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  • 79
    New England Biolabs strepavidin magnetic beads
    Strepavidin Magnetic Beads, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 79/100, based on 5 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    84
    New England Biolabs magnetic hydrophilic streptavidin beads
    Overview of 3-day generation of cDNA libraries. ( A ) On the first day, total RNA is ligated to a 3′ adapter and cDNA is generated by reverse transcription by tandem reactions in a single tube, RNA is degraded and cDNAs are isolated by ethanol precipitation. ( B ) On the second day, cDNAs are circularized, size selected by gel fractionation and eluted overnight in the presence of <t>streptavidin</t> beads. ( C ) PCR is done on bead-bound purified cDNAs to generate templates ready for high-throughput sequencing.
    Magnetic Hydrophilic Streptavidin Beads, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 84/100, based on 10 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    93
    Promega streptavidin coated magnetic beads
    Overview of 3-day generation of cDNA libraries. ( A ) On the first day, total RNA is ligated to a 3′ adapter and cDNA is generated by reverse transcription by tandem reactions in a single tube, RNA is degraded and cDNAs are isolated by ethanol precipitation. ( B ) On the second day, cDNAs are circularized, size selected by gel fractionation and eluted overnight in the presence of <t>streptavidin</t> beads. ( C ) PCR is done on bead-bound purified cDNAs to generate templates ready for high-throughput sequencing.
    Streptavidin Coated Magnetic Beads, supplied by Promega, used in various techniques. Bioz Stars score: 93/100, based on 838 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    96
    New England Biolabs streptavidin
    A catalytic RNA from the A. pernix genome that reacts with a disubstituted epoxide ( a ) PAGE <t>streptavidin</t> gel mobility shift following incubation of random sequence RNA (“random”), the A. pernix species from Round 6 of the selection (“selected”), and the A. pernix fragment corresponding to the reference genome sequence (“genomic”) with epoxide probe 1 (1 mM) for 16 h at room temperature (1 µM RNA). The complete gel is shown in Supplementary Figure 12 . ( b ) Secondary structure model of the minimized A. pernix catalytic RNA. The reactive guanosine (blue) was identified by RNAse T1 digestion and mass spectrometry. ( c ) Sequence logo based on high-throughput DNA sequencing of the RNA species surviving selection of a partially randomized RNA pool derived from the minimized 42-nt A. pernix catalytic RNA.
    Streptavidin, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 96/100, based on 276 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    86
    New England Biolabs nuclease bal 31
    A catalytic RNA from the A. pernix genome that reacts with a disubstituted epoxide ( a ) PAGE <t>streptavidin</t> gel mobility shift following incubation of random sequence RNA (“random”), the A. pernix species from Round 6 of the selection (“selected”), and the A. pernix fragment corresponding to the reference genome sequence (“genomic”) with epoxide probe 1 (1 mM) for 16 h at room temperature (1 µM RNA). The complete gel is shown in Supplementary Figure 12 . ( b ) Secondary structure model of the minimized A. pernix catalytic RNA. The reactive guanosine (blue) was identified by RNAse T1 digestion and mass spectrometry. ( c ) Sequence logo based on high-throughput DNA sequencing of the RNA species surviving selection of a partially randomized RNA pool derived from the minimized 42-nt A. pernix catalytic RNA.
    Nuclease Bal 31, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 86/100, based on 16 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    New England Biolabs m mulv reverse transcriptase
    A catalytic RNA from the A. pernix genome that reacts with a disubstituted epoxide ( a ) PAGE <t>streptavidin</t> gel mobility shift following incubation of random sequence RNA (“random”), the A. pernix species from Round 6 of the selection (“selected”), and the A. pernix fragment corresponding to the reference genome sequence (“genomic”) with epoxide probe 1 (1 mM) for 16 h at room temperature (1 µM RNA). The complete gel is shown in Supplementary Figure 12 . ( b ) Secondary structure model of the minimized A. pernix catalytic RNA. The reactive guanosine (blue) was identified by RNAse T1 digestion and mass spectrometry. ( c ) Sequence logo based on high-throughput DNA sequencing of the RNA species surviving selection of a partially randomized RNA pool derived from the minimized 42-nt A. pernix catalytic RNA.
    M Mulv Reverse Transcriptase, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 3431 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Image Search Results


    Overview of 3-day generation of cDNA libraries. ( A ) On the first day, total RNA is ligated to a 3′ adapter and cDNA is generated by reverse transcription by tandem reactions in a single tube, RNA is degraded and cDNAs are isolated by ethanol precipitation. ( B ) On the second day, cDNAs are circularized, size selected by gel fractionation and eluted overnight in the presence of streptavidin beads. ( C ) PCR is done on bead-bound purified cDNAs to generate templates ready for high-throughput sequencing.

