recjf  (New England Biolabs)


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    Name:
    RecJf
    Description:
    RecJf 5 000 units
    Catalog Number:
    m0264l
    Price:
    280
    Size:
    5 000 units
    Category:
    Exonucleases
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    Structured Review

    New England Biolabs recjf
    RecJf
    RecJf 5 000 units
    https://www.bioz.com/result/recjf/product/New England Biolabs
    Average 90 stars, based on 6 article reviews
    Price from $9.99 to $1999.99
    recjf - by Bioz Stars, 2020-01
    90/100 stars

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    Related Articles

    Amplification:

    Article Title: Sensing Self and Foreign Circular RNAs by Intron Identity
    Article Snippet: To remove excess linker, 30 Units of RecJf (New England Biolabs, Inc., M0264L) and 20 Units of 5′ Deadenylase (New England Biolabs, Inc., M0331S) in 1x RecJ buffer with Ribolock RNase Inhibitor were added to the reaction, and incubated for 1 hr at 37°C. .. Reverse transcription, biotin capture of ligated fragments, cDNA circularization, library amplification, and PAGE purification were carried out exactly as written in the previously published method ( ).

    Whole Genome Amplification:

    Article Title: Multiplex target capture with double-stranded DNA probes
    Article Snippet: Seventy femtomoles of cLPPs or ssLPPs (5 to 50 attomoles/probe) were mixed with 500 ng of genomic DNA (or WGA DNA) in 1× Ampligase buffer (Epicentre, Charlotte, NC, USA) and 0.9 M betaine (Sigma Aldrich, St Louis, MO, USA) in a 10 μl volume. .. To completely eliminate linear DNA molecules, 2 μl of a mixture of total of six exonucleases including 3.5 U exo I (Affymetrix, Santa Clara, CA, USA), 18 U exo III (Affymetrix), 4U exo T7 (Affymetrix), 0.4 U exo T (NEB), 3 U RecJf (NEB) and 0.2 U lambda exo (Epicentre, Charlotte, NC, USA) was added to the reaction and incubated at 37°C for 30 minutes, 80°C for 10 minutes and 95°C for 5 minutes.

    Autoradiography:

    Article Title: EXOG, a novel paralog of Endonuclease G in higher eukaryotes
    Article Snippet: The exonucleases RecJf and ExoI were used to digest the labeled oligonucleotides according to the recommendation of the supplier (NEB), leading to the production of mononucleotides (RecJf ) and dinucleotides (ExoI) used as size markers. .. After the separation of cleavage products by electrophoresis or on DEAE-cellulose thin layer plates at 65°C, data were collected by autoradiography.

    Electrophoresis:

    Article Title: Unusual Telomeric DNAs in Human Telomerase-Negative Immortalized Cells ▿Unusual Telomeric DNAs in Human Telomerase-Negative Immortalized Cells ▿ †
    Article Snippet: Digestion with a mixture of AluI and MboI was performed for samples in 2D gel electrophoresis, which was used in most of the similar experiments appearing in the literature. .. BAL-31 and Escherichia coli exonuclease III (Exo III) were purchased from Takara, and E. coli exonuclease I (Exo I), RecJf (RecJ), and T7 endonuclease I (Endo I) were from New England Biolabs.

    Article Title: EXOG, a novel paralog of Endonuclease G in higher eukaryotes
    Article Snippet: The exonucleases RecJf and ExoI were used to digest the labeled oligonucleotides according to the recommendation of the supplier (NEB), leading to the production of mononucleotides (RecJf ) and dinucleotides (ExoI) used as size markers. .. After the separation of cleavage products by electrophoresis or on DEAE-cellulose thin layer plates at 65°C, data were collected by autoradiography.

    Incubation:

    Article Title: Structural insights into the DNA-binding specificity of E2F family transcription factors
    Article Snippet: Cells were crosslinked with 1% formaldehyde, and incubated in hypotonic buffer for 15 min, and DNA then sonicated to 200–500-bp fragments in lysis buffer (50 mM HEPES, 2 mM EDTA, pH 8.0, 150 mM NaCl, 1% Triton X-100, 0.1% sodium deoxycholate, 0.2% SDS, pH 8.0). .. Immunoprecipitates were then subjected to the following enzymatic on-bead reactions for 30 min in 60 μl reaction volume: (a) end-polishing with T4 DNA polymerase (3 U, New England BioLabs, M0203L), (b) kinase reaction with T4 polynucleotide kinase (10 U, New England BioLabs, M0201L), (c) adenine addition reaction with Klenow fragment exo-(5 U, New England BioLabs, M0212L), (d) first adaptor ligation with 1.25 μM P2 adaptors ( , rows 3 and 4; Eurofins MWG Operon) and T4 DNA ligase (500 U, New England BioLabs, M0202L), (e) fill-in reaction with phi29 DNA polymerase (10 U, New England BioLabs, M0269L), (f) lambda exonuclease reaction (10 U, New England BioLabs, M0262L) and (f) RecJf exonuclease reaction with 30 U of RecJf exonuclease (New England BioLabs, M0264L).

    Article Title: Multiplex target capture with double-stranded DNA probes
    Article Snippet: .. To completely eliminate linear DNA molecules, 2 μl of a mixture of total of six exonucleases including 3.5 U exo I (Affymetrix, Santa Clara, CA, USA), 18 U exo III (Affymetrix), 4U exo T7 (Affymetrix), 0.4 U exo T (NEB), 3 U RecJf (NEB) and 0.2 U lambda exo (Epicentre, Charlotte, NC, USA) was added to the reaction and incubated at 37°C for 30 minutes, 80°C for 10 minutes and 95°C for 5 minutes. .. Total time for multiplex target capture is approximately 4 hours (Figure ).

