ecori New England Biolabs Search Results


  • Logo
  • About
  • News
  • Press Release
  • Team
  • Advisors
  • Partners
  • Contact
  • Bioz Stars
  • Bioz vStars
  • 78
    New England Biolabs ecori new england biolabs
    Ecori New England Biolabs, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 78/100, based on 3 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/ecori new england biolabs/product/New England Biolabs
    Average 78 stars, based on 3 article reviews
    Price from $9.99 to $1999.99
    ecori new england biolabs - by Bioz Stars, 2020-01
    78/100 stars
      Buy from Supplier

    87
    New England Biolabs ecor
    Ecor, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 87/100, based on 50 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/ecor/product/New England Biolabs
    Average 87 stars, based on 50 article reviews
    Price from $9.99 to $1999.99
    ecor - by Bioz Stars, 2020-01
    87/100 stars
      Buy from Supplier

    84
    New England Biolabs nebuffer ecori
    Nebuffer Ecori, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 84/100, based on 12 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/nebuffer ecori/product/New England Biolabs
    Average 84 stars, based on 12 article reviews
    Price from $9.99 to $1999.99
    nebuffer ecori - by Bioz Stars, 2020-01
    84/100 stars
      Buy from Supplier

    93
    TaKaRa ecorv
    Ecorv, supplied by TaKaRa, used in various techniques. Bioz Stars score: 93/100, based on 405 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/ecorv/product/TaKaRa
    Average 93 stars, based on 405 article reviews
    Price from $9.99 to $1999.99
    ecorv - by Bioz Stars, 2020-01
    93/100 stars
      Buy from Supplier

    99
    New England Biolabs ecori hf
    Ecori Hf, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 699 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/ecori hf/product/New England Biolabs
    Average 99 stars, based on 699 article reviews
    Price from $9.99 to $1999.99
    ecori hf - by Bioz Stars, 2020-01
    99/100 stars
      Buy from Supplier

    99
    New England Biolabs ecorv hf
    Ecorv Hf, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 133 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/ecorv hf/product/New England Biolabs
    Average 99 stars, based on 133 article reviews
    Price from $9.99 to $1999.99
    ecorv hf - by Bioz Stars, 2020-01
    99/100 stars
      Buy from Supplier

    87
    Thermo Fisher pyestrp
    Pyestrp, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 87/100, based on 53 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/pyestrp/product/Thermo Fisher
    Average 87 stars, based on 53 article reviews
    Price from $9.99 to $1999.99
    pyestrp - by Bioz Stars, 2020-01
    87/100 stars
      Buy from Supplier

    86
    New England Biolabs ecori mspi
    Ecori Mspi, 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
    https://www.bioz.com/result/ecori mspi/product/New England Biolabs
    Average 86 stars, based on 16 article reviews
    Price from $9.99 to $1999.99
    ecori mspi - by Bioz Stars, 2020-01
    86/100 stars
      Buy from Supplier

    78
    New England Biolabs ecori methyltransferase buffer
    Ecori Methyltransferase Buffer, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 78/100, based on 3 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/ecori methyltransferase buffer/product/New England Biolabs
    Average 78 stars, based on 3 article reviews
    Price from $9.99 to $1999.99
    ecori methyltransferase buffer - by Bioz Stars, 2020-01
    78/100 stars
      Buy from Supplier

    89
    TaKaRa ecori sali sites
    Ecori Sali Sites, supplied by TaKaRa, used in various techniques. Bioz Stars score: 89/100, based on 259 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/ecori sali sites/product/TaKaRa
    Average 89 stars, based on 259 article reviews
    Price from $9.99 to $1999.99
    ecori sali sites - by Bioz Stars, 2020-01
    89/100 stars
      Buy from Supplier

    99
    New England Biolabs bamhi
    Bamhi, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 8434 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/bamhi/product/New England Biolabs
    Average 99 stars, based on 8434 article reviews
    Price from $9.99 to $1999.99
    bamhi - by Bioz Stars, 2020-01
    99/100 stars
      Buy from Supplier

    99
    New England Biolabs nhei
    Nhei, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 2424 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/nhei/product/New England Biolabs
    Average 99 stars, based on 2424 article reviews
    Price from $9.99 to $1999.99
    nhei - by Bioz Stars, 2020-01
    99/100 stars
      Buy from Supplier

