dna ladder Search Results


  • Logo
  • About
  • News
  • Press Release
  • Team
  • Advisors
  • Partners
  • Contact
  • Bioz Stars
  • Bioz vStars
  • 80
    Thermo Fisher bp dna ladder
    Gel analysis of ChIA-PETs after PCR amplification ( STEP 32 ) A 25 bp <t>DNA</t> ladder is shown in lane 1 for size reference. Lanes 2 and 3 are the PCR products generated after 20 cycles of PCR amplification from 1 <t>µl</t> and 2 µl of bead-immobilized template respectively. 25 cycles were used to generate the PCR products in lanes 4 and 5 program, from 1 µl and 2 µl of beads respectively. ( A ) This is a successful library, as indicated by the bright, well-defined bands at the expected size of 166 bp. ( B ) PCR amplification has failed to yield sufficient ChIA-PET DNA, as seen from the very weak band present in lane 5. This could indicate that PCR conditions need to be optimized, or that library construction has failed.
    Bp Dna Ladder, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 80/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/bp dna ladder/product/Thermo Fisher
    Average 80 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    bp dna ladder - by Bioz Stars, 2022-11
    80/100 stars
      Buy from Supplier

    80
    Thermo Fisher kb plus dna ladder
    EHCas9 PAM screening and validation. ( A ) Sequence logo of the PAM region preferred by EHCas9 for target cleavage, as determined by in vivo screening of a PAM library. Nucleotide positions 3’ from the end of the spacer-matching strand of the target are indicated. Nucleotides from the 2nd to the 4th position were tested (the first position was kept invariable, corresponding to thymine). ( B ) Sequence logo of the consensus PAM preferred by EHCas9 for target cleavage as determined through in vitro screening. Nucleotide positions 3’ from the end of the spacer-matching strand of the target are indicated. Nucleotides from the 1st to the 7th position were tested. ( C ) In vivo PAM validation. The efficiency of transformation (number of colony-forming units – CFU - per mg of plasmid <t>DNA)</t> of E. coli cells expressing (+ EHCas9) or not (-EHCas9) EHCas9 in addition to a guide EH crRNA and the predicted EH tracrRNA, with plasmids carrying a target adjacent to sequences varying in the 2 nd , the 3 rd and the 4 th positions (ACC, GGA, GGC, GGG, GGT) of the PAM region, is represented. Data are the mean of three replicates (error bars correspond to the standard deviation).
    Kb Plus Dna Ladder, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 80/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/kb plus dna ladder/product/Thermo Fisher
    Average 80 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    kb plus dna ladder - by Bioz Stars, 2022-11
    80/100 stars
      Buy from Supplier

    80
    Thermo Fisher dna ladder
    EHCas9 PAM screening and validation. ( A ) Sequence logo of the PAM region preferred by EHCas9 for target cleavage, as determined by in vivo screening of a PAM library. Nucleotide positions 3’ from the end of the spacer-matching strand of the target are indicated. Nucleotides from the 2nd to the 4th position were tested (the first position was kept invariable, corresponding to thymine). ( B ) Sequence logo of the consensus PAM preferred by EHCas9 for target cleavage as determined through in vitro screening. Nucleotide positions 3’ from the end of the spacer-matching strand of the target are indicated. Nucleotides from the 1st to the 7th position were tested. ( C ) In vivo PAM validation. The efficiency of transformation (number of colony-forming units – CFU - per mg of plasmid <t>DNA)</t> of E. coli cells expressing (+ EHCas9) or not (-EHCas9) EHCas9 in addition to a guide EH crRNA and the predicted EH tracrRNA, with plasmids carrying a target adjacent to sequences varying in the 2 nd , the 3 rd and the 4 th positions (ACC, GGA, GGC, GGG, GGT) of the PAM region, is represented. Data are the mean of three replicates (error bars correspond to the standard deviation).
    Dna Ladder, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 80/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/dna ladder/product/Thermo Fisher
    Average 80 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    dna ladder - by Bioz Stars, 2022-11
    80/100 stars
      Buy from Supplier

