t7 express lysy iq cells  (New England Biolabs)


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    New England Biolabs t7 express lysy iq cells
    T7 Express Lysy Iq Cells, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 96/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    t7 express lysy iq competent e coli  (New England Biolabs)


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    New England Biolabs t7 express lysy iq competent e coli
    T7 Express Lysy Iq Competent E Coli, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    tn5 purification reagents t7 express lysy iq competent e coli  (New England Biolabs)


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    New England Biolabs tn5 purification reagents t7 express lysy iq competent e coli
    ATAC-Me is appropriate for use on a variety of cell types and treatment conditions, including flow sorted samples and in vitro differentiation systems. 200,000 cells are recommended as a starting point (compared to 50,000 in standard ATAC-seq protocols) to compensate for DNA input loss resulting from added experimental steps and sodium bisulfite degradation. Cells are pelleted by centrifugation and resuspended in a gentle lysis buffer to isolate nuclei with intact chromatin (procedure steps 7–14). Nuclei are incubated in <t>Tn5</t> transposition reaction buffer with Tn5 assembled with methylated adaptors, displayed here as a green circle (procedure step 15–20). Tn5 accessible DNA fragments (blue) undergo column-based <t>purification</t> (procedure steps 21–28) followed by oligo replacement (procedure step 29) and gap repair steps to incorporate asymmetric, sequencing-compatible adaptor ends and complete ligation of DNA bottom strands (procedure steps 30–34). Due to the subsequent bisulfite conversion, adaptor sequences and replacement oligonucleotides (green) are methylated to preserve the sequence of the Illumina compatible adaptor ends (sequences are included in Table 1). A small aliquot of the resulting fragment pool is reserved for a quality check PCR amplification prior to bisulfite conversion (procedure steps 35–37). Fragment distribution of high-quality libraries should reflect standard ATAC libraries with nucleosomal banding patterns (procedure step 38). Fragments undergo heat denaturation and sodium bisulfite conversion (procedure steps 39–58) followed by limited PCR amplification and indexing for next generation sequencing (procedure steps 59–68). Indexed primers are depicted as yellow and pink lines. Final libraries should display a fragment distribution between 200–600bp. Figure created with Biorender.com. This schematic is labeled with the corresponding procedure steps.
    Tn5 Purification Reagents T7 Express Lysy Iq Competent E Coli, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/tn5 purification reagents t7 express lysy iq competent e coli/product/New England Biolabs
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    1) Product Images from "Dual detection of chromatin accessibility and DNA methylation using ATAC-Me"

    Article Title: Dual detection of chromatin accessibility and DNA methylation using ATAC-Me

