r3104l  (New England Biolabs)


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    Name:
    HindIII HF
    Description:
    HindIII HF 50 000 units
    Catalog Number:
    R3104L
    Price:
    249
    Category:
    Restriction Enzymes
    Size:
    50 000 units
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    Structured Review

    New England Biolabs r3104l
    HindIII HF
    HindIII HF 50 000 units
    https://www.bioz.com/result/r3104l/product/New England Biolabs
    Average 99 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    r3104l - by Bioz Stars, 2021-06
    99/100 stars

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    Related Articles

    Southern Blot:

    Article Title: Endogenous viral element-derived piRNAs are not required for production of ping-pong-dependent piRNAs from Diaphorina citri densovirus
    Article Snippet: PCR products were purified with the Zymoclean Gel DNA Recovery Kit (Zymo Research, Irvine, California) and sequenced by Quintarabio using the Sanger method. .. Southern blotting 5 µg undigested CRF-CA D citri DNA or 5 µg CRF-CA D. citri DNA digested overnight with PstI-HF and HindIII-HF (New England Biolabs, Ibswich, Massachusetts) was electrophoresed in a 0.8% agarose/0.5x TAE gel and the gel was prepared for transfer by incubation in 0.25 M HCl for 30 minutes, then 0.5 M NaCl, 0.5 M NaOH for 30 minutes, and then 1.5 M NaCl, 0.5 M Tris-HCl pH 7 for 30 minutes. .. DNA was then transferred to an Amersham Hybond Nx membrane (GE Life Sciences, Boston, Massachusetts) for 24 hours in 20X SSC using the capillary method.

    Incubation:

    Article Title: Endogenous viral element-derived piRNAs are not required for production of ping-pong-dependent piRNAs from Diaphorina citri densovirus
    Article Snippet: PCR products were purified with the Zymoclean Gel DNA Recovery Kit (Zymo Research, Irvine, California) and sequenced by Quintarabio using the Sanger method. .. Southern blotting 5 µg undigested CRF-CA D citri DNA or 5 µg CRF-CA D. citri DNA digested overnight with PstI-HF and HindIII-HF (New England Biolabs, Ibswich, Massachusetts) was electrophoresed in a 0.8% agarose/0.5x TAE gel and the gel was prepared for transfer by incubation in 0.25 M HCl for 30 minutes, then 0.5 M NaCl, 0.5 M NaOH for 30 minutes, and then 1.5 M NaCl, 0.5 M Tris-HCl pH 7 for 30 minutes. .. DNA was then transferred to an Amersham Hybond Nx membrane (GE Life Sciences, Boston, Massachusetts) for 24 hours in 20X SSC using the capillary method.

    Purification:

    Article Title: CUTseq is a versatile method for preparing multiplexed DNA sequencing libraries from low-input samples
    Article Snippet: Afterwards, we added an equal volume of the corresponding antisense oligos pre-diluted at 10 μM in nuclease-free water and incubated the solution for 5 min at 95 °C, followed by cooling down to 25 °C over a period of 45 min in a PCR thermocycler. .. We digested purified gDNA with 20 U of HindIII (NEB, catalog number R3104) or NlaIII (NEB, catalog number R0125) enzyme in a final volume of 10 μl, by incubating for 14 h at 37 °C. .. Afterwards, we ligated HindIII or NlaIII cut sites with CUTseq adapters carrying the complementary staggered end, using 1000 U of T4 ligase (Thermo Fisher Scientific, catalog number EL0014) in a final volume of 30 μl, by incubating for 18 h at 16 °C.

    Article Title: An evaluation of new and established methods to determine T‐DNA copy number and homozygosity in transgenic plants.) An evaluation of new and established methods to determine T‐DNA copy number and homozygosity in transgenic plants.
    Article Snippet: The amplicons of all three reactions were separated on 1% agarose gels (General purpose agarose GP2, BE‐A125, MidSci, Valley Park, MO, USA) with Tris‐Borate‐EDTA buffer and visualized with ethidium bromide. .. Quantitative PCR (qPCR) DNA obtained as described above was digested overnight with Hind III (R3104, New England Biolabs, Ipswich, MA, USA), followed by purification with cleaning and concentrating columns (D4014, Zymo Research, Irvine, CA, USA). .. Reactions were prepared using 9 μ L of digested genomic DNA (20–25 ng μ L−1 ), 200 nmole of forward and reverse primersets AtPsbS_3, AtPsbS_4, AtVDE_1, AtVDE_4, AtZEP_1 or AtZEP_4 for T‐DNA amplicons and NtActin_1 and NtTubulin_1 for reference genes (for primer sequences, see Table S1) and 10 μ L of SsoAdvanced Universal SYBER Green Supermix (172‐5270; BioRad, Hercules, CA, USA).

