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    3 4 Difluorophenyl Isothiocyanate CAS 113028 75 4 is a useful research chemical
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    0610037L13Rik Myc DDK tagged Mouse RIKEN cDNA 0610037L13 gene 0610037L13Rik
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    Merck & Co pigcpb
    Pigcpb, supplied by Merck & Co, 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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    Santa Cruz Biotechnology anti bu 1 conjugated with phycoerythrin
    a. The <t>BU-1</t> locus as a model system to record G4-dependent replication stalling. The leading strand of a replication fork entering the locus from 3’ end stochastically stalls at the +3.5 G4, leading to the formation of a region of ssDNA, with interruption of parental histone recycling and of histone modifications necessary to maintain normal expression of the locus . b. Instability of BU-1 expression in timeless cells. FACS plots of wild type and timeless (clone 1) DT40 cells stained with anti-Bu-1 conjugated with phycoerythrin. Each line represents the Bu-1 expression profile of an individual clonal population. Unstained controls are shown in blue. c. Fluctuation analysis for Bu-1 loss in wild-type DT40 cells and two independent timeless clones generated by CRISPR-Cas9 targeting (clones 1 and 2; Supplementary Fig. 1), timeless (clone 1) complemented by expression of human Timeless cDNA and a timeless mutant on a background in which the endogenous +3.5 G4 has been deleted (ΔG4) . d. Fluctuation analysis for Bu-1 loss in DT40 wild-type and tipin cells. In c. and d., each symbol represents the percentage of cells in an individual clone expanded for 2-3 weeks that have lost Bu-1 high expression. At least two independent fluctuation analyses were performed, with 24-36 individual clones each cell line per repeat. Bars and whiskers represent median and interquartile range, respectively. **** p < 0.0001; one-way ANOVA.
    Anti Bu 1 Conjugated With Phycoerythrin, supplied by Santa Cruz Biotechnology, used in various techniques. Bioz Stars score: 93/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Lenti ORF clone of Human guanylate kinase 1 GUK1 transcript variant 3 Myc DDK tagged
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    a. The BU-1 locus as a model system to record G4-dependent replication stalling. The leading strand of a replication fork entering the locus from 3’ end stochastically stalls at the +3.5 G4, leading to the formation of a region of ssDNA, with interruption of parental histone recycling and of histone modifications necessary to maintain normal expression of the locus . b. Instability of BU-1 expression in timeless cells. FACS plots of wild type and timeless (clone 1) DT40 cells stained with anti-Bu-1 conjugated with phycoerythrin. Each line represents the Bu-1 expression profile of an individual clonal population. Unstained controls are shown in blue. c. Fluctuation analysis for Bu-1 loss in wild-type DT40 cells and two independent timeless clones generated by CRISPR-Cas9 targeting (clones 1 and 2; Supplementary Fig. 1), timeless (clone 1) complemented by expression of human Timeless cDNA and a timeless mutant on a background in which the endogenous +3.5 G4 has been deleted (ΔG4) . d. Fluctuation analysis for Bu-1 loss in DT40 wild-type and tipin cells. In c. and d., each symbol represents the percentage of cells in an individual clone expanded for 2-3 weeks that have lost Bu-1 high expression. At least two independent fluctuation analyses were performed, with 24-36 individual clones each cell line per repeat. Bars and whiskers represent median and interquartile range, respectively. **** p < 0.0001; one-way ANOVA.

    Journal: bioRxiv

    Article Title: Timeless couples G quadruplex detection with processing by DDX11 during DNA replication

    doi: 10.1101/826578

    Figure Lengend Snippet: a. The BU-1 locus as a model system to record G4-dependent replication stalling. The leading strand of a replication fork entering the locus from 3’ end stochastically stalls at the +3.5 G4, leading to the formation of a region of ssDNA, with interruption of parental histone recycling and of histone modifications necessary to maintain normal expression of the locus . b. Instability of BU-1 expression in timeless cells. FACS plots of wild type and timeless (clone 1) DT40 cells stained with anti-Bu-1 conjugated with phycoerythrin. Each line represents the Bu-1 expression profile of an individual clonal population. Unstained controls are shown in blue. c. Fluctuation analysis for Bu-1 loss in wild-type DT40 cells and two independent timeless clones generated by CRISPR-Cas9 targeting (clones 1 and 2; Supplementary Fig. 1), timeless (clone 1) complemented by expression of human Timeless cDNA and a timeless mutant on a background in which the endogenous +3.5 G4 has been deleted (ΔG4) . d. Fluctuation analysis for Bu-1 loss in DT40 wild-type and tipin cells. In c. and d., each symbol represents the percentage of cells in an individual clone expanded for 2-3 weeks that have lost Bu-1 high expression. At least two independent fluctuation analyses were performed, with 24-36 individual clones each cell line per repeat. Bars and whiskers represent median and interquartile range, respectively. **** p < 0.0001; one-way ANOVA.

    Article Snippet: Briefly, cells (confluency between 0.4 – 2 ×10 6 ) were directly stained with anti-Bu-1 conjugated with phycoerythrin (Santa Cruz 5K98-PE 70447 or Invitrogen 21-1A4-PE MA5-28754) at 1:100 dilution for 10 minutes at room temperature.

