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  • 99
    Integrated DNA Technologies dna oligonucleotides
    Dna Oligonucleotides, supplied by Integrated DNA Technologies, used in various techniques. Bioz Stars score: 99/100, based on 2965 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    New England Biolabs nebnext multiplex oligos for illumina
    Nebnext Multiplex Oligos For Illumina, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 96/100, based on 1655 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher oligo
    Oligo, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 33700 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher oligo dt
    Oligo Dt, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 25591 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher oligo dt primers
    Oligo Dt Primers, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 21392 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher oligo dt primer
    Oligo Dt Primer, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 18486 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Promega oligo
    Oligo, supplied by Promega, used in various techniques. Bioz Stars score: 99/100, based on 9287 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher oligo dt 12
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    New England Biolabs nebnext multiplex oligos
    Nebnext Multiplex Oligos, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 4694 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Millipore oligo
    Oligo, supplied by Millipore, used in various techniques. Bioz Stars score: 99/100, based on 1764 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    New England Biolabs oligos
    Oligos, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 1801 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Qiagen oligo dt primers
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    92
    Agilent technologies whole human genome oligo microarray
    TOP1MT has a wide expression range in the NCI-60 panel. ( A ) TOP1MT mRNA expression intensity across the cell line panel from the NCI (NCI-60), ranked from the highest TOP1MT expresser (leukemia RPMI-8226, top) to the lowest (lung NCI-H226, bottom). Tissues of origin are designated by colored circles (see legend below). Names of the individual cell lines are reported. Expression values were obtained with Agilent Whole Human Genome <t>Oligo</t> <t>Microarray</t> chips, and quality filtering and normalization were performed using GeneSpring GX 10.0 software (Agilent, Santa Clara, CA, USA). A value of one corresponds to a 2-fold higher intensity than the 75th percentile of expression for all probes on the entire array. Values are on a log 2 scale. ( B ) Normalized TOP1MT mRNA expressions sorted by level (highest to lowest) across the NCI-60. Individual cell lines (filled dots) are colored according to tissue of origin and arranged by the intensity values in panel A. Inset: frequency distribution plot showing the number of cell lines from the NCI-60 panel by TOP1MT normalized intensity. x -axis, normalized TOP1MT intensity; y -axis, frequency of cell lines for any given TOP1MT intensity in the x -axis.
    Whole Human Genome Oligo Microarray, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 92/100, based on 1382 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Integrated DNA Technologies rna oligonucleotides
    DDX1 Binds to G4 Structures in Intronic Switch RNAs (A) <t>RNA</t> oligonucleotides consisting of 4 tandem Sμ repeats <t>(Sμ4G)</t> or a G-to-C mutant (Sμ4Gmut). (B and C) RNA pull-down assays with protein extracts from (B) AID FLAG-HA or (C) AID KO CH12 cells, CIT stimulated for 48 hr. Western blots were analyzed for DDX1 and AID (FLAG tag) and RNA recovered from beads measured by dot blot. Representative results from at least 3 independent pull-downs. (D) Native electrophoretic mobility shift assays (EMSA) with 32 P-labeled Sμ4G and Sμ4Gmut RNA oligonucleotides and rDDX1 (WT) or rDDX1-K52A (ATPase mutant) proteins (1, 2, or 4 μg). Representative results from at least 3 independent assays. (E–H) CH12 cells were transfected with a pcDNA3 vector expressing GFP or N-terminal GFP-tagged human DDX1-K52A cDNA (GFP::DDX1-K52A), and cultured in UNS or CIT-stimulated conditions. (E) Percentage of GFP + cells 24 hr and 40 hr after transfection measured by flow cytometry (n = 4, mean ± SD). (F) Western blot of GFP + , fluorescence-activated cell sorted cells for DDX1 and Tubulin loading control (24 hr after transfection, 2 replicates). (G) Quantification of CSR in GFP – and GFP + -gated cell populations (40 hr after transfection; n = 4, mean ± SD). (H) DIP analyses with S9.6 antibody (IP) or no antibody control (–), 24 hr after transfection in CIT-stimulated conditions using Sα region probe 9. .
    Rna Oligonucleotides, supplied by Integrated DNA Technologies, used in various techniques. Bioz Stars score: 99/100, based on 655 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Trilencer 27 Fluorescent labeled transfection control siRNA duplex 1 nmol
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    Ik Rat 3 unique 27mer siRNA duplexes 2 nmol each
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    Image Search Results