    Nucleic Acid Electrophoresis:

    Article Title: Brassica yellows virus’ movement protein upregulates anthocyanin accumulation, leading to the development of purple leaf symptoms on Arabidopsis thaliana
    Article Snippet: The protocol established by E. M. Southern for Southern blot analysis was used to confirm the transformation events. .. Total genomic DNA (5 μg) of Arabidopsis seedlings was digested with Eco R I-HF or Hin d III-HF (New England Biolabs) overnight at 37 °C, fragments were separated by gel electrophoresis, transferred to N+ membrane (Amersham Biosciences, Roosendaal, The Netherlands) using the capillary transfer method, hybridized with a radioactive isotopes [α-32P] dCTP-labeled cDNA probe specific for nt 5,161 to 5,620 of the 3′ BrYV fragment, recorded by phosphor autoradiography, and finally scanned using a Typhoon 9000 (GE Healthcare). .. For the detection of BrYV RNAs generated by the BrYV amplicon-transformed Arabidopsis lines, 2 μg total RNA of Col-0, line 111, and line 412 were prepared and fractionated by electrophoresis with ~5 V/cm force in a denaturing agarose gel containing formaldehyde.

    Autoradiography:

    Article Title: Brassica yellows virus’ movement protein upregulates anthocyanin accumulation, leading to the development of purple leaf symptoms on Arabidopsis thaliana
    Article Snippet: The protocol established by E. M. Southern for Southern blot analysis was used to confirm the transformation events. .. Total genomic DNA (5 μg) of Arabidopsis seedlings was digested with Eco R I-HF or Hin d III-HF (New England Biolabs) overnight at 37 °C, fragments were separated by gel electrophoresis, transferred to N+ membrane (Amersham Biosciences, Roosendaal, The Netherlands) using the capillary transfer method, hybridized with a radioactive isotopes [α-32P] dCTP-labeled cDNA probe specific for nt 5,161 to 5,620 of the 3′ BrYV fragment, recorded by phosphor autoradiography, and finally scanned using a Typhoon 9000 (GE Healthcare). .. For the detection of BrYV RNAs generated by the BrYV amplicon-transformed Arabidopsis lines, 2 μg total RNA of Col-0, line 111, and line 412 were prepared and fractionated by electrophoresis with ~5 V/cm force in a denaturing agarose gel containing formaldehyde.

    Polymerase Chain Reaction:

    Article Title: Systematic evaluation of CRISPR-Cas systems reveals design principles for genome editing in human cells
    Article Snippet: For the RFLP analysis, 200 ng PCR products were digested overnight with either XbaI or HindIII-HF (New England Biolabs) in CutSmart buffer. .. For the RFLP analysis, 200 ng PCR products were digested overnight with either XbaI or HindIII-HF (New England Biolabs) in CutSmart buffer. .. The reactions were separated on a 2% agarose gel stained with GelRed (Biotium) and the gel bands were quantified using ImageJ.

    Real-time Polymerase Chain Reaction:

    Article Title: An evaluation of new and established methods to determine T‐DNA copy number and homozygosity in transgenic plants.) An evaluation of new and established methods to determine T‐DNA copy number and homozygosity in transgenic plants.
    Article Snippet: The amplicons of all three reactions were separated on 1% agarose gels (General purpose agarose GP2, BE‐A125, MidSci, Valley Park, MO, USA) with Tris‐Borate‐EDTA buffer and visualized with ethidium bromide. .. Quantitative PCR (qPCR) DNA obtained as described above was digested overnight with Hind III (R3104, New England Biolabs, Ipswich, MA, USA), followed by purification with cleaning and concentrating columns (D4014, Zymo Research, Irvine, CA, USA). .. Reactions were prepared using 9 μ L of digested genomic DNA (20–25 ng μ L−1 ), 200 nmole of forward and reverse primersets AtPsbS_3, AtPsbS_4, AtVDE_1, AtVDE_4, AtZEP_1 or AtZEP_4 for T‐DNA amplicons and NtActin_1 and NtTubulin_1 for reference genes (for primer sequences, see Table S1) and 10 μ L of SsoAdvanced Universal SYBER Green Supermix (172‐5270; BioRad, Hercules, CA, USA).