    87
    New England Biolabs nsp i
    Nsp I, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 87/100, based on 85 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/nsp i/product/New England Biolabs
    Average 87 stars, based on 85 article reviews
    Price from $9.99 to $1999.99
    nsp i - by Bioz Stars, 2020-01
    87/100 stars
      Buy from Supplier

    99
    New England Biolabs bamhi hf
    Bamhi Hf, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 955 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/bamhi hf/product/New England Biolabs
    Average 99 stars, based on 955 article reviews
    Price from $9.99 to $1999.99
    bamhi hf - by Bioz Stars, 2020-01
    99/100 stars
      Buy from Supplier

    99
    New England Biolabs ecori
    Ecori, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 8258 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/ecori/product/New England Biolabs
    Average 99 stars, based on 8258 article reviews
    Price from $9.99 to $1999.99
    ecori - by Bioz Stars, 2020-01
    99/100 stars
      Buy from Supplier

    97
    New England Biolabs acc65i
    Acc65i, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 97/100, based on 185 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/acc65i/product/New England Biolabs
    Average 97 stars, based on 185 article reviews
    Price from $9.99 to $1999.99
    acc65i - by Bioz Stars, 2020-01
    97/100 stars
      Buy from Supplier

    99
    New England Biolabs eagi
    Eagi, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 313 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/eagi/product/New England Biolabs
    Average 99 stars, based on 313 article reviews
    Price from $9.99 to $1999.99
    eagi - by Bioz Stars, 2020-01
    99/100 stars
      Buy from Supplier

    99
    New England Biolabs xhoi
    Xhoi, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 7087 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/xhoi/product/New England Biolabs
    Average 99 stars, based on 7087 article reviews
    Price from $9.99 to $1999.99
    xhoi - by Bioz Stars, 2020-01
    99/100 stars
      Buy from Supplier

    92
    New England Biolabs biobrick assembly kit
    Biobrick Assembly Kit, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 92/100, based on 14 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/biobrick assembly kit/product/New England Biolabs
    Average 92 stars, based on 14 article reviews
    Price from $9.99 to $1999.99
    biobrick assembly kit - by Bioz Stars, 2020-01
    92/100 stars
      Buy from Supplier

    99
    New England Biolabs bsm bi
    Bsm Bi, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 164 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/bsm bi/product/New England Biolabs
    Average 99 stars, based on 164 article reviews
    Price from $9.99 to $1999.99
    bsm bi - by Bioz Stars, 2020-01
    99/100 stars
      Buy from Supplier

    91
    New England Biolabs nebuffer ecor i
    Nebuffer Ecor I, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 91/100, based on 16 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/nebuffer ecor i/product/New England Biolabs
    Average 91 stars, based on 16 article reviews
    Price from $9.99 to $1999.99
    nebuffer ecor i - by Bioz Stars, 2020-01
    91/100 stars
      Buy from Supplier

    99
    New England Biolabs t5 exonuclease
    T5 Exonuclease, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 488 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/t5 exonuclease/product/New England Biolabs
    Average 99 stars, based on 488 article reviews
    Price from $9.99 to $1999.99
    t5 exonuclease - by Bioz Stars, 2020-01
    99/100 stars
      Buy from Supplier

    99
    New England Biolabs t4 pnk
    T4 Pnk, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 3038 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/t4 pnk/product/New England Biolabs
    Average 99 stars, based on 3038 article reviews
    Price from $9.99 to $1999.99
    t4 pnk - by Bioz Stars, 2020-01
    99/100 stars
      Buy from Supplier

    99
    New England Biolabs t4 polynucleotide kinase
    T4 Polynucleotide Kinase, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 22375 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/t4 polynucleotide kinase/product/New England Biolabs
    Average 99 stars, based on 22375 article reviews
    Price from $9.99 to $1999.99
    t4 polynucleotide kinase - by Bioz Stars, 2020-01
    99/100 stars
      Buy from Supplier

