1x t4 rna ligase buffer  (New England Biolabs)


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    Name:
    T4 RNA Ligase Reaction Buffer
    Description:
    T4 RNA Ligase Reaction Buffer 3 0 ml
    Catalog Number:
    b0216l
    Price:
    46
    Size:
    3 0 ml
    Category:
    Buffers
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    Structured Review

    New England Biolabs 1x t4 rna ligase buffer
    T4 RNA Ligase Reaction Buffer
    T4 RNA Ligase Reaction Buffer 3 0 ml
    https://www.bioz.com/result/1x t4 rna ligase buffer/product/New England Biolabs
    Average 99 stars, based on 2 article reviews
    Price from $9.99 to $1999.99
    1x t4 rna ligase buffer - by Bioz Stars, 2020-09
    99/100 stars

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    Related Articles

    Incubation:

    Article Title: Loss of a Universal tRNA Feature ▿
    Article Snippet: .. For rephosphorylation, dephosphorylated RNA was incubated at 125 ng/μl for 50 min at 37°C in RNA ligase buffer with 0.5 U of T4 polynucleotide kinase (New England Biolabs)/μl, purifying the product RNA as described above. .. Reverse transcription-PCR (RT-PCR) primers (-R and -F) are indicated in Fig. .

    Article Title: Late steps of ribosome assembly in E. coli are sensitive to a severe heat stress but are assisted by the HSP70 chaperone machine †
    Article Snippet: .. Thermo-denaturation of the RNA prior to the 3′5′ RACE Five micrograms of RNA in a total volume of 20 µl containing the T4 RNA ligase buffer (New England Biolabs, n° B0204S) were incubated for 4 min at 75°C, and then rapidly frozen in a solid CO2 (dry ice)-ethanol bath for 1 min. To allow the samples to thaw slowly, they were then placed on ice for about 15 min, as described in ref. 22, and then 2 µl of T4 RNA ligase was added to start the 3′5′ RNA ligation. ..

    Article Title: LOTTE-seq (Long hairpin oligonucleotide based tRNA high-throughput sequencing): specific selection of tRNAs with 3’-CCA end for high-throughput sequencing
    Article Snippet: .. The reaction was stopped by incubation at 65°C for 15 min. For ligation with T4 RNA ligase 2, 10 pmol of the tRNA in vitro transcripts was incubated with 50 pmol hairpin adapter, 1 x T4 RNA ligase buffer (NEB) and 10 units RNA ligase 2 (NEB) for 1 h at 37°C following an incubation overnight at 4°C. .. Reverse transcription tRNA ligated at the 3ʹ-end to the hairpin adapter was incubated with 100 pmol32P-labelled RT primer (5‘-CAAGC TCGGTACCGACAGTG-3‘; underlined sequence represents primer binding site for subsequent PCR) and 2 mM dNTPs for 5 min at 65°C and cooled down to room temperature.

    Article Title: Strand-specific deep sequencing of the transcriptome
    Article Snippet: .. We incubated the following reaction mixture for 30 min at 37°C: 10 μL of sample, 1 μL of 10× T4 RNA ligase buffer (as fresh ATP supply), 10 U of polynucleotide kinase (New England BioLabs), 3 μL of RNase free water. .. After addition of 2× loading dye and incubation for 5 min at 65°C, the reaction was loaded onto a denaturing urea-PAGE gel in order to separate the fragments with ligated 3′ adapter from nonligated adapter (band sizes: insert size + 23 nt for single end sequencing; insert size + 34 nt for paired end libraries).

    other:

    Article Title: Chromatin-associated RNA sequencing (ChAR-seq) maps genome-wide RNA-to-DNA contacts
    Article Snippet: Step 4B ( Optional additional step B ): RNase control Pre-mix and resuspend the pellet in the following 160 µL water 20 µL 10x T4 RNA ligase buffer 10 µL 10 mg/mL RNaseA 10 µL RNaseH (NEB) Incubate at 37C for 4 hr Centrifuge at 2.5 k x g for 2 min, discard supernatant Add 1000 µL DEPC-treated PBS, mix gently Centrifuge at 2.5 k x g for 2 min, discard supernatant Immediately proceed to the next step, with pre-mixed reaction buffer already prepared

    In Vitro:

    Article Title: LOTTE-seq (Long hairpin oligonucleotide based tRNA high-throughput sequencing): specific selection of tRNAs with 3’-CCA end for high-throughput sequencing
    Article Snippet: .. The reaction was stopped by incubation at 65°C for 15 min. For ligation with T4 RNA ligase 2, 10 pmol of the tRNA in vitro transcripts was incubated with 50 pmol hairpin adapter, 1 x T4 RNA ligase buffer (NEB) and 10 units RNA ligase 2 (NEB) for 1 h at 37°C following an incubation overnight at 4°C. .. Reverse transcription tRNA ligated at the 3ʹ-end to the hairpin adapter was incubated with 100 pmol32P-labelled RT primer (5‘-CAAGC TCGGTACCGACAGTG-3‘; underlined sequence represents primer binding site for subsequent PCR) and 2 mM dNTPs for 5 min at 65°C and cooled down to room temperature.