    88
    Thermo Fisher 100 bp dna ladder
    EHCas9 PAM screening and validation. ( A ) Sequence logo of the PAM region preferred by EHCas9 for target cleavage, as determined by in vivo screening of a PAM library. Nucleotide positions 3’ from the end of the spacer-matching strand of the target are indicated. Nucleotides from the 2nd to the 4th position were tested (the first position was kept invariable, corresponding to thymine). ( B ) Sequence logo of the consensus PAM preferred by EHCas9 for target cleavage as determined through in vitro screening. Nucleotide positions 3’ from the end of the spacer-matching strand of the target are indicated. Nucleotides from the 1st to the 7th position were tested. ( C ) In vivo PAM validation. The efficiency of transformation (number of colony-forming units – CFU - per mg of plasmid <t>DNA)</t> of E. coli cells expressing (+ EHCas9) or not (-EHCas9) EHCas9 in addition to a guide EH crRNA and the predicted EH tracrRNA, with plasmids carrying a target adjacent to sequences varying in the 2 nd , the 3 rd and the 4 th positions (ACC, GGA, GGC, GGG, GGT) of the PAM region, is represented. Data are the mean of three replicates (error bars correspond to the standard deviation).
    100 Bp Dna Ladder, supplied by Thermo Fisher, 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/100 bp dna ladder/product/Thermo Fisher
    Average 88 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    100 bp dna ladder - by Bioz Stars, 2022-11
    88/100 stars
      Buy from Supplier

    Image Search Results


    Gel analysis of ChIA-PETs after PCR amplification ( STEP 32 ) A 25 bp DNA ladder is shown in lane 1 for size reference. Lanes 2 and 3 are the PCR products generated after 20 cycles of PCR amplification from 1 µl and 2 µl of bead-immobilized template respectively. 25 cycles were used to generate the PCR products in lanes 4 and 5 program, from 1 µl and 2 µl of beads respectively. ( A ) This is a successful library, as indicated by the bright, well-defined bands at the expected size of 166 bp. ( B ) PCR amplification has failed to yield sufficient ChIA-PET DNA, as seen from the very weak band present in lane 5. This could indicate that PCR conditions need to be optimized, or that library construction has failed.

    Journal: Current protocols in molecular biology

    Article Title: Chromatin Interaction Analysis using Paired-End Tag Sequencing

    doi: 10.1002/0471142727.mb2115s89

    Figure Lengend Snippet: Gel analysis of ChIA-PETs after PCR amplification ( STEP 32 ) A 25 bp DNA ladder is shown in lane 1 for size reference. Lanes 2 and 3 are the PCR products generated after 20 cycles of PCR amplification from 1 µl and 2 µl of bead-immobilized template respectively. 25 cycles were used to generate the PCR products in lanes 4 and 5 program, from 1 µl and 2 µl of beads respectively. ( A ) This is a successful library, as indicated by the bright, well-defined bands at the expected size of 166 bp. ( B ) PCR amplification has failed to yield sufficient ChIA-PET DNA, as seen from the very weak band present in lane 5. This could indicate that PCR conditions need to be optimized, or that library construction has failed.

    Article Snippet: Annealed half-linkers A and B ( ) DNA fragment X of known size (blunt-ended, 5’-phosphorylated, ∼1 – 3 kb) Adapters A and B ( ) Primers ( ) 10 mM dNTPs Nuclease-free water T4 DNA ligase (30 U/µl) (Fermentas) 5× T4 DNA Ligase Buffer with PEG (Invitrogen) T4 DNA Polynucleotide Kinase (10 U/µl) (NEB) 10× T4 DNA Ligase Buffer (NEB) EB buffer (Qiagen) GlycoBlue (15 mg/ml) (Ambion) Absolute ethanol/ 75% ethanol (v/v) MmeI (2 U/µl) (NEB) S-adenosylmethionine (SAM) (NEB) 10× NEBuffer 4 (NEB) Dynabeads M-280 Streptavidin (Invitrogen) 1× and 2× B & W buffer (see recipe) E. coli DNA polymerase I (10 U/µl) (NEB) 10× NEBuffer 2 (NEB) HotStarTaq Master Mix (Qiagen) 25 bp DNA ladder (Invitrogen) 4–20% TBE PAGE gel (10 wells) (Invitrogen) 10× TBE buffer ( APPENDIX 2 ) DNA loading dye QIAquick PCR Purification Kit (Qiagen) TE buffer, pH 8.0 ( APPENDIX 2 ) 0.2-ml PCR tubes 0.6-ml tubes 1.7-ml microcentrifuge tubes DNA LoBind Tubes, 1.5-ml (Eppendorf) Novex Mini-Cell (Invitrogen) Intelli-Mixer RM-2L (Palico Biotech) Magnetic Particle Collector (Invitrogen)