    99
    New England Biolabs bsrgi
    Analysis of restriction sites over genic and intergenic regions. ( A ) Restriction fragment lengths over genic regions (gene bodies, exons, first exons) are significantly larger compared to intergenic regions. The plot shows the difference of genic (observed) and intergenic (expected) fragment sizes in base pairs. The following enzymes were applied in combination: <t>HindIII,</t> EcoRI, <t>BsrGI,</t> XbaI, and SspI. ( B – D ) The number of restriction sites over genic regions is significantly lower compared to intergenic regions. Colors indicate the proportion of cutting sites in each category. Red and blue slices, marking the rarest restriction site frequencies, are prevalent over genic elements in each pie chart. ( E ) Cutting efficiency of restriction enzymes applied in the indicated DRIP-seq experiments. Zero read: the restriction site was cut. Greater equal than one read: the restriction site was uncut in a fraction of cells. There were uncut reads (sites) over half of the theoretical restriction sites. The proportion of uncut reads was even higher within gene coding regions compared to intergenic regions. See the model of cutting efficiency in panel F .
    Bsrgi, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 483 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/bsrgi/product/New England Biolabs
    Average 99 stars, based on 483 article reviews
    Price from $9.99 to $1999.99
    bsrgi - by Bioz Stars, 2020-01
    99/100 stars
      Buy from Supplier

    95
    New England Biolabs sau96i
    RFLP profile of the URA5 genes from Cryptococcus sp obtained by double-digestion with HhaI and <t>Sau96I.</t> Column 1: Molecular maker (100 bp). Columns 2 to 7: isolated 2, 4, 5, 6, 7 and 8 (VNI), respectively; column 8: isolated 12 (VGI); Columns 9 to 13: isolates 13, 18, 22, 24 and 25 (VNI), respectively.
    Sau96i, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 95/100, based on 74 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/sau96i/product/New England Biolabs
    Average 95 stars, based on 74 article reviews
    Price from $9.99 to $1999.99
    sau96i - by Bioz Stars, 2020-01
    95/100 stars
      Buy from Supplier

    96
    New England Biolabs rnase inhibitor
    RFLP profile of the URA5 genes from Cryptococcus sp obtained by double-digestion with HhaI and <t>Sau96I.</t> Column 1: Molecular maker (100 bp). Columns 2 to 7: isolated 2, 4, 5, 6, 7 and 8 (VNI), respectively; column 8: isolated 12 (VGI); Columns 9 to 13: isolates 13, 18, 22, 24 and 25 (VNI), respectively.
    Rnase Inhibitor, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 96/100, based on 1529 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/rnase inhibitor/product/New England Biolabs
    Average 96 stars, based on 1529 article reviews
    Price from $9.99 to $1999.99
    rnase inhibitor - by Bioz Stars, 2020-01
    96/100 stars
      Buy from Supplier

    95
    New England Biolabs eco ri
    RFLP profile of the URA5 genes from Cryptococcus sp obtained by double-digestion with HhaI and <t>Sau96I.</t> Column 1: Molecular maker (100 bp). Columns 2 to 7: isolated 2, 4, 5, 6, 7 and 8 (VNI), respectively; column 8: isolated 12 (VGI); Columns 9 to 13: isolates 13, 18, 22, 24 and 25 (VNI), respectively.
    Eco Ri, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 95/100, based on 4671 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/eco ri/product/New England Biolabs
    Average 95 stars, based on 4671 article reviews
    Price from $9.99 to $1999.99
    eco ri - by Bioz Stars, 2020-01
    95/100 stars
      Buy from Supplier

    99
    New England Biolabs t4 dna ligase
    RFLP profile of the URA5 genes from Cryptococcus sp obtained by double-digestion with HhaI and <t>Sau96I.</t> Column 1: Molecular maker (100 bp). Columns 2 to 7: isolated 2, 4, 5, 6, 7 and 8 (VNI), respectively; column 8: isolated 12 (VGI); Columns 9 to 13: isolates 13, 18, 22, 24 and 25 (VNI), respectively.
    T4 Dna Ligase, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 36171 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/t4 dna ligase/product/New England Biolabs
    Average 99 stars, based on 36171 article reviews
    Price from $9.99 to $1999.99
    t4 dna ligase - by Bioz Stars, 2020-01
    99/100 stars
      Buy from Supplier