    Article Title: Nucleotide excision repair by dual incisions in plants
    Article Snippet: .. For 5′→3′ digestion, gel-purified, 3′-end-labeled DNA was incubated with 22.5 units of RecJf (New England Biolabs) for 1 h at 37 °C in a 5-µL reaction according to the recommendations of the manufacturer. .. Products were then ethanol-precipitated and resolved on an 11% sequencing gel.

    Article Title: Single-cell CAS-seq reveals a class of short PIWI-interacting RNAs in human oocytes
    Article Snippet: .. The CAS-seq protocol for the RIP sample was modified by adding 4 U of 5′ deadenylase (NEB, Massachusetts, USA) and 9 U of RecJf (NEB, Massachusetts, USA) immediately after the 3′ adapter ligation reaction, and the mixture was incubated at 30 °C for 30 min, then followed by 30 min at 37 °C. .. Antibody information The source and catalog number of the antibodies we used were as follows: rabbit IgG (Santa Cruz, SC2027); rabbit polyclonal anti-AGO1 (MBL, RN028PW); rat monoclonal anti-AGO2 (Sigma, SAB4200085); mouse monoclonal anti-AGO3 (Active Motif, 39787); mouse monoclonal anti-AGO4 (Merck Millipore, 05-967); mouse monoclonal anti-Flag (Sigma, A8592); rabbit polyclonal anti-GAPDH (glyceraldehyde 3-phosphate dehydrogenase) (Bioworld, AP0063); rabbit polyclonal anti-HIWI (custom-made by GL Biochem); rabbit polyclonal anti-HIWI3 (custom-made by GL Biochem); rabbit polyclonal anti-HILI (custom-made by GL Biochem).

    Article Title: Sensing Self and Foreign Circular RNAs by Intron Identity
    Article Snippet: .. To remove excess linker, 30 Units of RecJf (New England Biolabs, Inc., M0264L) and 20 Units of 5′ Deadenylase (New England Biolabs, Inc., M0331S) in 1x RecJ buffer with Ribolock RNase Inhibitor were added to the reaction, and incubated for 1 hr at 37°C. .. The reaction was cleaned with RNA Clean & Concentrator columns (Zymo Research, R1016).

    Article Title: Single-cell CAS-seq reveals a class of short PIWI-interacting RNAs in human oocytes
    Article Snippet: CAS-seq-2E cDNA library preparation The 2E-CAS-seq protocol was modified on the basis of CAS-seq by adding 4 U of 5′ deadenylase (NEB, Massachusetts, USA) and 9 U of RecJf (NEB, Massachusetts, USA) immediately after 3′ adapter ligation reaction. .. The reaction mixture was incubated at 30 °C for 30 min followed by at 37 °C for 30 min. Then, the 3′ adapter ligation product was used for 5′ adapter ligation following the same method described in CAS-seq.

    Article Title: Molecular mechanism of directional CTCF recognition of a diverse range of genomic sites
    Article Snippet: Beads-DNA samples were then treated with 20 U Lambda Exonuclease (NEB, M0262S) in the Exonuclease buffer (0.2% Triton X-100 and 1% DMSO in 100 μl of 1× Lambda buffer) by incubation at 37 °C for 1 h on thermomixer at 1 000 rpm. .. Samples were then digested by 75 U RecJf exonuclease (NEB, M0264S) in 100 μl of 1× NEB buffer 2 containing 0.2% Triton X-100 and 1% DMSO at 37 °C for 1 h on thermomixer at 1 000 rpm, and then washed three times with the RIPA buffer (50 mM HEPES, pH 7.5, 1 mM EDTA, 0.7% sodium deoxycholate, 1% NP-40, 0.5 M LiCl).

    Article Title: Systematic evaluation and optimization of the experimental steps in RNA G-quadruplex structure sequencing
    Article Snippet: Enzymatic digestion was conducted by adding 1 μl of 50 U/μl of 5′ deadenylase (50 U final) (NEB, M0331S) and 1 μl of 30 U/μl RecJf (30U final) (NEB, M0264S) directly into the sample. .. To carry out both enzymatic digestion and column purification steps, after the incubation, 28 μl of nuclease-free water was added to the reaction mixture to dilute the PEG concentration, and then purified with RNA Clean & Concentrator™ (Zymo Research) by following manufacturer’s protocol.

    Activity Assay:

    Article Title: EXOG, a novel paralog of Endonuclease G in higher eukaryotes
    Article Snippet: Paragraph title: Enzymatic activity assays ... The exonucleases RecJf and ExoI were used to digest the labeled oligonucleotides according to the recommendation of the supplier (NEB), leading to the production of mononucleotides (RecJf ) and dinucleotides (ExoI) used as size markers.