    Journal: Nucleic Acids Research

    Article Title: An efficient and sensitive method for preparing cDNA libraries from scarce biological samples

    doi: 10.1093/nar/gku637

    Figure Lengend Snippet: Overview of 3-day generation of cDNA libraries. ( A ) On the first day, total RNA is ligated to a 3′ adapter and cDNA is generated by reverse transcription by tandem reactions in a single tube, RNA is degraded and cDNAs are isolated by ethanol precipitation. ( B ) On the second day, cDNAs are circularized, size selected by gel fractionation and eluted overnight in the presence of streptavidin beads. ( C ) PCR is done on bead-bound purified cDNAs to generate templates ready for high-throughput sequencing.

    Article Snippet: 5.0 μl magnetic hydrophilic streptavidin beads (New England Biolabs) were washed three times with 50 μl buffer WB (0.5M NaCl, 20 mM Tris-HCl pH 7.5, 1.0 mM EDTA), resuspended in 5.0 μl TE + 0.3M NaCl and added to each sample.

    Techniques: Generated, Isolation, Ethanol Precipitation, Fractionation, Polymerase Chain Reaction, Purification, Next-Generation Sequencing

    Detailed LQ cloning method. ( A ) A pre-adenylated (rApp) 3′-terminal dideoxy-C (ddC) blocked adapter (gray) is annealed to a ssDNA reverse transcription (RT) oligo (black) in a 1:1 molar ratio. The annealed adapter is ligated to 3′-hydroxyl-containing RNA (orange) using T4 RNA Ligase 2 (truncated K227Q) without ATP. Each RT oligo contains a 5′ Guanine (G) followed by a 4 or 6 nucleotide randomer (N X ), a 3–6 nucleotide barcode (BAR) and 3 internal deoxyUridine (dU) nucleotides. The adapter::RT oligo hybrid is in excess over RNA, resulting in free adapter::primer material present in the completed reaction. ( B ) Reverse transcription of ligated RNA is carried out in the same tube as the ligation reaction generating ‘+ insert’ and ‘no insert’ cDNA products (red and black line) using dGTP, dTTP, dATP, dCTP as well as biotinylated dATP and dCTP (yellow ‘B’-containing circles). The RNA template is degraded (dashed orange line) by base hydrolysis and cDNA is ethanol precipitated with ammonium acetate to facilitate maximum removal of free adapter and unincorporated nucleotides ( C ). Ethanol precipitated cDNAs are circularized ( D ) and resolved on a 10% denaturing polyacrylamide gel. ‘+ insert’ circularized cDNAs are isolated by excising and eluting them from the gel overnight in the presence of magnetic streptavidin beads ( E ). Bead-bound ‘+ insert’ cDNAs serve as templates in the first round of PCR. Amplification is done using a mix containing uracil-N-deglycosylase (UNG) to remove dU nucleotides, thereby generating a linear template through strand scission, and with primers complimentary to the 3′ adapter (blue) and 5′ end of the RT oligo (tan) ( F ). First round PCR products are resolved on an 8% native polyacrylamide gel, the 60–70 nucleotide products are excised and a portion is used as the template for second round PCR. Second round PCR products are generated using primers complimentary to the 3′ adapter (dark blue) and 5′ end of the RT oligo (brown) that contain the full Illumina or Ion Torrent adapter sequences (dark blue and brown) ( G ).