    99
    New England Biolabs phi29 dna polymerase
    Effect of Tth SSB-255 protein on the efficiency and specificity of RCA. ( a ) Top: RCAs were performed in the absence of the SSB proteins using pUC19 <t>DNA</t> as template and <t>phi29</t> DNA polymerase for the indicated reaction times. Bottom: Signals of spot hybridization of the same samples. ( b ) Top and Bottom: same as (a), except for the absence of template DNA. ( c ) Top and Bottom: same as (a), except for the presence of the Tth SSB protein (3.0 µg/20 µl reaction volume). ( d ) Top and Bottom: same as (c), except for the absence of template DNA. ( e ) Top and Bottom: same as (a), except for the presence of the Tth SSB-255 protein (3.0 µg/20 µl reaction volume). ( f ) Top and Bottom: same as (e), except for the absence of template DNA.
    Phi29 Dna Polymerase, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 558 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/phi29 dna polymerase/product/New England Biolabs
    Average 99 stars, based on 558 article reviews
    Price from $9.99 to $1999.99
    phi29 dna polymerase - by Bioz Stars, 2020-01
    99/100 stars
      Buy from Supplier

    97
    New England Biolabs restriction endonuclease dpni
    Effect of Tth SSB-255 protein on the efficiency and specificity of RCA. ( a ) Top: RCAs were performed in the absence of the SSB proteins using pUC19 <t>DNA</t> as template and <t>phi29</t> DNA polymerase for the indicated reaction times. Bottom: Signals of spot hybridization of the same samples. ( b ) Top and Bottom: same as (a), except for the absence of template DNA. ( c ) Top and Bottom: same as (a), except for the presence of the Tth SSB protein (3.0 µg/20 µl reaction volume). ( d ) Top and Bottom: same as (c), except for the absence of template DNA. ( e ) Top and Bottom: same as (a), except for the presence of the Tth SSB-255 protein (3.0 µg/20 µl reaction volume). ( f ) Top and Bottom: same as (e), except for the absence of template DNA.
    Restriction Endonuclease Dpni, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 97/100, based on 54 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/restriction endonuclease dpni/product/New England Biolabs
    Average 97 stars, based on 54 article reviews
    Price from $9.99 to $1999.99
    restriction endonuclease dpni - by Bioz Stars, 2020-01
    97/100 stars
      Buy from Supplier

    Image Search Results


    Analysis of restriction sites over genic and intergenic regions. ( A ) Restriction fragment lengths over genic regions (gene bodies, exons, first exons) are significantly larger compared to intergenic regions. The plot shows the difference of genic (observed) and intergenic (expected) fragment sizes in base pairs. The following enzymes were applied in combination: HindIII, EcoRI, BsrGI, XbaI, and SspI. ( B – D ) The number of restriction sites over genic regions is significantly lower compared to intergenic regions. Colors indicate the proportion of cutting sites in each category. Red and blue slices, marking the rarest restriction site frequencies, are prevalent over genic elements in each pie chart. ( E ) Cutting efficiency of restriction enzymes applied in the indicated DRIP-seq experiments. Zero read: the restriction site was cut. Greater equal than one read: the restriction site was uncut in a fraction of cells. There were uncut reads (sites) over half of the theoretical restriction sites. The proportion of uncut reads was even higher within gene coding regions compared to intergenic regions. See the model of cutting efficiency in panel F .

    Journal: Genome Research

    Article Title: RNA-DNA hybrid (R-loop) immunoprecipitation mapping: an analytical workflow to evaluate inherent biases

    doi: 10.1101/gr.219394.116

    Figure Lengend Snippet: Analysis of restriction sites over genic and intergenic regions. ( A ) Restriction fragment lengths over genic regions (gene bodies, exons, first exons) are significantly larger compared to intergenic regions. The plot shows the difference of genic (observed) and intergenic (expected) fragment sizes in base pairs. The following enzymes were applied in combination: HindIII, EcoRI, BsrGI, XbaI, and SspI. ( B – D ) The number of restriction sites over genic regions is significantly lower compared to intergenic regions. Colors indicate the proportion of cutting sites in each category. Red and blue slices, marking the rarest restriction site frequencies, are prevalent over genic elements in each pie chart. ( E ) Cutting efficiency of restriction enzymes applied in the indicated DRIP-seq experiments. Zero read: the restriction site was cut. Greater equal than one read: the restriction site was uncut in a fraction of cells. There were uncut reads (sites) over half of the theoretical restriction sites. The proportion of uncut reads was even higher within gene coding regions compared to intergenic regions. See the model of cutting efficiency in panel F .