    Modification:

    Article Title: Single-cell CAS-seq reveals a class of short PIWI-interacting RNAs in human oocytes
    Article Snippet: .. The CAS-seq protocol for the RIP sample was modified by adding 4 U of 5′ deadenylase (NEB, Massachusetts, USA) and 9 U of RecJf (NEB, Massachusetts, USA) immediately after the 3′ adapter ligation reaction, and the mixture was incubated at 30 °C for 30 min, then followed by 30 min at 37 °C. .. Antibody information The source and catalog number of the antibodies we used were as follows: rabbit IgG (Santa Cruz, SC2027); rabbit polyclonal anti-AGO1 (MBL, RN028PW); rat monoclonal anti-AGO2 (Sigma, SAB4200085); mouse monoclonal anti-AGO3 (Active Motif, 39787); mouse monoclonal anti-AGO4 (Merck Millipore, 05-967); mouse monoclonal anti-Flag (Sigma, A8592); rabbit polyclonal anti-GAPDH (glyceraldehyde 3-phosphate dehydrogenase) (Bioworld, AP0063); rabbit polyclonal anti-HIWI (custom-made by GL Biochem); rabbit polyclonal anti-HIWI3 (custom-made by GL Biochem); rabbit polyclonal anti-HILI (custom-made by GL Biochem).

    Article Title: Single-cell CAS-seq reveals a class of short PIWI-interacting RNAs in human oocytes
    Article Snippet: .. CAS-seq-2E cDNA library preparation The 2E-CAS-seq protocol was modified on the basis of CAS-seq by adding 4 U of 5′ deadenylase (NEB, Massachusetts, USA) and 9 U of RecJf (NEB, Massachusetts, USA) immediately after 3′ adapter ligation reaction. .. RecJf is an exonuclease that only digests single-strand DNA oligos with monophosphate at the 5′ end, but not the 3′ adapter bearing 5′ rApp modification, a 5′ deadenylase is used to remove the rApp modification from the 5′ end of the 3′ adapter, which convert the 3′ adapter to be a suitable substrate for RecJf digestion.

    Chromatography:

    Article Title: EXOG, a novel paralog of Endonuclease G in higher eukaryotes
    Article Snippet: The cleavage of radioactively labeled oligonucleotides was analyzed by denaturing polyacrylamide gel electrophoresis as well as thin layer anion-exchange chromatography under denaturing conditions. .. The exonucleases RecJf and ExoI were used to digest the labeled oligonucleotides according to the recommendation of the supplier (NEB), leading to the production of mononucleotides (RecJf ) and dinucleotides (ExoI) used as size markers.

    Ligation:

    Article Title: Structural insights into the DNA-binding specificity of E2F family transcription factors
    Article Snippet: .. Immunoprecipitates were then subjected to the following enzymatic on-bead reactions for 30 min in 60 μl reaction volume: (a) end-polishing with T4 DNA polymerase (3 U, New England BioLabs, M0203L), (b) kinase reaction with T4 polynucleotide kinase (10 U, New England BioLabs, M0201L), (c) adenine addition reaction with Klenow fragment exo-(5 U, New England BioLabs, M0212L), (d) first adaptor ligation with 1.25 μM P2 adaptors ( , rows 3 and 4; Eurofins MWG Operon) and T4 DNA ligase (500 U, New England BioLabs, M0202L), (e) fill-in reaction with phi29 DNA polymerase (10 U, New England BioLabs, M0269L), (f) lambda exonuclease reaction (10 U, New England BioLabs, M0262L) and (f) RecJf exonuclease reaction with 30 U of RecJf exonuclease (New England BioLabs, M0264L). ..

    Article Title: MACE: model based analysis of ChIP-exo
    Article Snippet: .. After ligation, the DNA was nick-repaired with phi29 polymerase, and digested by lambda (λ) and RecJf exonucleases (NEB). .. DNA samples were eluted from the beads by performing reverse cross-linking overnight at 65°C, followed by RNaseA (Ambion) and ProteinaseK (Invitrogen) treatments.

    Article Title: Multiplex target capture with double-stranded DNA probes
    Article Snippet: For probe extension and ligation, a 10 μl mixture of 0.3 mM dNTP, 2 mM NAD, 1.1 M betaine, 1× Ampligase buffer, 5 U Ampligase (Epicentre, Madison, WI, USA) and 0.8 U Phusion polymerase (NEB, Ipswich, MA, USA) was added to the reaction and incubated at 56°C for 60 minutes followed by 68°C for 20 minutes. .. To completely eliminate linear DNA molecules, 2 μl of a mixture of total of six exonucleases including 3.5 U exo I (Affymetrix, Santa Clara, CA, USA), 18 U exo III (Affymetrix), 4U exo T7 (Affymetrix), 0.4 U exo T (NEB), 3 U RecJf (NEB) and 0.2 U lambda exo (Epicentre, Charlotte, NC, USA) was added to the reaction and incubated at 37°C for 30 minutes, 80°C for 10 minutes and 95°C for 5 minutes.

    Article Title: Brg1 modulates enhancer activation in mesoderm lineage commitment
    Article Snippet: The resulting DNA was digested with Exo I and RecJf exonucleases (NEB). .. DNA was purified using Agencourt Ampure XP beads (Beckman Coulter), denatured, and the single-stranded DNA was used to synthesize the second strand using P7 primer, followed by ligation of P5 adapter.

    Article Title: Single-cell CAS-seq reveals a class of short PIWI-interacting RNAs in human oocytes
    Article Snippet: .. The CAS-seq protocol for the RIP sample was modified by adding 4 U of 5′ deadenylase (NEB, Massachusetts, USA) and 9 U of RecJf (NEB, Massachusetts, USA) immediately after the 3′ adapter ligation reaction, and the mixture was incubated at 30 °C for 30 min, then followed by 30 min at 37 °C. .. Antibody information The source and catalog number of the antibodies we used were as follows: rabbit IgG (Santa Cruz, SC2027); rabbit polyclonal anti-AGO1 (MBL, RN028PW); rat monoclonal anti-AGO2 (Sigma, SAB4200085); mouse monoclonal anti-AGO3 (Active Motif, 39787); mouse monoclonal anti-AGO4 (Merck Millipore, 05-967); mouse monoclonal anti-Flag (Sigma, A8592); rabbit polyclonal anti-GAPDH (glyceraldehyde 3-phosphate dehydrogenase) (Bioworld, AP0063); rabbit polyclonal anti-HIWI (custom-made by GL Biochem); rabbit polyclonal anti-HIWI3 (custom-made by GL Biochem); rabbit polyclonal anti-HILI (custom-made by GL Biochem).

