t4 rna ligase 2  (New England Biolabs)


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    New England Biolabs t4 rna ligase 2
    T4 Rna Ligase 2, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 152 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/t4 rna ligase 2/product/New England Biolabs
    Average 99 stars, based on 152 article reviews
    Price from $9.99 to $1999.99
    t4 rna ligase 2 - by Bioz Stars, 2020-01
    99/100 stars

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    Immunoprecipitation:

    Article Title: The RNA-binding complex ESCRT-II in Xenopus laevis eggs recognizes purine-rich sequences through its subunit, Vps25
    Article Snippet: The samples were heated at 70 °C for 10 min and then diluted 1:2 with PBS plus 1% Triton to reduce the SDS concentration for immunoprecipitation. .. To construct the CLIP-Seq library, UV cross-linking and denaturing immunoprecipitations were performed as described above except with a low RNase A concentration (1 μg/ml); and instead of 3′-end labeling with pCp, the samples were resuspended in a 20-μl mix containing 1× T4 RNA ligase 2, truncated buffer (NEB), 6 μl of PEG 8000, 1 μl of RNase inhibitor (Roche Applied Science), 1 μl of truncated T4 RNA ligase 2 (NEB), and 30 pmol of adenylated DNA oligo (Blower lab oligo database number oMB1863: 5′-rAppCGGCCGCCACCATCAAT-3ddC-3′).

    Ligation:

    Article Title: The RNA-binding complex ESCRT-II in Xenopus laevis eggs recognizes purine-rich sequences through its subunit, Vps25
    Article Snippet: To construct the CLIP-Seq library, UV cross-linking and denaturing immunoprecipitations were performed as described above except with a low RNase A concentration (1 μg/ml); and instead of 3′-end labeling with pCp, the samples were resuspended in a 20-μl mix containing 1× T4 RNA ligase 2, truncated buffer (NEB), 6 μl of PEG 8000, 1 μl of RNase inhibitor (Roche Applied Science), 1 μl of truncated T4 RNA ligase 2 (NEB), and 30 pmol of adenylated DNA oligo (Blower lab oligo database number oMB1863: 5′-rAppCGGCCGCCACCATCAAT-3ddC-3′). .. The ligation reaction was incubated overnight at 16 °C with agitation in a ThermoMixer.

    Autoradiography:

    Article Title: The RNA-binding complex ESCRT-II in Xenopus laevis eggs recognizes purine-rich sequences through its subunit, Vps25
    Article Snippet: The reactions proceeded for 2 h at room temperature and were then washed three times in PBS, transferred to a fresh tube, resuspended in protein loading buffer, run on SDS-PAGE, transferred to a nitrocellulose membrane, and analyzed by autoradiography on a Typhoon Trio scanner (GE Healthcare). .. To construct the CLIP-Seq library, UV cross-linking and denaturing immunoprecipitations were performed as described above except with a low RNase A concentration (1 μg/ml); and instead of 3′-end labeling with pCp, the samples were resuspended in a 20-μl mix containing 1× T4 RNA ligase 2, truncated buffer (NEB), 6 μl of PEG 8000, 1 μl of RNase inhibitor (Roche Applied Science), 1 μl of truncated T4 RNA ligase 2 (NEB), and 30 pmol of adenylated DNA oligo (Blower lab oligo database number oMB1863: 5′-rAppCGGCCGCCACCATCAAT-3ddC-3′).

    Labeling:

    Article Title: The RNA-binding complex ESCRT-II in Xenopus laevis eggs recognizes purine-rich sequences through its subunit, Vps25
    Article Snippet: .. To construct the CLIP-Seq library, UV cross-linking and denaturing immunoprecipitations were performed as described above except with a low RNase A concentration (1 μg/ml); and instead of 3′-end labeling with pCp, the samples were resuspended in a 20-μl mix containing 1× T4 RNA ligase 2, truncated buffer (NEB), 6 μl of PEG 8000, 1 μl of RNase inhibitor (Roche Applied Science), 1 μl of truncated T4 RNA ligase 2 (NEB), and 30 pmol of adenylated DNA oligo (Blower lab oligo database number oMB1863: 5′-rAppCGGCCGCCACCATCAAT-3ddC-3′). .. The ligation reaction was incubated overnight at 16 °C with agitation in a ThermoMixer.