    Article Snippet: 2, 4, 6, 8, 10, 12, 14, and 16, purified DNA samples (∼25 µg each) were fragmented using a restriction enzyme cocktail of 1 µL HindIII (20 U/µL), 1 µL EcoRI (20 U/µL), 2 µL BsrGI (10 U/µL), 1 µL XbaI (20 U/µL), and 4 µL SspI (5 U/µL) in NEB Buffer 2 (NEB) (V = 300 µL) at 37°C for 4 h. The fragmented DNA samples were repurified either by phenol-chloroform extraction (experiments 1–4, 9–12) or by the NucleoSpin Gel and PCR Clean-up kit (Macherey-Nagel) (experiments 5–8, 13–16).

    Techniques:

    Experimental design: constructing DRIP schemes. ( A ) Experiments 1–16 explore the effect of formaldehyde-fixation (Step 1), nucleic acid isolation (Step 2), removal of free RNA (Step 3), and nucleic acid fragmentation (Step 4) on the outcome of RNA-DNA hybrid detection. Each experiment was performed at two parallel cell lysis temperatures (65°C and 37°C), respectively. The temperature variable is not depicted in the cartoon, but it is referred in the main text. ( B ) Experiments 17–24 test the impact of acoustic sharing performed on a chromatin prep rather than on naked nucleic acid, similarly to the ChIP protocol. Each experiment was performed at 65°C cell lysis temperature. ( C ) Workflow of a ChIP experiment (shown only for comparison with the DRIP pipeline). (HCHO) Formaldehyde fixation, (Phe/Chl) phenol-chloroform extraction, (Kit) silica membrane-based nucleic acid purification, (RNase A) Ribonuclease A digestion performed at high (300 mM) NaCl concentration, (Son) sonication, (RE) restriction enzyme cocktail digestion (HindIII, EcoRI, BsrGI, XbaI, and SspI). As a negative control, RNase H digestion was applied in all DRIP experiments (not indicated in the cartoon).

    Journal: Genome Research

    Article Title: RNA-DNA hybrid (R-loop) immunoprecipitation mapping: an analytical workflow to evaluate inherent biases

    doi: 10.1101/gr.219394.116

    Figure Lengend Snippet: Experimental design: constructing DRIP schemes. ( A ) Experiments 1–16 explore the effect of formaldehyde-fixation (Step 1), nucleic acid isolation (Step 2), removal of free RNA (Step 3), and nucleic acid fragmentation (Step 4) on the outcome of RNA-DNA hybrid detection. Each experiment was performed at two parallel cell lysis temperatures (65°C and 37°C), respectively. The temperature variable is not depicted in the cartoon, but it is referred in the main text. ( B ) Experiments 17–24 test the impact of acoustic sharing performed on a chromatin prep rather than on naked nucleic acid, similarly to the ChIP protocol. Each experiment was performed at 65°C cell lysis temperature. ( C ) Workflow of a ChIP experiment (shown only for comparison with the DRIP pipeline). (HCHO) Formaldehyde fixation, (Phe/Chl) phenol-chloroform extraction, (Kit) silica membrane-based nucleic acid purification, (RNase A) Ribonuclease A digestion performed at high (300 mM) NaCl concentration, (Son) sonication, (RE) restriction enzyme cocktail digestion (HindIII, EcoRI, BsrGI, XbaI, and SspI). As a negative control, RNase H digestion was applied in all DRIP experiments (not indicated in the cartoon).