    Ligation:

    Article Title: Late steps of ribosome assembly in E. coli are sensitive to a severe heat stress but are assisted by the HSP70 chaperone machine †
    Article Snippet: .. Thermo-denaturation of the RNA prior to the 3′5′ RACE Five micrograms of RNA in a total volume of 20 µl containing the T4 RNA ligase buffer (New England Biolabs, n° B0204S) were incubated for 4 min at 75°C, and then rapidly frozen in a solid CO2 (dry ice)-ethanol bath for 1 min. To allow the samples to thaw slowly, they were then placed on ice for about 15 min, as described in ref. 22, and then 2 µl of T4 RNA ligase was added to start the 3′5′ RNA ligation. ..

    Article Title: LOTTE-seq (Long hairpin oligonucleotide based tRNA high-throughput sequencing): specific selection of tRNAs with 3’-CCA end for high-throughput sequencing
    Article Snippet: .. The reaction was stopped by incubation at 65°C for 15 min. For ligation with T4 RNA ligase 2, 10 pmol of the tRNA in vitro transcripts was incubated with 50 pmol hairpin adapter, 1 x T4 RNA ligase buffer (NEB) and 10 units RNA ligase 2 (NEB) for 1 h at 37°C following an incubation overnight at 4°C. .. Reverse transcription tRNA ligated at the 3ʹ-end to the hairpin adapter was incubated with 100 pmol32P-labelled RT primer (5‘-CAAGC TCGGTACCGACAGTG-3‘; underlined sequence represents primer binding site for subsequent PCR) and 2 mM dNTPs for 5 min at 65°C and cooled down to room temperature.

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    New England Biolabs t4 rna ligase 2 truncated buffer
    Graphical Visualization of the 3′ RACE-Seq Approach, Related to Figure 2 (A) Graphical representation of 3′ RACE-seq library preparation and the oligonucleotides used. First, the 3′ adaptor RA3_15N was joined to the 3′ end of RNA by enzymatic ligation. The adaptor has: (i) 5′ rApp modification for efficient and specific ligation by the truncated <t>T4</t> RNA ligase 2, (ii) delimiter sequence to be used in bioinformatics analyses to exclude RT and PCR artifacts (CTGAC, highlighted in violet), (iii) unique 15N barcode for individual transcript barcoding (highlighted in green), (iv) anchor sequence to pair with the reverse transcription primer (underlined) and (v) dideoxyC on the 3′ end to prevent concatamer formation. The RNA ligated to the adaptor sequence was purified from excess adaptor and reverse transcription was performed with the RT primer, which is compatible with Illumina sequencing and has: (i) sequences to base-pair with the adaptor (underlined), (ii) 6-nucleotide barcode for sample barcoding (highlighted in red), (iii) sequences that base pair with the universal outer primer for nested PCR (blue). Libraries were generated by nested PCR with 2 outer forward primers (F1 and F2) and a single universal reverse primer (uni rev). PCR amplicons of first and second PCRs were purified from excess primers on AmPure beads (Agencourt) before beginning the next step. (B) Flowchart of the bioinformatics approach to 3′ RACE-seq data analysis. The procedure starts at the top. Datasets are shown in rectangles. Software used is depicted in hexagons.
    T4 Rna Ligase 2 Truncated Buffer, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 2 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/t4 rna ligase 2 truncated buffer/product/New England Biolabs
    Average 99 stars, based on 2 article reviews
    Price from $9.99 to $1999.99
    t4 rna ligase 2 truncated buffer - by Bioz Stars, 2020-09
    99/100 stars
      Buy from Supplier