    Concentration Assay:

    Article Title: The RNA-binding complex ESCRT-II in Xenopus laevis eggs recognizes purine-rich sequences through its subunit, Vps25
    Article Snippet: .. To construct the CLIP-Seq library, UV cross-linking and denaturing immunoprecipitations were performed as described above except with a low RNase A concentration (1 μg/ml); and instead of 3′-end labeling with pCp, the samples were resuspended in a 20-μl mix containing 1× T4 RNA ligase 2, truncated buffer (NEB), 6 μl of PEG 8000, 1 μl of RNase inhibitor (Roche Applied Science), 1 μl of truncated T4 RNA ligase 2 (NEB), and 30 pmol of adenylated DNA oligo (Blower lab oligo database number oMB1863: 5′-rAppCGGCCGCCACCATCAAT-3ddC-3′). .. The ligation reaction was incubated overnight at 16 °C with agitation in a ThermoMixer.

    Incubation:

    Article Title: The RNA-binding complex ESCRT-II in Xenopus laevis eggs recognizes purine-rich sequences through its subunit, Vps25
    Article Snippet: Samples resuspended in 1× PNK buffer (NEB) with 1 unit/μl RNase inhibitor (Roche Applied Science) and 0.75 unit/μl T4 PNK (NEB) were incubated for 45 min at 37 °C to dephosphorylate the 3′-ends of the RNA. .. To construct the CLIP-Seq library, UV cross-linking and denaturing immunoprecipitations were performed as described above except with a low RNase A concentration (1 μg/ml); and instead of 3′-end labeling with pCp, the samples were resuspended in a 20-μl mix containing 1× T4 RNA ligase 2, truncated buffer (NEB), 6 μl of PEG 8000, 1 μl of RNase inhibitor (Roche Applied Science), 1 μl of truncated T4 RNA ligase 2 (NEB), and 30 pmol of adenylated DNA oligo (Blower lab oligo database number oMB1863: 5′-rAppCGGCCGCCACCATCAAT-3ddC-3′).

    Construct:

    Article Title: The RNA-binding complex ESCRT-II in Xenopus laevis eggs recognizes purine-rich sequences through its subunit, Vps25
    Article Snippet: .. To construct the CLIP-Seq library, UV cross-linking and denaturing immunoprecipitations were performed as described above except with a low RNase A concentration (1 μg/ml); and instead of 3′-end labeling with pCp, the samples were resuspended in a 20-μl mix containing 1× T4 RNA ligase 2, truncated buffer (NEB), 6 μl of PEG 8000, 1 μl of RNase inhibitor (Roche Applied Science), 1 μl of truncated T4 RNA ligase 2 (NEB), and 30 pmol of adenylated DNA oligo (Blower lab oligo database number oMB1863: 5′-rAppCGGCCGCCACCATCAAT-3ddC-3′). .. The ligation reaction was incubated overnight at 16 °C with agitation in a ThermoMixer.

    Cross-linking Immunoprecipitation:

    Article Title: The RNA-binding complex ESCRT-II in Xenopus laevis eggs recognizes purine-rich sequences through its subunit, Vps25
    Article Snippet: .. To construct the CLIP-Seq library, UV cross-linking and denaturing immunoprecipitations were performed as described above except with a low RNase A concentration (1 μg/ml); and instead of 3′-end labeling with pCp, the samples were resuspended in a 20-μl mix containing 1× T4 RNA ligase 2, truncated buffer (NEB), 6 μl of PEG 8000, 1 μl of RNase inhibitor (Roche Applied Science), 1 μl of truncated T4 RNA ligase 2 (NEB), and 30 pmol of adenylated DNA oligo (Blower lab oligo database number oMB1863: 5′-rAppCGGCCGCCACCATCAAT-3ddC-3′). .. The ligation reaction was incubated overnight at 16 °C with agitation in a ThermoMixer.