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    New England Biolabs hindiii hf
    ENS is a transcribed EVE that is unevenly distributed among distinct D. citri populations. (A) Upper: PCR products produced using primers flanking ENS (primers 2 and 8). Lower: PCR products produced using primers specific to D. citri actin (primers 9 and 10). (B) Southern blot of D. citri genomic DNA using an RNA probe based on the sequence of ENS; U = undigested, D = digested with PstI and <t>HindIII.</t> Upper arrow denotes ENS in undigested genomic DNA. Lower arrows denote cleavage products. (C) PCR products produced using primers 3 and 7 and the indicated DNA samples. “Plasmid” is a plasmid containing the full ENS sequence and “Plasmid HindIII + SbfI” is the same plasmid digested with HindIII and SbfI. DNA was left intact or digested with an exonuclease (Exo.) prior to PCR. (D) Primers 3 or 7 were used to generate cDNA from antisense or sense transcripts, respectively. cDNAs were used as templates for PCR using primers 3 and 7. DNA or cDNA prepared without reverse transcriptase (RT) served as controls.
    Hindiii Hf, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/hindiii hf/product/New England Biolabs
    Average 99 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
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    ENS is a transcribed EVE that is unevenly distributed among distinct D. citri populations. (A) Upper: PCR products produced using primers flanking ENS (primers 2 and 8). Lower: PCR products produced using primers specific to D. citri actin (primers 9 and 10). (B) Southern blot of D. citri genomic DNA using an RNA probe based on the sequence of ENS; U = undigested, D = digested with PstI and HindIII. Upper arrow denotes ENS in undigested genomic DNA. Lower arrows denote cleavage products. (C) PCR products produced using primers 3 and 7 and the indicated DNA samples. “Plasmid” is a plasmid containing the full ENS sequence and “Plasmid HindIII + SbfI” is the same plasmid digested with HindIII and SbfI. DNA was left intact or digested with an exonuclease (Exo.) prior to PCR. (D) Primers 3 or 7 were used to generate cDNA from antisense or sense transcripts, respectively. cDNAs were used as templates for PCR using primers 3 and 7. DNA or cDNA prepared without reverse transcriptase (RT) served as controls.

    Journal: bioRxiv

    Article Title: Endogenous viral element-derived piRNAs are not required for production of ping-pong-dependent piRNAs from Diaphorina citri densovirus

    doi: 10.1101/2020.05.20.105924

    Figure Lengend Snippet: ENS is a transcribed EVE that is unevenly distributed among distinct D. citri populations. (A) Upper: PCR products produced using primers flanking ENS (primers 2 and 8). Lower: PCR products produced using primers specific to D. citri actin (primers 9 and 10). (B) Southern blot of D. citri genomic DNA using an RNA probe based on the sequence of ENS; U = undigested, D = digested with PstI and HindIII. Upper arrow denotes ENS in undigested genomic DNA. Lower arrows denote cleavage products. (C) PCR products produced using primers 3 and 7 and the indicated DNA samples. “Plasmid” is a plasmid containing the full ENS sequence and “Plasmid HindIII + SbfI” is the same plasmid digested with HindIII and SbfI. DNA was left intact or digested with an exonuclease (Exo.) prior to PCR. (D) Primers 3 or 7 were used to generate cDNA from antisense or sense transcripts, respectively. cDNAs were used as templates for PCR using primers 3 and 7. DNA or cDNA prepared without reverse transcriptase (RT) served as controls.

    Article Snippet: Southern blotting 5 µg undigested CRF-CA D citri DNA or 5 µg CRF-CA D. citri DNA digested overnight with PstI-HF and HindIII-HF (New England Biolabs, Ibswich, Massachusetts) was electrophoresed in a 0.8% agarose/0.5x TAE gel and the gel was prepared for transfer by incubation in 0.25 M HCl for 30 minutes, then 0.5 M NaCl, 0.5 M NaOH for 30 minutes, and then 1.5 M NaCl, 0.5 M Tris-HCl pH 7 for 30 minutes.

    Techniques: Polymerase Chain Reaction, Produced, Southern Blot, Sequencing, Plasmid Preparation

    Characterization of BrYV amplicon-transformed Arabidopsis. ( a ) Southern blot analysis indicating that the cDNA of BrYV was inserted into the Arabidopsis genome. The genomic DNA of transgenic Arabidopsis plants was digested with either Eco R I or Hin d III. (b) Northern blot results showing the constitutive expression of BrYV-encoded genomic RNA (gRNA) and subgenomic RNAs (sgRNAs). (c) Western blot analysis demonstrating the expression of the BrYV coat protein in lines 111 and 412.