    Techniques: Expressing, Staining, Clone Assay, Generated, CRISPR, Mutagenesis

    Fluctuation analysis for the generation of Bu-1 loss variants in wild-type cells, timeless (clone 1) cells, timeless (clone 1) complemented with human Timeless ΔDBD cDNA (hTimΔ81-965) and timeless (clone 1) complemented with human Timeless truncated at the PARP binding domain (hTim[1:1000]) cDNA and timeless cells generated by CRISPR-Cas9 targeting exon 16 which truncates the protein removing the CTD containing both the DBD and the PARP binding domains. At least two independent fluctuation analyses were performed with 24-36 individual clones each cell line per repeat. Bars and whiskers represent median and interquartile range, respectively. * p < 0.05 and **** p < 0.0001; one-way ANOVA for comparison with the wild-type cells.

    Journal: bioRxiv

    Article Title: Timeless couples G quadruplex detection with processing by DDX11 during DNA replication

    doi: 10.1101/826578

    Figure Lengend Snippet: Fluctuation analysis for the generation of Bu-1 loss variants in wild-type cells, timeless (clone 1) cells, timeless (clone 1) complemented with human Timeless ΔDBD cDNA (hTimΔ81-965) and timeless (clone 1) complemented with human Timeless truncated at the PARP binding domain (hTim[1:1000]) cDNA and timeless cells generated by CRISPR-Cas9 targeting exon 16 which truncates the protein removing the CTD containing both the DBD and the PARP binding domains. At least two independent fluctuation analyses were performed with 24-36 individual clones each cell line per repeat. Bars and whiskers represent median and interquartile range, respectively. * p < 0.05 and **** p < 0.0001; one-way ANOVA for comparison with the wild-type cells.

    Article Snippet: Briefly, cells (confluency between 0.4 – 2 ×10 6 ) were directly stained with anti-Bu-1 conjugated with phycoerythrin (Santa Cruz 5K98-PE 70447 or Invitrogen 21-1A4-PE MA5-28754) at 1:100 dilution for 10 minutes at room temperature.

    Techniques: Binding Assay, Generated, CRISPR, Clone Assay

    a. Fluctuation analysis for Bu-1a loss in wild-type DT40 cells, two independent ddx11 clones generated by CRISPR-Cas9 targeting (clones 1 and 2) and one ddx11 clone generated by conventional homologous recombination gene targeting (clone 3). Each symbol represents the percentage of cells in an individual clone expanded for 2-3 weeks that have lost Bu-1a high expression. b. Fluctuation analysis for Bu-1a loss variant generation in wild-type cells, ddx11 (clone 1) cells, ddx11 (clone 1) complemented by expression of chicken DDX11 WT cDNA, ddx11 (clone 1) complemented by expression of helicase-dead form of chicken DDX11 (K87A) cDNA, and a ddx11 clone generated in cells in which the endogenous +3.5 G4 has been deleted (ΔG4). c. Fluctuation analysis for Bu-1 loss in two independent ddx11/timeless double-mutant clones. Fluctuation analyses for wild type, timeless (clone 1) and ddx11 (clone 1) are shown for comparison, as are fluctuation analyses fancj and fancj / ddx11 double-mutants. In all cases, at least two independent fluctuation analyses were performed, with 24-36 individual clones each cell line per repeat. Bars and whiskers represent median and interquartile range, respectively. ** p < 0.01 and **** p < 0.0001; one-way ANOVA for comparison with wild-type cells.

    Journal: bioRxiv

    Article Title: Timeless couples G quadruplex detection with processing by DDX11 during DNA replication

    doi: 10.1101/826578

    Figure Lengend Snippet: a. Fluctuation analysis for Bu-1a loss in wild-type DT40 cells, two independent ddx11 clones generated by CRISPR-Cas9 targeting (clones 1 and 2) and one ddx11 clone generated by conventional homologous recombination gene targeting (clone 3). Each symbol represents the percentage of cells in an individual clone expanded for 2-3 weeks that have lost Bu-1a high expression. b. Fluctuation analysis for Bu-1a loss variant generation in wild-type cells, ddx11 (clone 1) cells, ddx11 (clone 1) complemented by expression of chicken DDX11 WT cDNA, ddx11 (clone 1) complemented by expression of helicase-dead form of chicken DDX11 (K87A) cDNA, and a ddx11 clone generated in cells in which the endogenous +3.5 G4 has been deleted (ΔG4). c. Fluctuation analysis for Bu-1 loss in two independent ddx11/timeless double-mutant clones. Fluctuation analyses for wild type, timeless (clone 1) and ddx11 (clone 1) are shown for comparison, as are fluctuation analyses fancj and fancj / ddx11 double-mutants. In all cases, at least two independent fluctuation analyses were performed, with 24-36 individual clones each cell line per repeat. Bars and whiskers represent median and interquartile range, respectively. ** p < 0.01 and **** p < 0.0001; one-way ANOVA for comparison with wild-type cells.

    Article Snippet: Briefly, cells (confluency between 0.4 – 2 ×10 6 ) were directly stained with anti-Bu-1 conjugated with phycoerythrin (Santa Cruz 5K98-PE 70447 or Invitrogen 21-1A4-PE MA5-28754) at 1:100 dilution for 10 minutes at room temperature.

    Techniques: Clone Assay, Generated, CRISPR, Homologous Recombination, Expressing, Variant Assay, Mutagenesis