    Journal: Nucleic Acids Research

    Article Title: An efficient and sensitive method for preparing cDNA libraries from scarce biological samples

    doi: 10.1093/nar/gku637

    Figure Lengend Snippet: Detailed LQ cloning method. ( A ) A pre-adenylated (rApp) 3′-terminal dideoxy-C (ddC) blocked adapter (gray) is annealed to a ssDNA reverse transcription (RT) oligo (black) in a 1:1 molar ratio. The annealed adapter is ligated to 3′-hydroxyl-containing RNA (orange) using T4 RNA Ligase 2 (truncated K227Q) without ATP. Each RT oligo contains a 5′ Guanine (G) followed by a 4 or 6 nucleotide randomer (N X ), a 3–6 nucleotide barcode (BAR) and 3 internal deoxyUridine (dU) nucleotides. The adapter::RT oligo hybrid is in excess over RNA, resulting in free adapter::primer material present in the completed reaction. ( B ) Reverse transcription of ligated RNA is carried out in the same tube as the ligation reaction generating ‘+ insert’ and ‘no insert’ cDNA products (red and black line) using dGTP, dTTP, dATP, dCTP as well as biotinylated dATP and dCTP (yellow ‘B’-containing circles). The RNA template is degraded (dashed orange line) by base hydrolysis and cDNA is ethanol precipitated with ammonium acetate to facilitate maximum removal of free adapter and unincorporated nucleotides ( C ). Ethanol precipitated cDNAs are circularized ( D ) and resolved on a 10% denaturing polyacrylamide gel. ‘+ insert’ circularized cDNAs are isolated by excising and eluting them from the gel overnight in the presence of magnetic streptavidin beads ( E ). Bead-bound ‘+ insert’ cDNAs serve as templates in the first round of PCR. Amplification is done using a mix containing uracil-N-deglycosylase (UNG) to remove dU nucleotides, thereby generating a linear template through strand scission, and with primers complimentary to the 3′ adapter (blue) and 5′ end of the RT oligo (tan) ( F ). First round PCR products are resolved on an 8% native polyacrylamide gel, the 60–70 nucleotide products are excised and a portion is used as the template for second round PCR. Second round PCR products are generated using primers complimentary to the 3′ adapter (dark blue) and 5′ end of the RT oligo (brown) that contain the full Illumina or Ion Torrent adapter sequences (dark blue and brown) ( G ).

    Article Snippet: 5.0 μl magnetic hydrophilic streptavidin beads (New England Biolabs) were washed three times with 50 μl buffer WB (0.5M NaCl, 20 mM Tris-HCl pH 7.5, 1.0 mM EDTA), resuspended in 5.0 μl TE + 0.3M NaCl and added to each sample.

    Techniques: Clone Assay, Ligation, Isolation, Polymerase Chain Reaction, Amplification, Generated

    A catalytic RNA from the A. pernix genome that reacts with a disubstituted epoxide ( a ) PAGE streptavidin gel mobility shift following incubation of random sequence RNA (“random”), the A. pernix species from Round 6 of the selection (“selected”), and the A. pernix fragment corresponding to the reference genome sequence (“genomic”) with epoxide probe 1 (1 mM) for 16 h at room temperature (1 µM RNA). The complete gel is shown in Supplementary Figure 12 . ( b ) Secondary structure model of the minimized A. pernix catalytic RNA. The reactive guanosine (blue) was identified by RNAse T1 digestion and mass spectrometry. ( c ) Sequence logo based on high-throughput DNA sequencing of the RNA species surviving selection of a partially randomized RNA pool derived from the minimized 42-nt A. pernix catalytic RNA.

    Journal: Nature chemical biology

    Article Title: Electrophilic activity-based RNA probes reveal a self-alkylating RNA for RNA labeling

    doi: 10.1038/nchembio.1655

    Figure Lengend Snippet: A catalytic RNA from the A. pernix genome that reacts with a disubstituted epoxide ( a ) PAGE streptavidin gel mobility shift following incubation of random sequence RNA (“random”), the A. pernix species from Round 6 of the selection (“selected”), and the A. pernix fragment corresponding to the reference genome sequence (“genomic”) with epoxide probe 1 (1 mM) for 16 h at room temperature (1 µM RNA). The complete gel is shown in Supplementary Figure 12 . ( b ) Secondary structure model of the minimized A. pernix catalytic RNA. The reactive guanosine (blue) was identified by RNAse T1 digestion and mass spectrometry. ( c ) Sequence logo based on high-throughput DNA sequencing of the RNA species surviving selection of a partially randomized RNA pool derived from the minimized 42-nt A. pernix catalytic RNA.