    Techniques: Polymerase Chain Reaction, Amplification, Generated, ChIA Pet Assay

    EHCas9 PAM screening and validation. ( A ) Sequence logo of the PAM region preferred by EHCas9 for target cleavage, as determined by in vivo screening of a PAM library. Nucleotide positions 3’ from the end of the spacer-matching strand of the target are indicated. Nucleotides from the 2nd to the 4th position were tested (the first position was kept invariable, corresponding to thymine). ( B ) Sequence logo of the consensus PAM preferred by EHCas9 for target cleavage as determined through in vitro screening. Nucleotide positions 3’ from the end of the spacer-matching strand of the target are indicated. Nucleotides from the 1st to the 7th position were tested. ( C ) In vivo PAM validation. The efficiency of transformation (number of colony-forming units – CFU - per mg of plasmid DNA) of E. coli cells expressing (+ EHCas9) or not (-EHCas9) EHCas9 in addition to a guide EH crRNA and the predicted EH tracrRNA, with plasmids carrying a target adjacent to sequences varying in the 2 nd , the 3 rd and the 4 th positions (ACC, GGA, GGC, GGG, GGT) of the PAM region, is represented. Data are the mean of three replicates (error bars correspond to the standard deviation).

    Journal: bioRxiv

    Article Title: Identification of the EH CRISPR-Cas9 system on a metagenome and its application to genome engineering

    doi: 10.1101/2022.10.31.514646

    Figure Lengend Snippet: EHCas9 PAM screening and validation. ( A ) Sequence logo of the PAM region preferred by EHCas9 for target cleavage, as determined by in vivo screening of a PAM library. Nucleotide positions 3’ from the end of the spacer-matching strand of the target are indicated. Nucleotides from the 2nd to the 4th position were tested (the first position was kept invariable, corresponding to thymine). ( B ) Sequence logo of the consensus PAM preferred by EHCas9 for target cleavage as determined through in vitro screening. Nucleotide positions 3’ from the end of the spacer-matching strand of the target are indicated. Nucleotides from the 1st to the 7th position were tested. ( C ) In vivo PAM validation. The efficiency of transformation (number of colony-forming units – CFU - per mg of plasmid DNA) of E. coli cells expressing (+ EHCas9) or not (-EHCas9) EHCas9 in addition to a guide EH crRNA and the predicted EH tracrRNA, with plasmids carrying a target adjacent to sequences varying in the 2 nd , the 3 rd and the 4 th positions (ACC, GGA, GGC, GGG, GGT) of the PAM region, is represented. Data are the mean of three replicates (error bars correspond to the standard deviation).

    Article Snippet: The 1 Kb Plus DNA Ladder (Invitrogen) was included in the agarose gels as a DNA weight marker.

    Techniques: Sequencing, In Vivo, In Vitro, Transformation Assay, Plasmid Preparation, Expressing, Standard Deviation

    EH sgRNA design. ( A ) RNA sequence alignments of the EH repeat, the predicted EH tracrRNA gene region and the designed EH sgRNA with the S. donghicola (Sdo) repeat, tracrRNA coding sequence and sgRNA, correspondingly. Matching positions are marked with asterisks. Promoter and terminator regions predicted for the EH tracrRNA gene are grey shaded. The constant region of the EH sgRNA sequence was conceived by joining the EH repeat sequence in orange and the EH tracrRNA sequence in blue. ( B ) Scheme of the EH sgRNA including a generic 23-nt spacer base-paired to the target strand in a DNA substrate containing a spacer-matching sequence and a compatible PAM (underlined). The EH sgRNA anti-repeat and tracrRNA sequences comprising the linker (tetraloop 5’-GAAA-3’), the anti-repeat and the two stem-loop forming segments, are coloured as in panel A.