    Article Title: Sensing Self and Foreign Circular RNAs by Intron Identity
    Article Snippet: For the ligation of the 3′ end adaptor, 0.8 µM of 3′ end biotin blocked preadenylated adaptor, 6.6 Units of T4 RNA ligase 1, high concentration (New England Biolabs, Inc., M0437M), in 1x RNA ligase buffer with 5 mM DTT and 50% PEG8000, were added, and the reaction was incubated at RT for 3 hr. .. To remove excess linker, 30 Units of RecJf (New England Biolabs, Inc., M0264L) and 20 Units of 5′ Deadenylase (New England Biolabs, Inc., M0331S) in 1x RecJ buffer with Ribolock RNase Inhibitor were added to the reaction, and incubated for 1 hr at 37°C.

    Article Title: Single-cell CAS-seq reveals a class of short PIWI-interacting RNAs in human oocytes
    Article Snippet: .. CAS-seq-2E cDNA library preparation The 2E-CAS-seq protocol was modified on the basis of CAS-seq by adding 4 U of 5′ deadenylase (NEB, Massachusetts, USA) and 9 U of RecJf (NEB, Massachusetts, USA) immediately after 3′ adapter ligation reaction. .. RecJf is an exonuclease that only digests single-strand DNA oligos with monophosphate at the 5′ end, but not the 3′ adapter bearing 5′ rApp modification, a 5′ deadenylase is used to remove the rApp modification from the 5′ end of the 3′ adapter, which convert the 3′ adapter to be a suitable substrate for RecJf digestion.

    Article Title: Systematic evaluation and optimization of the experimental steps in RNA G-quadruplex structure sequencing
    Article Snippet: Excess 3′-adapter digestion and removal Ten microliters of the reaction mixture from 3′-adapter ligation was then used for enzymatic digestion and removal of the excess 3′-adapter. .. Enzymatic digestion was conducted by adding 1 μl of 50 U/μl of 5′ deadenylase (50 U final) (NEB, M0331S) and 1 μl of 30 U/μl RecJf (30U final) (NEB, M0264S) directly into the sample.

    Cell Culture:

    Article Title: Structural insights into the DNA-binding specificity of E2F family transcription factors
    Article Snippet: ChIP-exo LoVo (ATCC, catalogue no. CCL229TM) cells were cultured in DMEM supplemented with 10% fetal bovine serum and antibiotics. .. Immunoprecipitates were then subjected to the following enzymatic on-bead reactions for 30 min in 60 μl reaction volume: (a) end-polishing with T4 DNA polymerase (3 U, New England BioLabs, M0203L), (b) kinase reaction with T4 polynucleotide kinase (10 U, New England BioLabs, M0201L), (c) adenine addition reaction with Klenow fragment exo-(5 U, New England BioLabs, M0212L), (d) first adaptor ligation with 1.25 μM P2 adaptors ( , rows 3 and 4; Eurofins MWG Operon) and T4 DNA ligase (500 U, New England BioLabs, M0202L), (e) fill-in reaction with phi29 DNA polymerase (10 U, New England BioLabs, M0269L), (f) lambda exonuclease reaction (10 U, New England BioLabs, M0262L) and (f) RecJf exonuclease reaction with 30 U of RecJf exonuclease (New England BioLabs, M0264L).

    Polymerase Chain Reaction:

    Article Title: Brg1 modulates enhancer activation in mesoderm lineage commitment
    Article Snippet: The resulting DNA was digested with Exo I and RecJf exonucleases (NEB). .. The resulting DNA fragment was PCR-amplified, gel-purified and sequenced using an Illumina HiSeq 2500 sequencer at a minimum depth of 25 million mapped reads, with most exceeding 30 million.

    Article Title: Translation Readthrough Mitigation
    Article Snippet: Unligated AF-JA-34.2 was removed by sequential treatment with 5'deadenylase (M0331S, NEB), then RecJf (M0264S, NEB). .. Circular ligase treatment and PCR were as previously described .

    Sonication:

    Article Title: Structural insights into the DNA-binding specificity of E2F family transcription factors
    Article Snippet: Cells were crosslinked with 1% formaldehyde, and incubated in hypotonic buffer for 15 min, and DNA then sonicated to 200–500-bp fragments in lysis buffer (50 mM HEPES, 2 mM EDTA, pH 8.0, 150 mM NaCl, 1% Triton X-100, 0.1% sodium deoxycholate, 0.2% SDS, pH 8.0). .. Immunoprecipitates were then subjected to the following enzymatic on-bead reactions for 30 min in 60 μl reaction volume: (a) end-polishing with T4 DNA polymerase (3 U, New England BioLabs, M0203L), (b) kinase reaction with T4 polynucleotide kinase (10 U, New England BioLabs, M0201L), (c) adenine addition reaction with Klenow fragment exo-(5 U, New England BioLabs, M0212L), (d) first adaptor ligation with 1.25 μM P2 adaptors ( , rows 3 and 4; Eurofins MWG Operon) and T4 DNA ligase (500 U, New England BioLabs, M0202L), (e) fill-in reaction with phi29 DNA polymerase (10 U, New England BioLabs, M0269L), (f) lambda exonuclease reaction (10 U, New England BioLabs, M0262L) and (f) RecJf exonuclease reaction with 30 U of RecJf exonuclease (New England BioLabs, M0264L).