    TOP1MT has a wide expression range in the NCI-60 panel. ( A ) TOP1MT mRNA expression intensity across the cell line panel from the NCI (NCI-60), ranked from the highest TOP1MT expresser (leukemia RPMI-8226, top) to the lowest (lung NCI-H226, bottom). Tissues of origin are designated by colored circles (see legend below). Names of the individual cell lines are reported. Expression values were obtained with Agilent Whole Human Genome Oligo Microarray chips, and quality filtering and normalization were performed using GeneSpring GX 10.0 software (Agilent, Santa Clara, CA, USA). A value of one corresponds to a 2-fold higher intensity than the 75th percentile of expression for all probes on the entire array. Values are on a log 2 scale. ( B ) Normalized TOP1MT mRNA expressions sorted by level (highest to lowest) across the NCI-60. Individual cell lines (filled dots) are colored according to tissue of origin and arranged by the intensity values in panel A. Inset: frequency distribution plot showing the number of cell lines from the NCI-60 panel by TOP1MT normalized intensity. x -axis, normalized TOP1MT intensity; y -axis, frequency of cell lines for any given TOP1MT intensity in the x -axis.

    Journal: Nucleic Acids Research

    Article Title: Coordinated regulation of mitochondrial topoisomerase IB with mitochondrial nuclear encoded genes and MYC

    doi: 10.1093/nar/gkr208

    Figure Lengend Snippet: TOP1MT has a wide expression range in the NCI-60 panel. ( A ) TOP1MT mRNA expression intensity across the cell line panel from the NCI (NCI-60), ranked from the highest TOP1MT expresser (leukemia RPMI-8226, top) to the lowest (lung NCI-H226, bottom). Tissues of origin are designated by colored circles (see legend below). Names of the individual cell lines are reported. Expression values were obtained with Agilent Whole Human Genome Oligo Microarray chips, and quality filtering and normalization were performed using GeneSpring GX 10.0 software (Agilent, Santa Clara, CA, USA). A value of one corresponds to a 2-fold higher intensity than the 75th percentile of expression for all probes on the entire array. Values are on a log 2 scale. ( B ) Normalized TOP1MT mRNA expressions sorted by level (highest to lowest) across the NCI-60. Individual cell lines (filled dots) are colored according to tissue of origin and arranged by the intensity values in panel A. Inset: frequency distribution plot showing the number of cell lines from the NCI-60 panel by TOP1MT normalized intensity. x -axis, normalized TOP1MT intensity; y -axis, frequency of cell lines for any given TOP1MT intensity in the x -axis.

    Article Snippet: All 132 labeled samples were hybridized to the Agilent Whole Human Genome Oligo Microarray (WHG; G4112F, design ID 014850, Agilent Technologies, Santa Clara, CA, USA), containing 41 000 probes (22 144 unique gene IDs).

    Techniques: Expressing, Microarray, Software

    DDX1 Binds to G4 Structures in Intronic Switch RNAs (A) RNA oligonucleotides consisting of 4 tandem Sμ repeats (Sμ4G) or a G-to-C mutant (Sμ4Gmut). (B and C) RNA pull-down assays with protein extracts from (B) AID FLAG-HA or (C) AID KO CH12 cells, CIT stimulated for 48 hr. Western blots were analyzed for DDX1 and AID (FLAG tag) and RNA recovered from beads measured by dot blot. Representative results from at least 3 independent pull-downs. (D) Native electrophoretic mobility shift assays (EMSA) with 32 P-labeled Sμ4G and Sμ4Gmut RNA oligonucleotides and rDDX1 (WT) or rDDX1-K52A (ATPase mutant) proteins (1, 2, or 4 μg). Representative results from at least 3 independent assays. (E–H) CH12 cells were transfected with a pcDNA3 vector expressing GFP or N-terminal GFP-tagged human DDX1-K52A cDNA (GFP::DDX1-K52A), and cultured in UNS or CIT-stimulated conditions. (E) Percentage of GFP + cells 24 hr and 40 hr after transfection measured by flow cytometry (n = 4, mean ± SD). (F) Western blot of GFP + , fluorescence-activated cell sorted cells for DDX1 and Tubulin loading control (24 hr after transfection, 2 replicates). (G) Quantification of CSR in GFP – and GFP + -gated cell populations (40 hr after transfection; n = 4, mean ± SD). (H) DIP analyses with S9.6 antibody (IP) or no antibody control (–), 24 hr after transfection in CIT-stimulated conditions using Sα region probe 9. .