    Journal: Scientific Reports

    Article Title: Brassica yellows virus’ movement protein upregulates anthocyanin accumulation, leading to the development of purple leaf symptoms on Arabidopsis thaliana

    doi: 10.1038/s41598-018-34591-5

    Figure Lengend Snippet: Characterization of BrYV amplicon-transformed Arabidopsis. ( a ) Southern blot analysis indicating that the cDNA of BrYV was inserted into the Arabidopsis genome. The genomic DNA of transgenic Arabidopsis plants was digested with either Eco R I or Hin d III. (b) Northern blot results showing the constitutive expression of BrYV-encoded genomic RNA (gRNA) and subgenomic RNAs (sgRNAs). (c) Western blot analysis demonstrating the expression of the BrYV coat protein in lines 111 and 412.

    Article Snippet: Total genomic DNA (5 μg) of Arabidopsis seedlings was digested with Eco R I-HF or Hin d III-HF (New England Biolabs) overnight at 37 °C, fragments were separated by gel electrophoresis, transferred to N+ membrane (Amersham Biosciences, Roosendaal, The Netherlands) using the capillary transfer method, hybridized with a radioactive isotopes [α-32P] dCTP-labeled cDNA probe specific for nt 5,161 to 5,620 of the 3′ BrYV fragment, recorded by phosphor autoradiography, and finally scanned using a Typhoon 9000 (GE Healthcare).

    Techniques: Amplification, Transformation Assay, Southern Blot, Transgenic Assay, Northern Blot, Expressing, Western Blot

    CUTseq implementation and reproducibility. a CUTseq workflow. (1) RE, restriction enzyme. T7, T7 phage promoter. IVT, in vitro transcription. RA5, RA3, SP7, and SP9: Illumina’s sequencing adapters. b BT474 cells copy number profiles (100 kb resolution). ρ , Pearson’s correlation. c Pearson’s correlation ( ρ ) between the copy number profiles (100 kb resolution) of five cancer cell lines digested with HindIII (rows) or NlaIII (columns). d Chr17 copy number profiles (NlaIII, 100 kb resolution) in two HER2-positive (SKBR3 and BT474) and one HER2-negative cell line (MCF7). ERBB2/HER2 is highlighted in red. e Copy number profiles (NlaIII, 100 kb resolution) in five replicates (Rep) from FFPE tumor samples. COAD, colon adenocarcinoma. MELA, melanoma. ρ , Pearson’s correlation. f Pearson’s correlation ( ρ ) between the replicates shown in e at different resolutions. Each dot represents one pair of replicates. Error bars indicate the median and interquartile range. g Pearson’s correlation ( ρ ) between the fraction of the genome (100 kb resolution) either amplified or deleted in the replicates (Rep) shown in e . Each dot represents one pair of replicates. Dashed line: linear regression. h , i Length of amplified (AMP) or deleted (DEL) genomic segments in Rep1 ( h ) and Rep2 ( i ) samples shown in e , at various resolutions. j Zoom-in view on chr9 q-arm in sample TRN4 shown in e . Arrows indicate focal amplifications detected only at 10 kb resolution in both replicates. Red: centromeric region. The p-arm is not shown. k Copy number profiles (NlaIII, 100 kb resolution) determined using 120 pg of gDNA extracted from one FFPE breast cancer (BRCA) sample and three different numbers of PCR cycles. l Pearson’s correlation ( ρ ) between copy number profiles (100 kb resolution) determined using different amounts of gDNA extracted from the sample shown in k . In all the profiles, gray dots represent individual genomic windows, whereas black lines indicate segmented genomic intervals after circular binary segmentation 37 . The numbers below each box indicate chromosomes from chr1 (leftmost) to chr22 (rightmost). In all the cases, TRN refers to the ID of Turin samples, as shown in Supplementary Table 2 . All the source data for this figure are provided as a Source Data file