    Article Snippet: 2, 4, 6, 8, 10, 12, 14, and 16, purified DNA samples (∼25 µg each) were fragmented using a restriction enzyme cocktail of 1 µL HindIII (20 U/µL), 1 µL EcoRI (20 U/µL), 2 µL BsrGI (10 U/µL), 1 µL XbaI (20 U/µL), and 4 µL SspI (5 U/µL) in NEB Buffer 2 (NEB) (V = 300 µL) at 37°C for 4 h. The fragmented DNA samples were repurified either by phenol-chloroform extraction (experiments 1–4, 9–12) or by the NucleoSpin Gel and PCR Clean-up kit (Macherey-Nagel) (experiments 5–8, 13–16).

    Techniques: Isolation, Lysis, Chromatin Immunoprecipitation, Nucleic Acid Purification, Concentration Assay, Sonication, Negative Control

    Large restriction fragments over gene bodies cause uncertainty in the precise localization of R-loops, potentially impeding their functional annotation. ( A – C ) Genome browser tracks showing three representative examples ( MYC , BCL6 , and VIM ). Upper two tracks: restriction fragment-sized R-loops are prevalent over the 5′ end of genes, vastly exceeding the gene borders in the case of MYC . Lower two tracks: the precise genomic position of R-loops was resolved in the sonicated group of samples. Green boxes represent R-loop enriched regions predicted by the peak callers. Blue dashed lines represent cutting sites for restriction enzymes (HindIII, EcoRI, BsrGI, XbaI, and SspI).

    Journal: Genome Research

    Article Title: RNA-DNA hybrid (R-loop) immunoprecipitation mapping: an analytical workflow to evaluate inherent biases

    doi: 10.1101/gr.219394.116

    Figure Lengend Snippet: Large restriction fragments over gene bodies cause uncertainty in the precise localization of R-loops, potentially impeding their functional annotation. ( A – C ) Genome browser tracks showing three representative examples ( MYC , BCL6 , and VIM ). Upper two tracks: restriction fragment-sized R-loops are prevalent over the 5′ end of genes, vastly exceeding the gene borders in the case of MYC . Lower two tracks: the precise genomic position of R-loops was resolved in the sonicated group of samples. Green boxes represent R-loop enriched regions predicted by the peak callers. Blue dashed lines represent cutting sites for restriction enzymes (HindIII, EcoRI, BsrGI, XbaI, and SspI).

    Article Snippet: 2, 4, 6, 8, 10, 12, 14, and 16, purified DNA samples (∼25 µg each) were fragmented using a restriction enzyme cocktail of 1 µL HindIII (20 U/µL), 1 µL EcoRI (20 U/µL), 2 µL BsrGI (10 U/µL), 1 µL XbaI (20 U/µL), and 4 µL SspI (5 U/µL) in NEB Buffer 2 (NEB) (V = 300 µL) at 37°C for 4 h. The fragmented DNA samples were repurified either by phenol-chloroform extraction (experiments 1–4, 9–12) or by the NucleoSpin Gel and PCR Clean-up kit (Macherey-Nagel) (experiments 5–8, 13–16).

    Techniques: Functional Assay, Sonication

    RFLP profile of the URA5 genes from Cryptococcus sp obtained by double-digestion with HhaI and Sau96I. Column 1: Molecular maker (100 bp). Columns 2 to 7: isolated 2, 4, 5, 6, 7 and 8 (VNI), respectively; column 8: isolated 12 (VGI); Columns 9 to 13: isolates 13, 18, 22, 24 and 25 (VNI), respectively.

    Journal: Revista do Instituto de Medicina Tropical de São Paulo

    Article Title: The epidemiology of cryptococcosis and the characterization of Cryptococcus neoformans isolated in a Brazilian University Hospital

    doi: 10.1590/S1678-9946201759013

    Figure Lengend Snippet: RFLP profile of the URA5 genes from Cryptococcus sp obtained by double-digestion with HhaI and Sau96I. Column 1: Molecular maker (100 bp). Columns 2 to 7: isolated 2, 4, 5, 6, 7 and 8 (VNI), respectively; column 8: isolated 12 (VGI); Columns 9 to 13: isolates 13, 18, 22, 24 and 25 (VNI), respectively.

    Article Snippet: Thirty microliters of the reaction amplicon were doubly digested with Sau96I (10 U/µL) and HhaI (20 U/µL) (New England Biolabs, Uniscience, SP, Brazil), and incubated at 37 °C for 3 hours.

