of DNA ( > 10 ng) for generating ChIP-Seq libraries as recommended by the Illumina ChIP-Seq Library Preparation Protocol.

    Techniques: Chromogenic In Situ Hybridization, Chromatin Immunoprecipitation, Real-time Polymerase Chain Reaction, Negative Control

    ChIP identifies p300 and HDAC3 on Socs2 , Cish , and Bcl6 . 3T3-F442A adipocytes were treated without (open bars) or with GH (gray bars) for (A) 24 h or (B) 30 min. ChIP was performed with antibodies against BCL6, STAT5, p300, or HDAC3. ChIP DNA was analyzed by qPCR with primers for the BCL6/STAT5 sites on Socs2 , Cish , and Bcl6 . Signals were normalized to input DNA from respective treatment conditions. Each bar shows the mean ± SE for 7 (BCL6 and STAT5) or 3 (p300 and HDAC3) independent experiments. Asterisks (*) indicate responses to GH that are statistically significant ( P

    Journal: Molecular and cellular endocrinology

    Article Title: Reciprocal occupancy of BCL6 and STAT5 on Growth Hormone target genes: contrasting transcriptional outcomes and promoter-specific roles of p300 and HDAC3

    doi: 10.1016/j.mce.2014.07.020

    Figure Lengend Snippet: ChIP identifies p300 and HDAC3 on Socs2 , Cish , and Bcl6 . 3T3-F442A adipocytes were treated without (open bars) or with GH (gray bars) for (A) 24 h or (B) 30 min. ChIP was performed with antibodies against BCL6, STAT5, p300, or HDAC3. ChIP DNA was analyzed by qPCR with primers for the BCL6/STAT5 sites on Socs2 , Cish , and Bcl6 . Signals were normalized to input DNA from respective treatment conditions. Each bar shows the mean ± SE for 7 (BCL6 and STAT5) or 3 (p300 and HDAC3) independent experiments. Asterisks (*) indicate responses to GH that are statistically significant ( P

    Article Snippet: ChIP DNA samples were pre-tested for quality by PCR using primers specific for the BCL6/STAT5 binding site in murine Socs2 , and multiple ChIP DNA samples immunoprecipitated (IP) with the same antibody under the same GH treatment conditions were pooled to obtain a sufficient amount of DNA ( > 10 ng) for generating ChIP-Seq libraries as recommended by the Illumina ChIP-Seq Library Preparation Protocol.

    Techniques: Chromatin Immunoprecipitation, Chromogenic In Situ Hybridization, Real-time Polymerase Chain Reaction