    92
    New England Biolabs ligation mix
    Graphical Visualization of the 3′ RACE-Seq Approach, Related to Figure 2 (A) Graphical representation of 3′ RACE-seq library preparation and the oligonucleotides used. First, the 3′ adaptor RA3_15N was joined to the 3′ end of RNA by enzymatic ligation. The adaptor has: (i) 5′ rApp modification for efficient and specific ligation by the truncated <t>T4</t> RNA ligase 2, (ii) delimiter sequence to be used in bioinformatics analyses to exclude RT and PCR artifacts (CTGAC, highlighted in violet), (iii) unique 15N barcode for individual transcript barcoding (highlighted in green), (iv) anchor sequence to pair with the reverse transcription primer (underlined) and (v) dideoxyC on the 3′ end to prevent concatamer formation. The RNA ligated to the adaptor sequence was purified from excess adaptor and reverse transcription was performed with the RT primer, which is compatible with Illumina sequencing and has: (i) sequences to base-pair with the adaptor (underlined), (ii) 6-nucleotide barcode for sample barcoding (highlighted in red), (iii) sequences that base pair with the universal outer primer for nested PCR (blue). Libraries were generated by nested PCR with 2 outer forward primers (F1 and F2) and a single universal reverse primer (uni rev). PCR amplicons of first and second PCRs were purified from excess primers on AmPure beads (Agencourt) before beginning the next step. (B) Flowchart of the bioinformatics approach to 3′ RACE-seq data analysis. The procedure starts at the top. Datasets are shown in rectangles. Software used is depicted in hexagons.
    Ligation Mix, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 92/100, based on 93 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/ligation mix/product/New England Biolabs
    Average 92 stars, based on 93 article reviews
    Price from $9.99 to $1999.99
    ligation mix - by Bioz Stars, 2020-09
    92/100 stars
      Buy from Supplier

    Image Search Results


    Graphical Visualization of the 3′ RACE-Seq Approach, Related to Figure 2 (A) Graphical representation of 3′ RACE-seq library preparation and the oligonucleotides used. First, the 3′ adaptor RA3_15N was joined to the 3′ end of RNA by enzymatic ligation. The adaptor has: (i) 5′ rApp modification for efficient and specific ligation by the truncated T4 RNA ligase 2, (ii) delimiter sequence to be used in bioinformatics analyses to exclude RT and PCR artifacts (CTGAC, highlighted in violet), (iii) unique 15N barcode for individual transcript barcoding (highlighted in green), (iv) anchor sequence to pair with the reverse transcription primer (underlined) and (v) dideoxyC on the 3′ end to prevent concatamer formation. The RNA ligated to the adaptor sequence was purified from excess adaptor and reverse transcription was performed with the RT primer, which is compatible with Illumina sequencing and has: (i) sequences to base-pair with the adaptor (underlined), (ii) 6-nucleotide barcode for sample barcoding (highlighted in red), (iii) sequences that base pair with the universal outer primer for nested PCR (blue). Libraries were generated by nested PCR with 2 outer forward primers (F1 and F2) and a single universal reverse primer (uni rev). PCR amplicons of first and second PCRs were purified from excess primers on AmPure beads (Agencourt) before beginning the next step. (B) Flowchart of the bioinformatics approach to 3′ RACE-seq data analysis. The procedure starts at the top. Datasets are shown in rectangles. Software used is depicted in hexagons.

    Journal: Cell

    Article Title: Uridylation by TUT4/7 Restricts Retrotransposition of Human LINE-1s

    doi: 10.1016/j.cell.2018.07.022

    Figure Lengend Snippet: Graphical Visualization of the 3′ RACE-Seq Approach, Related to Figure 2 (A) Graphical representation of 3′ RACE-seq library preparation and the oligonucleotides used. First, the 3′ adaptor RA3_15N was joined to the 3′ end of RNA by enzymatic ligation. The adaptor has: (i) 5′ rApp modification for efficient and specific ligation by the truncated T4 RNA ligase 2, (ii) delimiter sequence to be used in bioinformatics analyses to exclude RT and PCR artifacts (CTGAC, highlighted in violet), (iii) unique 15N barcode for individual transcript barcoding (highlighted in green), (iv) anchor sequence to pair with the reverse transcription primer (underlined) and (v) dideoxyC on the 3′ end to prevent concatamer formation. The RNA ligated to the adaptor sequence was purified from excess adaptor and reverse transcription was performed with the RT primer, which is compatible with Illumina sequencing and has: (i) sequences to base-pair with the adaptor (underlined), (ii) 6-nucleotide barcode for sample barcoding (highlighted in red), (iii) sequences that base pair with the universal outer primer for nested PCR (blue). Libraries were generated by nested PCR with 2 outer forward primers (F1 and F2) and a single universal reverse primer (uni rev). PCR amplicons of first and second PCRs were purified from excess primers on AmPure beads (Agencourt) before beginning the next step. (B) Flowchart of the bioinformatics approach to 3′ RACE-seq data analysis. The procedure starts at the top. Datasets are shown in rectangles. Software used is depicted in hexagons.

    Article Snippet: The reactions were carried out in 20 μL with 1x T4 RNA ligase 2 truncated buffer (NEB) supplemented with PEG-8000 at 10% final concentration, 0.25 U/μl RiboLock inhibitor (Thermo Fisher Scientific), 3 pmol of the 5′ FAM-labeled 44-mer oligonucleotide RNA44 (Future Synthesis) and 300 U T4 RNA ligase 2 truncated (NEB) for 18h at 18°C.

    Techniques: Ligation, Modification, Sequencing, Polymerase Chain Reaction, Purification, Nested PCR, Generated, Software