    Article Snippet: The RNA (7 µL) and streptavidin (NEB; 1 µg) were incubated at room temperature for 25 minutes and then combined with gel electrophoresis loading buffer.

    Techniques: Polyacrylamide Gel Electrophoresis, Mobility Shift, Incubation, Sequencing, Selection, Mass Spectrometry, High Throughput Screening Assay, DNA Sequencing, Derivative Assay

    Application of the epoxide-opening catalytic RNA to enrich RNAs of interest from total cellular RNA and to capture RNA-binding proteins ( a ) Transcriptional fusion of a self-labeling catalytic RNA to an RNA of interest may enable selective, covalent RNA modification in a complex biological sample. ( b ) Total RNA from HEK 293T cells was reacted with epoxide-azide 14 , followed by DBCO-TAMRA. Total RNA was analyzed by PAGE and TAMRA-modified RNAs were visualized by fluorescence imaging. Lanes 1 and 6: in vitro transcribed catalytic RNA-fused 5S rRNA containing one or three copies of the catalytic RNA, respectively, rather than cellular RNA. Lanes 2 and 3: the inactive C9-G35 mutant RNA. Lanes 4–8: 5S rRNA fused to one copy (lanes 4–5) or three copies (lanes 6–8) of the active optimized catalytic RNA. Bands at the top of the gel result from incomplete removal of excess DBCO-TAMRA probe or background labeling of cellular rRNAs/mRNAs. The complete gel is shown in Supplementary Figure 14 . ( c ) Western blot probing the presence of three known ASH1 mRNA-binding proteins (Puf6, Khd1, and She2) and one non-binding protein control (Guk1) in yeast cell lysate. Lanes 1 and 2: Lysate incubated overnight with streptavidin-coated magnetic beads only (lane 1) or pre-incubated with 5 µg of epoxide 1 -modified ASH1 -catalytic RNA (lane 2). Unbound proteins were washed away and captured proteins were eluted at 95 °C. Lane 3: Input lysate prior to incubation with beads. The complete gel is shown in Supplementary Figure 15 .

    Journal: Nature chemical biology

    Article Title: Electrophilic activity-based RNA probes reveal a self-alkylating RNA for RNA labeling

    doi: 10.1038/nchembio.1655

    Figure Lengend Snippet: Application of the epoxide-opening catalytic RNA to enrich RNAs of interest from total cellular RNA and to capture RNA-binding proteins ( a ) Transcriptional fusion of a self-labeling catalytic RNA to an RNA of interest may enable selective, covalent RNA modification in a complex biological sample. ( b ) Total RNA from HEK 293T cells was reacted with epoxide-azide 14 , followed by DBCO-TAMRA. Total RNA was analyzed by PAGE and TAMRA-modified RNAs were visualized by fluorescence imaging. Lanes 1 and 6: in vitro transcribed catalytic RNA-fused 5S rRNA containing one or three copies of the catalytic RNA, respectively, rather than cellular RNA. Lanes 2 and 3: the inactive C9-G35 mutant RNA. Lanes 4–8: 5S rRNA fused to one copy (lanes 4–5) or three copies (lanes 6–8) of the active optimized catalytic RNA. Bands at the top of the gel result from incomplete removal of excess DBCO-TAMRA probe or background labeling of cellular rRNAs/mRNAs. The complete gel is shown in Supplementary Figure 14 . ( c ) Western blot probing the presence of three known ASH1 mRNA-binding proteins (Puf6, Khd1, and She2) and one non-binding protein control (Guk1) in yeast cell lysate. Lanes 1 and 2: Lysate incubated overnight with streptavidin-coated magnetic beads only (lane 1) or pre-incubated with 5 µg of epoxide 1 -modified ASH1 -catalytic RNA (lane 2). Unbound proteins were washed away and captured proteins were eluted at 95 °C. Lane 3: Input lysate prior to incubation with beads. The complete gel is shown in Supplementary Figure 15 .

    Article Snippet: The RNA (7 µL) and streptavidin (NEB; 1 µg) were incubated at room temperature for 25 minutes and then combined with gel electrophoresis loading buffer.

    Techniques: RNA Binding Assay, Labeling, Modification, Polyacrylamide Gel Electrophoresis, Fluorescence, Imaging, In Vitro, Mutagenesis, Western Blot, Binding Assay, Incubation, Magnetic Beads