    ChIP-sequencing:

    Article Title: Brg1 modulates enhancer activation in mesoderm lineage commitment
    Article Snippet: ChIP-seq analysis pipeline and statistical methods are provided in the supplementary material Methods . .. The resulting DNA was digested with Exo I and RecJf exonucleases (NEB).

    Article Title: Centromere DNA Destabilizes H3 Nucleosomes to Promote CENP-A Deposition during the Cell Cycle
    Article Snippet: Paragraph title: ChIP-Seq and ChIP-Nexus ... Blunted DNA was then sequentially digested by lambda exonuclease (NEB, M0262S) and RecJf (NEB, M0264L).

    Nucleic Acid Electrophoresis:

    Article Title: Unusual Telomeric DNAs in Human Telomerase-Negative Immortalized Cells ▿Unusual Telomeric DNAs in Human Telomerase-Negative Immortalized Cells ▿ †
    Article Snippet: HinfI was used to liberate T-DNA and to measure its length in 1D gel electrophoresis in this study. .. BAL-31 and Escherichia coli exonuclease III (Exo III) were purchased from Takara, and E. coli exonuclease I (Exo I), RecJf (RecJ), and T7 endonuclease I (Endo I) were from New England Biolabs.

    RNA Sequencing Assay:

    Article Title: Sensing Self and Foreign Circular RNAs by Intron Identity
    Article Snippet: The following notes are minor deviations for RNA-seq: Ribo-depleted RNA was fragmented to ~100 nt by incubation for 45 s at 95°C with Zinc chloride buffer (10 mM ZnCl2 ,10mM Tris-HCl, pH 7.0). .. To remove excess linker, 30 Units of RecJf (New England Biolabs, Inc., M0264L) and 20 Units of 5′ Deadenylase (New England Biolabs, Inc., M0331S) in 1x RecJ buffer with Ribolock RNase Inhibitor were added to the reaction, and incubated for 1 hr at 37°C.

    Article Title: Translation Readthrough Mitigation
    Article Snippet: Paragraph title: RNA Sequencing ... Unligated AF-JA-34.2 was removed by sequential treatment with 5'deadenylase (M0331S, NEB), then RecJf (M0264S, NEB).

    Magnetic Beads:

    Article Title: MACE: model based analysis of ChIP-exo
    Article Snippet: After ligation, the DNA was nick-repaired with phi29 polymerase, and digested by lambda (λ) and RecJf exonucleases (NEB). .. After ligation, the DNA was nick-repaired with phi29 polymerase, and digested by lambda (λ) and RecJf exonucleases (NEB).

    Article Title: Brg1 modulates enhancer activation in mesoderm lineage commitment
    Article Snippet: Briefly, Brg1 ChIP was performed, and, while still on magnetic beads, the immunoprecipitated DNA was polished, ligated with P7 adapter and nicks were repaired. .. The resulting DNA was digested with Exo I and RecJf exonucleases (NEB).

    Multiplex Assay:

    Article Title: Multiplex target capture with double-stranded DNA probes
    Article Snippet: Paragraph title: Multiplex target capture with LPPs ... To completely eliminate linear DNA molecules, 2 μl of a mixture of total of six exonucleases including 3.5 U exo I (Affymetrix, Santa Clara, CA, USA), 18 U exo III (Affymetrix), 4U exo T7 (Affymetrix), 0.4 U exo T (NEB), 3 U RecJf (NEB) and 0.2 U lambda exo (Epicentre, Charlotte, NC, USA) was added to the reaction and incubated at 37°C for 30 minutes, 80°C for 10 minutes and 95°C for 5 minutes.

    Labeling:

    Article Title: EXOG, a novel paralog of Endonuclease G in higher eukaryotes
    Article Snippet: .. The exonucleases RecJf and ExoI were used to digest the labeled oligonucleotides according to the recommendation of the supplier (NEB), leading to the production of mononucleotides (RecJf ) and dinucleotides (ExoI) used as size markers. .. After the separation of cleavage products by electrophoresis or on DEAE-cellulose thin layer plates at 65°C, data were collected by autoradiography.

    Purification:

    Article Title: Brg1 modulates enhancer activation in mesoderm lineage commitment
    Article Snippet: The resulting DNA was digested with Exo I and RecJf exonucleases (NEB). .. DNA was purified using Agencourt Ampure XP beads (Beckman Coulter), denatured, and the single-stranded DNA was used to synthesize the second strand using P7 primer, followed by ligation of P5 adapter.

    Article Title: Sensing Self and Foreign Circular RNAs by Intron Identity
    Article Snippet: To remove excess linker, 30 Units of RecJf (New England Biolabs, Inc., M0264L) and 20 Units of 5′ Deadenylase (New England Biolabs, Inc., M0331S) in 1x RecJ buffer with Ribolock RNase Inhibitor were added to the reaction, and incubated for 1 hr at 37°C. .. Reverse transcription, biotin capture of ligated fragments, cDNA circularization, library amplification, and PAGE purification were carried out exactly as written in the previously published method ( ).