    Techniques: Isolation

    Effect of Tth SSB-255 protein on the efficiency and specificity of RCA. ( a ) Top: RCAs were performed in the absence of the SSB proteins using pUC19 DNA as template and phi29 DNA polymerase for the indicated reaction times. Bottom: Signals of spot hybridization of the same samples. ( b ) Top and Bottom: same as (a), except for the absence of template DNA. ( c ) Top and Bottom: same as (a), except for the presence of the Tth SSB protein (3.0 µg/20 µl reaction volume). ( d ) Top and Bottom: same as (c), except for the absence of template DNA. ( e ) Top and Bottom: same as (a), except for the presence of the Tth SSB-255 protein (3.0 µg/20 µl reaction volume). ( f ) Top and Bottom: same as (e), except for the absence of template DNA.

    Journal: Nucleic Acids Research

    Article Title: Improvements of rolling circle amplification (RCA) efficiency and accuracy using Thermus thermophilus SSB mutant protein

    doi: 10.1093/nar/gkl350

    Figure Lengend Snippet: Effect of Tth SSB-255 protein on the efficiency and specificity of RCA. ( a ) Top: RCAs were performed in the absence of the SSB proteins using pUC19 DNA as template and phi29 DNA polymerase for the indicated reaction times. Bottom: Signals of spot hybridization of the same samples. ( b ) Top and Bottom: same as (a), except for the absence of template DNA. ( c ) Top and Bottom: same as (a), except for the presence of the Tth SSB protein (3.0 µg/20 µl reaction volume). ( d ) Top and Bottom: same as (c), except for the absence of template DNA. ( e ) Top and Bottom: same as (a), except for the presence of the Tth SSB-255 protein (3.0 µg/20 µl reaction volume). ( f ) Top and Bottom: same as (e), except for the absence of template DNA.

    Article Snippet: The denatured DNA was amplified using 0.3 µl Phi29 DNA polymerase (10 U/µl, New England Biolabs) complemented with 2 µl of 10× Phi29 DNA polymerase buffer, 0.2 µl of 100× BSA, 3.2 µl of 2.5 mM dNTP and 1 µl of 20% DMSO (Sigma Aldrich) in a volume of 20 µl at 30°C for ∼24 h. The phi29 DNA polymerase was inactivated at 65°C for 10 min and the amplification product was purified using a spin-column (Sephadex G-50, Amersham Biosciences) to eliminate the un-reacted primers.

    Techniques: Hybridization

    Effect of Tth SSB-255 protein on RCA assays. ( a ) RCAs were carried out in the absence or presence of the indicated SSB proteins using pUC19 DNA as a template and phi29 DNA polymerase. ( b ) Same as (a), except for using linearized ( Eco RI) pUC19 DNA as the template. ( c ) Same as (a), except that the amplifications were carried out in the absence of template DNA. Lane M: molecular weight markers (100 and 12 kb).

    Journal: Nucleic Acids Research

    Article Title: Improvements of rolling circle amplification (RCA) efficiency and accuracy using Thermus thermophilus SSB mutant protein

    doi: 10.1093/nar/gkl350

    Figure Lengend Snippet: Effect of Tth SSB-255 protein on RCA assays. ( a ) RCAs were carried out in the absence or presence of the indicated SSB proteins using pUC19 DNA as a template and phi29 DNA polymerase. ( b ) Same as (a), except for using linearized ( Eco RI) pUC19 DNA as the template. ( c ) Same as (a), except that the amplifications were carried out in the absence of template DNA. Lane M: molecular weight markers (100 and 12 kb).

    Article Snippet: The denatured DNA was amplified using 0.3 µl Phi29 DNA polymerase (10 U/µl, New England Biolabs) complemented with 2 µl of 10× Phi29 DNA polymerase buffer, 0.2 µl of 100× BSA, 3.2 µl of 2.5 mM dNTP and 1 µl of 20% DMSO (Sigma Aldrich) in a volume of 20 µl at 30°C for ∼24 h. The phi29 DNA polymerase was inactivated at 65°C for 10 min and the amplification product was purified using a spin-column (Sephadex G-50, Amersham Biosciences) to eliminate the un-reacted primers.

    Techniques: Molecular Weight