    SDS Page:

    Article Title: The RNA-binding complex ESCRT-II in Xenopus laevis eggs recognizes purine-rich sequences through its subunit, Vps25
    Article Snippet: The reactions proceeded for 2 h at room temperature and were then washed three times in PBS, transferred to a fresh tube, resuspended in protein loading buffer, run on SDS-PAGE, transferred to a nitrocellulose membrane, and analyzed by autoradiography on a Typhoon Trio scanner (GE Healthcare). .. To construct the CLIP-Seq library, UV cross-linking and denaturing immunoprecipitations were performed as described above except with a low RNase A concentration (1 μg/ml); and instead of 3′-end labeling with pCp, the samples were resuspended in a 20-μl mix containing 1× T4 RNA ligase 2, truncated buffer (NEB), 6 μl of PEG 8000, 1 μl of RNase inhibitor (Roche Applied Science), 1 μl of truncated T4 RNA ligase 2 (NEB), and 30 pmol of adenylated DNA oligo (Blower lab oligo database number oMB1863: 5′-rAppCGGCCGCCACCATCAAT-3ddC-3′).

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    New England Biolabs t4 rnl2
    Optimization of the 3´ adapter ligation step. Synthetic Let-7d-5p (NNN) miRNA was ligated to the 3´ adapter using the same ligation conditions as the CleanTag library prep workflow step 1. A) Yield increase with addition of PEG 8000 using <t>T4</t> RNA Ligase 2, truncated KQ and modified 3´ adapter (MP (n-1)). B) Specificity comparison between ligases used in 3´ ligation step: 1) T4 RNA Ligase 2, truncated; 2) T4 RNA Ligase 2, truncated KQ; 3) T4 RNA Ligase 1; 4) No Ligase. Both unmodified and modified (MP (n-1)) 3´ adapters were tested. Side products indicated with red arrows.
    T4 Rnl2, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 90/100, based on 153 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/t4 rnl2/product/New England Biolabs
    Average 90 stars, based on 153 article reviews
    Price from $9.99 to $1999.99
    t4 rnl2 - by Bioz Stars, 2020-01
    90/100 stars
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    Optimization of the 3´ adapter ligation step. Synthetic Let-7d-5p (NNN) miRNA was ligated to the 3´ adapter using the same ligation conditions as the CleanTag library prep workflow step 1. A) Yield increase with addition of PEG 8000 using T4 RNA Ligase 2, truncated KQ and modified 3´ adapter (MP (n-1)). B) Specificity comparison between ligases used in 3´ ligation step: 1) T4 RNA Ligase 2, truncated; 2) T4 RNA Ligase 2, truncated KQ; 3) T4 RNA Ligase 1; 4) No Ligase. Both unmodified and modified (MP (n-1)) 3´ adapters were tested. Side products indicated with red arrows.

    Journal: PLoS ONE

    Article Title: Small RNA Library Preparation Method for Next-Generation Sequencing Using Chemical Modifications to Prevent Adapter Dimer Formation

    doi: 10.1371/journal.pone.0167009

    Figure Lengend Snippet: Optimization of the 3´ adapter ligation step. Synthetic Let-7d-5p (NNN) miRNA was ligated to the 3´ adapter using the same ligation conditions as the CleanTag library prep workflow step 1. A) Yield increase with addition of PEG 8000 using T4 RNA Ligase 2, truncated KQ and modified 3´ adapter (MP (n-1)). B) Specificity comparison between ligases used in 3´ ligation step: 1) T4 RNA Ligase 2, truncated; 2) T4 RNA Ligase 2, truncated KQ; 3) T4 RNA Ligase 1; 4) No Ligase. Both unmodified and modified (MP (n-1)) 3´ adapters were tested. Side products indicated with red arrows.

    Article Snippet: The truncation derivatives tested include T4 RNA Ligase 2, truncated (T42t); T4 RNA Ligase 2, truncated K227Q; and T4 RNA Ligase 2, truncated KQ [ ].

    Techniques: Ligation, Modification