    Journal: Molecular Cell

    Article Title: RNA Helicase DDX1 Converts RNA G-Quadruplex Structures into R-Loops to Promote IgH Class Switch Recombination

    doi: 10.1016/j.molcel.2018.04.001

    Figure Lengend Snippet: DDX1 Binds to G4 Structures in Intronic Switch RNAs (A) RNA oligonucleotides consisting of 4 tandem Sμ repeats (Sμ4G) or a G-to-C mutant (Sμ4Gmut). (B and C) RNA pull-down assays with protein extracts from (B) AID FLAG-HA or (C) AID KO CH12 cells, CIT stimulated for 48 hr. Western blots were analyzed for DDX1 and AID (FLAG tag) and RNA recovered from beads measured by dot blot. Representative results from at least 3 independent pull-downs. (D) Native electrophoretic mobility shift assays (EMSA) with 32 P-labeled Sμ4G and Sμ4Gmut RNA oligonucleotides and rDDX1 (WT) or rDDX1-K52A (ATPase mutant) proteins (1, 2, or 4 μg). Representative results from at least 3 independent assays. (E–H) CH12 cells were transfected with a pcDNA3 vector expressing GFP or N-terminal GFP-tagged human DDX1-K52A cDNA (GFP::DDX1-K52A), and cultured in UNS or CIT-stimulated conditions. (E) Percentage of GFP + cells 24 hr and 40 hr after transfection measured by flow cytometry (n = 4, mean ± SD). (F) Western blot of GFP + , fluorescence-activated cell sorted cells for DDX1 and Tubulin loading control (24 hr after transfection, 2 replicates). (G) Quantification of CSR in GFP – and GFP + -gated cell populations (40 hr after transfection; n = 4, mean ± SD). (H) DIP analyses with S9.6 antibody (IP) or no antibody control (–), 24 hr after transfection in CIT-stimulated conditions using Sα region probe 9. .

    Article Snippet: Synthetic 5′-biotinylated Sμ4G and Sμ4Gmut RNA oligonucleotides (Integrated DNA technologies) were diluted to 5 μM in folding buffer (20 mM Tris-HCl pH 7.6, 1 mM EDTA and 100 mM KCl or 100 mM LiCl), heated at 95°C for 5 min and then allowed to cool at room temperature.

    Techniques: Mutagenesis, Western Blot, FLAG-tag, Dot Blot, Electrophoretic Mobility Shift Assay, Labeling, Transfection, Plasmid Preparation, Expressing, Cell Culture, Flow Cytometry, Cytometry, Fluorescence

    DDX1 and G4 RNA-Dependent R-Loops in IgH S-Regions (A and B) CH12 cells transduced with shCtrl or shDDX1 were analyzed by DIP with S9.6 antibody (IP) or no antibody control (–). Cells were cultured in CIT-stimulated conditions with DMSO (Control), the G4 stabilizer pyridostatin (PDS, 10 μM), the G4 RNA-specific derivative carboxypyridostatin (cPDS, 10–40 μM) or the splicing inhibitor Pladienolide B (PlaB, 1 μM) for 4 hr. DIP signals shown for upstream Sμ region (probe 4) (A) and Sα region (probe 10) (B). Values were normalized to shCtrl DMSO (n ≥ 3, mean ± SD). (C–E) In vitro RNA:DNA hybrid assay using 32 .

    Journal: Molecular Cell

    Article Title: RNA Helicase DDX1 Converts RNA G-Quadruplex Structures into R-Loops to Promote IgH Class Switch Recombination

    doi: 10.1016/j.molcel.2018.04.001

    Figure Lengend Snippet: DDX1 and G4 RNA-Dependent R-Loops in IgH S-Regions (A and B) CH12 cells transduced with shCtrl or shDDX1 were analyzed by DIP with S9.6 antibody (IP) or no antibody control (–). Cells were cultured in CIT-stimulated conditions with DMSO (Control), the G4 stabilizer pyridostatin (PDS, 10 μM), the G4 RNA-specific derivative carboxypyridostatin (cPDS, 10–40 μM) or the splicing inhibitor Pladienolide B (PlaB, 1 μM) for 4 hr. DIP signals shown for upstream Sμ region (probe 4) (A) and Sα region (probe 10) (B). Values were normalized to shCtrl DMSO (n ≥ 3, mean ± SD). (C–E) In vitro RNA:DNA hybrid assay using 32 .

    Article Snippet: Synthetic 5′-biotinylated Sμ4G and Sμ4Gmut RNA oligonucleotides (Integrated DNA technologies) were diluted to 5 μM in folding buffer (20 mM Tris-HCl pH 7.6, 1 mM EDTA and 100 mM KCl or 100 mM LiCl), heated at 95°C for 5 min and then allowed to cool at room temperature.

    Techniques: Transduction, Cell Culture, In Vitro, Hybrid Assay