    Journal: bioRxiv

    Article Title: Identification of the EH CRISPR-Cas9 system on a metagenome and its application to genome engineering

    doi: 10.1101/2022.10.31.514646

    Figure Lengend Snippet: EH sgRNA design. ( A ) RNA sequence alignments of the EH repeat, the predicted EH tracrRNA gene region and the designed EH sgRNA with the S. donghicola (Sdo) repeat, tracrRNA coding sequence and sgRNA, correspondingly. Matching positions are marked with asterisks. Promoter and terminator regions predicted for the EH tracrRNA gene are grey shaded. The constant region of the EH sgRNA sequence was conceived by joining the EH repeat sequence in orange and the EH tracrRNA sequence in blue. ( B ) Scheme of the EH sgRNA including a generic 23-nt spacer base-paired to the target strand in a DNA substrate containing a spacer-matching sequence and a compatible PAM (underlined). The EH sgRNA anti-repeat and tracrRNA sequences comprising the linker (tetraloop 5’-GAAA-3’), the anti-repeat and the two stem-loop forming segments, are coloured as in panel A.

    Article Snippet: The 1 Kb Plus DNA Ladder (Invitrogen) was included in the agarose gels as a DNA weight marker.

    Techniques: Sequencing

    Representative agarose gel electrophoreses of in vitro EHCas9-mediated DNA cleavage reactions. Except indicated otherwise, experiments were performed under the following standard conditions: 30 min reaction time at 37°C, 20 mM MgCl 2 , 25 nM of an 840 bp linear DNA containing a target sequence and a compatible PAM, preincubated (15 min at 37°C) EHCas9:EH sgRNA mixtures (0.5 mM EHCas9 and 0.5 mM EH sgRNA concentration in the digestion reaction). The length of relevant bands (in kb) of a linear dsDNA molecular weight marker (M) and the position of bands corresponding to expected cut and uncut DNA substrates are indicated. (A) Samples from standard digestion reactions, mixed either after protein:guide preincubation (lane 2) or without preincubation (lane 7), and from reactions with a missing component (MgCl 2 , lane 3; a compatible PAM next to the target, lane 4; a guide, lane 5; the protein, lane 6) are included. (B) Samples from digestion reactions under standard conditions but for the protein concentration (up to 500 nM). (C) Samples from standard reactions incubated for up to 40 min. (D) Samples of digestions carried out under standard conditions except by the incubation temperature (from 20°C to 45 °C).

    Journal: bioRxiv

    Article Title: Identification of the EH CRISPR-Cas9 system on a metagenome and its application to genome engineering

    doi: 10.1101/2022.10.31.514646

    Figure Lengend Snippet: Representative agarose gel electrophoreses of in vitro EHCas9-mediated DNA cleavage reactions. Except indicated otherwise, experiments were performed under the following standard conditions: 30 min reaction time at 37°C, 20 mM MgCl 2 , 25 nM of an 840 bp linear DNA containing a target sequence and a compatible PAM, preincubated (15 min at 37°C) EHCas9:EH sgRNA mixtures (0.5 mM EHCas9 and 0.5 mM EH sgRNA concentration in the digestion reaction). The length of relevant bands (in kb) of a linear dsDNA molecular weight marker (M) and the position of bands corresponding to expected cut and uncut DNA substrates are indicated. (A) Samples from standard digestion reactions, mixed either after protein:guide preincubation (lane 2) or without preincubation (lane 7), and from reactions with a missing component (MgCl 2 , lane 3; a compatible PAM next to the target, lane 4; a guide, lane 5; the protein, lane 6) are included. (B) Samples from digestion reactions under standard conditions but for the protein concentration (up to 500 nM). (C) Samples from standard reactions incubated for up to 40 min. (D) Samples of digestions carried out under standard conditions except by the incubation temperature (from 20°C to 45 °C).

    Article Snippet: The 1 Kb Plus DNA Ladder (Invitrogen) was included in the agarose gels as a DNA weight marker.