    Article Title: Systematic evaluation and optimization of the experimental steps in RNA G-quadruplex structure sequencing
    Article Snippet: Enzymatic digestion was conducted by adding 1 μl of 50 U/μl of 5′ deadenylase (50 U final) (NEB, M0331S) and 1 μl of 30 U/μl RecJf (30U final) (NEB, M0264S) directly into the sample. .. To carry out both enzymatic digestion and column purification steps, after the incubation, 28 μl of nuclease-free water was added to the reaction mixture to dilute the PEG concentration, and then purified with RNA Clean & Concentrator™ (Zymo Research) by following manufacturer’s protocol.

    Article Title: Translation Readthrough Mitigation
    Article Snippet: RNA fragments were gel purified, then treated with T4 PNK NEB). .. Unligated AF-JA-34.2 was removed by sequential treatment with 5'deadenylase (M0331S, NEB), then RecJf (M0264S, NEB).

    Sequencing:

    Article Title: MACE: model based analysis of ChIP-exo
    Article Snippet: The P7 adapter (150 pmol) was designed based on the adapter sequence provided by NEB: 5′-Phos-TGACTGGAGTTCAGACGTGTGCTCTTCCGATCT-OH-3′ and 5′-OH-AGATCGGAAGAGCACACGTCTGAACTCC-OH-3′. .. After ligation, the DNA was nick-repaired with phi29 polymerase, and digested by lambda (λ) and RecJf exonucleases (NEB).

    Article Title: Nucleotide excision repair by dual incisions in plants
    Article Snippet: For 5′→3′ digestion, gel-purified, 3′-end-labeled DNA was incubated with 22.5 units of RecJf (New England Biolabs) for 1 h at 37 °C in a 5-µL reaction according to the recommendations of the manufacturer. .. Products were then ethanol-precipitated and resolved on an 11% sequencing gel.

    Article Title: Sensing Self and Foreign Circular RNAs by Intron Identity
    Article Snippet: Paragraph title: RNA extraction, selection, library preparation, and sequencing ... To remove excess linker, 30 Units of RecJf (New England Biolabs, Inc., M0264L) and 20 Units of 5′ Deadenylase (New England Biolabs, Inc., M0331S) in 1x RecJ buffer with Ribolock RNase Inhibitor were added to the reaction, and incubated for 1 hr at 37°C.

    Immunoprecipitation:

    Article Title: Structural insights into the DNA-binding specificity of E2F family transcription factors
    Article Snippet: The immune-complexes were precipitated using 40 μl protein G-Sepharose beads for 3 h at 4 °C, and washed successively with 0.5 ml of immunoprecipitation buffer (100 mM NaCl, 5 mM EDTA, 0.33% SDS and 1.5% Triton X-100 in 50 mM Tris-Cl, pH 8.0), 1 ml of mixed micelle buffer (150 mM NaCl, 5 mM EDTA, 5.2% sucrose, 1.0% Triton X-100 and 0.2% SDS in 20 mM Tris-Cl, pH 8.0), 1 ml of buffer 500 (250 mM NaCl, 25 mM HEPES, 0.5% Triton X-100, 0.05% sodium deoxycholate and 0.5 mM EDTA in 5 mM Tris-Cl, pH 8.0), 1 ml of lithium chloride/detergent buffer (250 mM lithium chloride, 0.5% IGEPAL CA-630, 0.5% sodium deoxycholate and 10 mM EDTA in 10 mM Tris-Cl, pH 8.0), 1 ml of TE buffer (1 mM EDTA in 10 mM Tris-Cl, pH 8.0) and 1 ml of Tris-Cl buffer (10 mM, pH 7.5, 8.0 or 9.2 according to the requirements for the enzymatic reaction steps detailed below). .. Immunoprecipitates were then subjected to the following enzymatic on-bead reactions for 30 min in 60 μl reaction volume: (a) end-polishing with T4 DNA polymerase (3 U, New England BioLabs, M0203L), (b) kinase reaction with T4 polynucleotide kinase (10 U, New England BioLabs, M0201L), (c) adenine addition reaction with Klenow fragment exo-(5 U, New England BioLabs, M0212L), (d) first adaptor ligation with 1.25 μM P2 adaptors ( , rows 3 and 4; Eurofins MWG Operon) and T4 DNA ligase (500 U, New England BioLabs, M0202L), (e) fill-in reaction with phi29 DNA polymerase (10 U, New England BioLabs, M0269L), (f) lambda exonuclease reaction (10 U, New England BioLabs, M0262L) and (f) RecJf exonuclease reaction with 30 U of RecJf exonuclease (New England BioLabs, M0264L).

    Article Title: MACE: model based analysis of ChIP-exo
    Article Snippet: After ligation, the DNA was nick-repaired with phi29 polymerase, and digested by lambda (λ) and RecJf exonucleases (NEB). .. After ligation, the DNA was nick-repaired with phi29 polymerase, and digested by lambda (λ) and RecJf exonucleases (NEB).

    Article Title: Brg1 modulates enhancer activation in mesoderm lineage commitment
    Article Snippet: Briefly, Brg1 ChIP was performed, and, while still on magnetic beads, the immunoprecipitated DNA was polished, ligated with P7 adapter and nicks were repaired. .. The resulting DNA was digested with Exo I and RecJf exonucleases (NEB).

    Article Title: Single-cell CAS-seq reveals a class of short PIWI-interacting RNAs in human oocytes
    Article Snippet: The supernatant containing immunoprecipitated RNA was collected for CAS-seq library construction. .. The CAS-seq protocol for the RIP sample was modified by adding 4 U of 5′ deadenylase (NEB, Massachusetts, USA) and 9 U of RecJf (NEB, Massachusetts, USA) immediately after the 3′ adapter ligation reaction, and the mixture was incubated at 30 °C for 30 min, then followed by 30 min at 37 °C.