    Journal: Nature Communications

    Article Title: CUTseq is a versatile method for preparing multiplexed DNA sequencing libraries from low-input samples

    doi: 10.1038/s41467-019-12570-2

    Figure Lengend Snippet: CUTseq implementation and reproducibility. a CUTseq workflow. (1) RE, restriction enzyme. T7, T7 phage promoter. IVT, in vitro transcription. RA5, RA3, SP7, and SP9: Illumina’s sequencing adapters. b BT474 cells copy number profiles (100 kb resolution). ρ , Pearson’s correlation. c Pearson’s correlation ( ρ ) between the copy number profiles (100 kb resolution) of five cancer cell lines digested with HindIII (rows) or NlaIII (columns). d Chr17 copy number profiles (NlaIII, 100 kb resolution) in two HER2-positive (SKBR3 and BT474) and one HER2-negative cell line (MCF7). ERBB2/HER2 is highlighted in red. e Copy number profiles (NlaIII, 100 kb resolution) in five replicates (Rep) from FFPE tumor samples. COAD, colon adenocarcinoma. MELA, melanoma. ρ , Pearson’s correlation. f Pearson’s correlation ( ρ ) between the replicates shown in e at different resolutions. Each dot represents one pair of replicates. Error bars indicate the median and interquartile range. g Pearson’s correlation ( ρ ) between the fraction of the genome (100 kb resolution) either amplified or deleted in the replicates (Rep) shown in e . Each dot represents one pair of replicates. Dashed line: linear regression. h , i Length of amplified (AMP) or deleted (DEL) genomic segments in Rep1 ( h ) and Rep2 ( i ) samples shown in e , at various resolutions. j Zoom-in view on chr9 q-arm in sample TRN4 shown in e . Arrows indicate focal amplifications detected only at 10 kb resolution in both replicates. Red: centromeric region. The p-arm is not shown. k Copy number profiles (NlaIII, 100 kb resolution) determined using 120 pg of gDNA extracted from one FFPE breast cancer (BRCA) sample and three different numbers of PCR cycles. l Pearson’s correlation ( ρ ) between copy number profiles (100 kb resolution) determined using different amounts of gDNA extracted from the sample shown in k . In all the profiles, gray dots represent individual genomic windows, whereas black lines indicate segmented genomic intervals after circular binary segmentation 37 . The numbers below each box indicate chromosomes from chr1 (leftmost) to chr22 (rightmost). In all the cases, TRN refers to the ID of Turin samples, as shown in Supplementary Table 2 . All the source data for this figure are provided as a Source Data file

    Article Snippet: We then used I-DOT One to dispense first 5 ng diluted in 350 nl of gDNA extracted from HeLa cells, followed by 100 nl of 20 U/μl of HindIII (NEB, catalog number R3104) and 50 nl of CutSmart buffer (NEB, catalog number R3104), in 96 of the 384 wells.

    Techniques: In Vitro, Sequencing, Formalin-fixed Paraffin-Embedded, Amplification, Polymerase Chain Reaction

    (a) Southern blot (b) TAIL‐PCR analyses for T 0 plant VPZ‐23, five segregating T 1 plants, two homozygous T 2 plants and wild type control (WT). The final three lanes show 25 and 50 pg digested VPZ plasmid DNA with 10 μ g of digested WT DNA and 50 pg of VPZ plasmid without WT DNA. Arrows in panel b indicate the bands that were absent in WT and show a size shift between reaction 2 and 3 in the TAIL‐PCR and scored in Table 1 . TAIL‐PCR was performed with AD3 and T‐DNA specific primers RB3.

    Journal: Plant, Cell & Environment

    Article Title: An evaluation of new and established methods to determine T‐DNA copy number and homozygosity in transgenic plants.) An evaluation of new and established methods to determine T‐DNA copy number and homozygosity in transgenic plants.

    doi: 10.1111/pce.12693

    Figure Lengend Snippet: (a) Southern blot (b) TAIL‐PCR analyses for T 0 plant VPZ‐23, five segregating T 1 plants, two homozygous T 2 plants and wild type control (WT). The final three lanes show 25 and 50 pg digested VPZ plasmid DNA with 10 μ g of digested WT DNA and 50 pg of VPZ plasmid without WT DNA. Arrows in panel b indicate the bands that were absent in WT and show a size shift between reaction 2 and 3 in the TAIL‐PCR and scored in Table 1 . TAIL‐PCR was performed with AD3 and T‐DNA specific primers RB3.

    Article Snippet: Quantitative PCR (qPCR) DNA obtained as described above was digested overnight with Hind III (R3104, New England Biolabs, Ipswich, MA, USA), followed by purification with cleaning and concentrating columns (D4014, Zymo Research, Irvine, CA, USA).

    Techniques: Southern Blot, Polymerase Chain Reaction, Plasmid Preparation