    Techniques: Agarose Gel Electrophoresis, In Vitro, Sequencing, Concentration Assay, Molecular Weight, Marker, Protein Concentration, Incubation

    Prokaryotic genome editing with EHCas9. (A) Overview of the single-step general procedure for positive selection of genome-edited E. coli. E. coli cells harbouring a plasmid ( e.g ., pKD46; ampicillin resistance, Amp R ) encoding Lambda Red recombination proteins (Gam, Beta, Exo) are co-transformed with an antibiotic resistance (Ab R ) selectable plasmid carrying inducible ehcas9 gene and a sgRNA targeting a sequence within the gene of interest (GOI) and a linear dsDNA template matching both sides of the target (flanking sites, FS). Recombination between the template and the flanking sites in the gene mediated by the Lambda Red recombination machinery (RM) will result in the deletion of the target sequence. The Cas9:sgRNA ribonucleoprotein complex will produce double-strand breaks in the non-edited target, often leading to cell death. Colonies grown at 37°C expressing Cas9 are selected on plates ( i.e ., arabinose and antibiotic-containing medium) and screened through PCR amplification and agarose gel electrophoresis to confirm the deletion. (B) An agarose gel electrophoresis of PCR products from the region surrounding pyrF (the gene of interest) in E. coli cells expressing the Lambda Red system from pKD46. DNA used for amplification was purified from chloramphenicol-resistant colonies grown in the presence of arabinose after co-transformation with a recombination template matching the flanks of pyrF (recombination would lead to a ca. 0.6 kb deletion), and a pBAD33-derivative plasmid (providing chloramphenicol resistance) encoding either both EHCas9 and an EH sgRNA that targets the pyrF gene (+ EHCas9) or only the EH sgRNA (-EHCas9). Each lane corresponds to a transformant clone. Bands running as linear DNA fragments with the length of the original (ca. 1 kb; WT) and the recombinant (ca. 0.5 kb; Mutant) pyrF region are indicated. The length of relevant bands of a linear dsDNA molecular weight marker is indicated.

    Journal: bioRxiv

    Article Title: Identification of the EH CRISPR-Cas9 system on a metagenome and its application to genome engineering

    doi: 10.1101/2022.10.31.514646

    Figure Lengend Snippet: Prokaryotic genome editing with EHCas9. (A) Overview of the single-step general procedure for positive selection of genome-edited E. coli. E. coli cells harbouring a plasmid ( e.g ., pKD46; ampicillin resistance, Amp R ) encoding Lambda Red recombination proteins (Gam, Beta, Exo) are co-transformed with an antibiotic resistance (Ab R ) selectable plasmid carrying inducible ehcas9 gene and a sgRNA targeting a sequence within the gene of interest (GOI) and a linear dsDNA template matching both sides of the target (flanking sites, FS). Recombination between the template and the flanking sites in the gene mediated by the Lambda Red recombination machinery (RM) will result in the deletion of the target sequence. The Cas9:sgRNA ribonucleoprotein complex will produce double-strand breaks in the non-edited target, often leading to cell death. Colonies grown at 37°C expressing Cas9 are selected on plates ( i.e ., arabinose and antibiotic-containing medium) and screened through PCR amplification and agarose gel electrophoresis to confirm the deletion. (B) An agarose gel electrophoresis of PCR products from the region surrounding pyrF (the gene of interest) in E. coli cells expressing the Lambda Red system from pKD46. DNA used for amplification was purified from chloramphenicol-resistant colonies grown in the presence of arabinose after co-transformation with a recombination template matching the flanks of pyrF (recombination would lead to a ca. 0.6 kb deletion), and a pBAD33-derivative plasmid (providing chloramphenicol resistance) encoding either both EHCas9 and an EH sgRNA that targets the pyrF gene (+ EHCas9) or only the EH sgRNA (-EHCas9). Each lane corresponds to a transformant clone. Bands running as linear DNA fragments with the length of the original (ca. 1 kb; WT) and the recombinant (ca. 0.5 kb; Mutant) pyrF region are indicated. The length of relevant bands of a linear dsDNA molecular weight marker is indicated.

    Article Snippet: The 1 Kb Plus DNA Ladder (Invitrogen) was included in the agarose gels as a DNA weight marker.

    Techniques: Selection, Plasmid Preparation, Transformation Assay, Sequencing, Expressing, Polymerase Chain Reaction, Amplification, Agarose Gel Electrophoresis, Purification, Recombinant, Mutagenesis, Molecular Weight, Marker