    Polyacrylamide Gel Electrophoresis:

    Article Title: Sensing Self and Foreign Circular RNAs by Intron Identity
    Article Snippet: To remove excess linker, 30 Units of RecJf (New England Biolabs, Inc., M0264L) and 20 Units of 5′ Deadenylase (New England Biolabs, Inc., M0331S) in 1x RecJ buffer with Ribolock RNase Inhibitor were added to the reaction, and incubated for 1 hr at 37°C. .. Reverse transcription, biotin capture of ligated fragments, cDNA circularization, library amplification, and PAGE purification were carried out exactly as written in the previously published method ( ).

    Article Title: EXOG, a novel paralog of Endonuclease G in higher eukaryotes
    Article Snippet: Denaturing polyacrylamide gel electrophoresis was performed using 25% polyacrylamide gels containing 7 M urea in 1 × TBE-buffer. .. The exonucleases RecJf and ExoI were used to digest the labeled oligonucleotides according to the recommendation of the supplier (NEB), leading to the production of mononucleotides (RecJf ) and dinucleotides (ExoI) used as size markers.

    cDNA Library Assay:

    Article Title: Single-cell CAS-seq reveals a class of short PIWI-interacting RNAs in human oocytes
    Article Snippet: .. CAS-seq-2E cDNA library preparation The 2E-CAS-seq protocol was modified on the basis of CAS-seq by adding 4 U of 5′ deadenylase (NEB, Massachusetts, USA) and 9 U of RecJf (NEB, Massachusetts, USA) immediately after 3′ adapter ligation reaction. .. RecJf is an exonuclease that only digests single-strand DNA oligos with monophosphate at the 5′ end, but not the 3′ adapter bearing 5′ rApp modification, a 5′ deadenylase is used to remove the rApp modification from the 5′ end of the 3′ adapter, which convert the 3′ adapter to be a suitable substrate for RecJf digestion.

    Chromatin Immunoprecipitation:

    Article Title: Structural insights into the DNA-binding specificity of E2F family transcription factors
    Article Snippet: Paragraph title: ChIP-exo ... Immunoprecipitates were then subjected to the following enzymatic on-bead reactions for 30 min in 60 μl reaction volume: (a) end-polishing with T4 DNA polymerase (3 U, New England BioLabs, M0203L), (b) kinase reaction with T4 polynucleotide kinase (10 U, New England BioLabs, M0201L), (c) adenine addition reaction with Klenow fragment exo-(5 U, New England BioLabs, M0212L), (d) first adaptor ligation with 1.25 μM P2 adaptors ( , rows 3 and 4; Eurofins MWG Operon) and T4 DNA ligase (500 U, New England BioLabs, M0202L), (e) fill-in reaction with phi29 DNA polymerase (10 U, New England BioLabs, M0269L), (f) lambda exonuclease reaction (10 U, New England BioLabs, M0262L) and (f) RecJf exonuclease reaction with 30 U of RecJf exonuclease (New England BioLabs, M0264L).

    Article Title: MACE: model based analysis of ChIP-exo
    Article Snippet: Paragraph title: Mouse ONECUT1 ChIP-exo data ... After ligation, the DNA was nick-repaired with phi29 polymerase, and digested by lambda (λ) and RecJf exonucleases (NEB).

    Article Title: Brg1 modulates enhancer activation in mesoderm lineage commitment
    Article Snippet: Paragraph title: ChIP-seq/ChIP-exo ... The resulting DNA was digested with Exo I and RecJf exonucleases (NEB).

    Article Title: Molecular mechanism of directional CTCF recognition of a diverse range of genomic sites
    Article Snippet: Paragraph title: ChIP-nexus ... Samples were then digested by 75 U RecJf exonuclease (NEB, M0264S) in 100 μl of 1× NEB buffer 2 containing 0.2% Triton X-100 and 1% DMSO at 37 °C for 1 h on thermomixer at 1 000 rpm, and then washed three times with the RIPA buffer (50 mM HEPES, pH 7.5, 1 mM EDTA, 0.7% sodium deoxycholate, 1% NP-40, 0.5 M LiCl).

    Article Title: Centromere DNA Destabilizes H3 Nucleosomes to Promote CENP-A Deposition during the Cell Cycle
    Article Snippet: Paragraph title: ChIP-Seq and ChIP-Nexus ... Blunted DNA was then sequentially digested by lambda exonuclease (NEB, M0262S) and RecJf (NEB, M0264L).

    RNA Extraction:

    Article Title: Single-cell CAS-seq reveals a class of short PIWI-interacting RNAs in human oocytes
    Article Snippet: The input and sample supernatants after RIP were mixed with 2 × 10−9 pmol spike-in RNA oligos before RNA extraction with 600 μl TRIzol (Ambion, USA). .. The CAS-seq protocol for the RIP sample was modified by adding 4 U of 5′ deadenylase (NEB, Massachusetts, USA) and 9 U of RecJf (NEB, Massachusetts, USA) immediately after the 3′ adapter ligation reaction, and the mixture was incubated at 30 °C for 30 min, then followed by 30 min at 37 °C.

    Article Title: Sensing Self and Foreign Circular RNAs by Intron Identity
    Article Snippet: Paragraph title: RNA extraction, selection, library preparation, and sequencing ... To remove excess linker, 30 Units of RecJf (New England Biolabs, Inc., M0264L) and 20 Units of 5′ Deadenylase (New England Biolabs, Inc., M0331S) in 1x RecJ buffer with Ribolock RNase Inhibitor were added to the reaction, and incubated for 1 hr at 37°C.

    Selection:

    Article Title: Sensing Self and Foreign Circular RNAs by Intron Identity
    Article Snippet: Paragraph title: RNA extraction, selection, library preparation, and sequencing ... To remove excess linker, 30 Units of RecJf (New England Biolabs, Inc., M0264L) and 20 Units of 5′ Deadenylase (New England Biolabs, Inc., M0331S) in 1x RecJ buffer with Ribolock RNase Inhibitor were added to the reaction, and incubated for 1 hr at 37°C.

    Ethanol Precipitation:

    Article Title: MACE: model based analysis of ChIP-exo
    Article Snippet: After ligation, the DNA was nick-repaired with phi29 polymerase, and digested by lambda (λ) and RecJf exonucleases (NEB). .. DNA was extracted using a phenol-chloroform-isoamyl protocol and ethanol precipitation.

    Produced:

    Article Title: EXOG, a novel paralog of Endonuclease G in higher eukaryotes
    Article Snippet: Double stranded oligonucleotide substrates were produced by annealing of the unlabeled complementary strand. .. The exonucleases RecJf and ExoI were used to digest the labeled oligonucleotides according to the recommendation of the supplier (NEB), leading to the production of mononucleotides (RecJf ) and dinucleotides (ExoI) used as size markers.

    Concentration Assay:

    Article Title: Sensing Self and Foreign Circular RNAs by Intron Identity
    Article Snippet: For the ligation of the 3′ end adaptor, 0.8 µM of 3′ end biotin blocked preadenylated adaptor, 6.6 Units of T4 RNA ligase 1, high concentration (New England Biolabs, Inc., M0437M), in 1x RNA ligase buffer with 5 mM DTT and 50% PEG8000, were added, and the reaction was incubated at RT for 3 hr. .. To remove excess linker, 30 Units of RecJf (New England Biolabs, Inc., M0264L) and 20 Units of 5′ Deadenylase (New England Biolabs, Inc., M0331S) in 1x RecJ buffer with Ribolock RNase Inhibitor were added to the reaction, and incubated for 1 hr at 37°C.

    Article Title: Systematic evaluation and optimization of the experimental steps in RNA G-quadruplex structure sequencing
    Article Snippet: Enzymatic digestion was conducted by adding 1 μl of 50 U/μl of 5′ deadenylase (50 U final) (NEB, M0331S) and 1 μl of 30 U/μl RecJf (30U final) (NEB, M0264S) directly into the sample. .. To carry out both enzymatic digestion and column purification steps, after the incubation, 28 μl of nuclease-free water was added to the reaction mixture to dilute the PEG concentration, and then purified with RNA Clean & Concentrator™ (Zymo Research) by following manufacturer’s protocol.

    Thin Layer Chromatography:

    Article Title: EXOG, a novel paralog of Endonuclease G in higher eukaryotes
    Article Snippet: Thin layer chromatography was performed using a lysate of total yeast RNA in 7 M urea as the eluens. .. The exonucleases RecJf and ExoI were used to digest the labeled oligonucleotides according to the recommendation of the supplier (NEB), leading to the production of mononucleotides (RecJf ) and dinucleotides (ExoI) used as size markers.

    Two-Dimensional Gel Electrophoresis:

    Article Title: Unusual Telomeric DNAs in Human Telomerase-Negative Immortalized Cells ▿Unusual Telomeric DNAs in Human Telomerase-Negative Immortalized Cells ▿ †
    Article Snippet: Digestion with a mixture of AluI and MboI was performed for samples in 2D gel electrophoresis, which was used in most of the similar experiments appearing in the literature. .. BAL-31 and Escherichia coli exonuclease III (Exo III) were purchased from Takara, and E. coli exonuclease I (Exo I), RecJf (RecJ), and T7 endonuclease I (Endo I) were from New England Biolabs.

    Lysis:

    Article Title: Structural insights into the DNA-binding specificity of E2F family transcription factors
    Article Snippet: Cells were crosslinked with 1% formaldehyde, and incubated in hypotonic buffer for 15 min, and DNA then sonicated to 200–500-bp fragments in lysis buffer (50 mM HEPES, 2 mM EDTA, pH 8.0, 150 mM NaCl, 1% Triton X-100, 0.1% sodium deoxycholate, 0.2% SDS, pH 8.0). .. Immunoprecipitates were then subjected to the following enzymatic on-bead reactions for 30 min in 60 μl reaction volume: (a) end-polishing with T4 DNA polymerase (3 U, New England BioLabs, M0203L), (b) kinase reaction with T4 polynucleotide kinase (10 U, New England BioLabs, M0201L), (c) adenine addition reaction with Klenow fragment exo-(5 U, New England BioLabs, M0212L), (d) first adaptor ligation with 1.25 μM P2 adaptors ( , rows 3 and 4; Eurofins MWG Operon) and T4 DNA ligase (500 U, New England BioLabs, M0202L), (e) fill-in reaction with phi29 DNA polymerase (10 U, New England BioLabs, M0269L), (f) lambda exonuclease reaction (10 U, New England BioLabs, M0262L) and (f) RecJf exonuclease reaction with 30 U of RecJf exonuclease (New England BioLabs, M0264L).

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    New England Biolabs recjf
    Recjf, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 90/100, based on 6 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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