    Journal: Nature protocols

    doi: 10.1038/s41596-021-00608-z

    ATAC-Me is appropriate for use on a variety of cell types and treatment conditions, including flow sorted samples and in vitro differentiation systems. 200,000 cells are recommended as a starting point (compared to 50,000 in standard ATAC-seq protocols) to compensate for DNA input loss resulting from added experimental steps and sodium bisulfite degradation. Cells are pelleted by centrifugation and resuspended in a gentle lysis buffer to isolate nuclei with intact chromatin (procedure steps 7–14). Nuclei are incubated in Tn5 transposition reaction buffer with Tn5 assembled with methylated adaptors, displayed here as a green circle (procedure step 15–20). Tn5 accessible DNA fragments (blue) undergo column-based purification (procedure steps 21–28) followed by oligo replacement (procedure step 29) and gap repair steps to incorporate asymmetric, sequencing-compatible adaptor ends and complete ligation of DNA bottom strands (procedure steps 30–34). Due to the subsequent bisulfite conversion, adaptor sequences and replacement oligonucleotides (green) are methylated to preserve the sequence of the Illumina compatible adaptor ends (sequences are included in Table 1). A small aliquot of the resulting fragment pool is reserved for a quality check PCR amplification prior to bisulfite conversion (procedure steps 35–37). Fragment distribution of high-quality libraries should reflect standard ATAC libraries with nucleosomal banding patterns (procedure step 38). Fragments undergo heat denaturation and sodium bisulfite conversion (procedure steps 39–58) followed by limited PCR amplification and indexing for next generation sequencing (procedure steps 59–68). Indexed primers are depicted as yellow and pink lines. Final libraries should display a fragment distribution between 200–600bp. Figure created with Biorender.com. This schematic is labeled with the corresponding procedure steps.
    Figure Legend Snippet: ATAC-Me is appropriate for use on a variety of cell types and treatment conditions, including flow sorted samples and in vitro differentiation systems. 200,000 cells are recommended as a starting point (compared to 50,000 in standard ATAC-seq protocols) to compensate for DNA input loss resulting from added experimental steps and sodium bisulfite degradation. Cells are pelleted by centrifugation and resuspended in a gentle lysis buffer to isolate nuclei with intact chromatin (procedure steps 7–14). Nuclei are incubated in Tn5 transposition reaction buffer with Tn5 assembled with methylated adaptors, displayed here as a green circle (procedure step 15–20). Tn5 accessible DNA fragments (blue) undergo column-based purification (procedure steps 21–28) followed by oligo replacement (procedure step 29) and gap repair steps to incorporate asymmetric, sequencing-compatible adaptor ends and complete ligation of DNA bottom strands (procedure steps 30–34). Due to the subsequent bisulfite conversion, adaptor sequences and replacement oligonucleotides (green) are methylated to preserve the sequence of the Illumina compatible adaptor ends (sequences are included in Table 1). A small aliquot of the resulting fragment pool is reserved for a quality check PCR amplification prior to bisulfite conversion (procedure steps 35–37). Fragment distribution of high-quality libraries should reflect standard ATAC libraries with nucleosomal banding patterns (procedure step 38). Fragments undergo heat denaturation and sodium bisulfite conversion (procedure steps 39–58) followed by limited PCR amplification and indexing for next generation sequencing (procedure steps 59–68). Indexed primers are depicted as yellow and pink lines. Final libraries should display a fragment distribution between 200–600bp. Figure created with Biorender.com. This schematic is labeled with the corresponding procedure steps.

    Techniques Used: In Vitro, Centrifugation, Gentle, Lysis, Incubation, Methylation, Purification, Sequencing, Ligation, Amplification, Next-Generation Sequencing, Labeling

    tn5 purification reagents t7 express lysy iq competent e coli  (New England Biolabs)


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    New England Biolabs tn5 purification reagents t7 express lysy iq competent e coli
    ATAC-Me is appropriate for use on a variety of cell types and treatment conditions, including flow sorted samples and in vitro differentiation systems. 200,000 cells are recommended as a starting point (compared to 50,000 in standard ATAC-seq protocols) to compensate for DNA input loss resulting from added experimental steps and sodium bisulfite degradation. Cells are pelleted by centrifugation and resuspended in a gentle lysis buffer to isolate nuclei with intact chromatin (procedure steps 7–14). Nuclei are incubated in <t>Tn5</t> transposition reaction buffer with Tn5 assembled with methylated adaptors, displayed here as a green circle (procedure step 15–20). Tn5 accessible DNA fragments (blue) undergo column-based <t>purification</t> (procedure steps 21–28) followed by oligo replacement (procedure step 29) and gap repair steps to incorporate asymmetric, sequencing-compatible adaptor ends and complete ligation of DNA bottom strands (procedure steps 30–34). Due to the subsequent bisulfite conversion, adaptor sequences and replacement oligonucleotides (green) are methylated to preserve the sequence of the Illumina compatible adaptor ends (sequences are included in Table 1). A small aliquot of the resulting fragment pool is reserved for a quality check PCR amplification prior to bisulfite conversion (procedure steps 35–37). Fragment distribution of high-quality libraries should reflect standard ATAC libraries with nucleosomal banding patterns (procedure step 38). Fragments undergo heat denaturation and sodium bisulfite conversion (procedure steps 39–58) followed by limited PCR amplification and indexing for next generation sequencing (procedure steps 59–68). Indexed primers are depicted as yellow and pink lines. Final libraries should display a fragment distribution between 200–600bp. Figure created with Biorender.com. This schematic is labeled with the corresponding procedure steps.
    Tn5 Purification Reagents T7 Express Lysy Iq Competent E Coli, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/tn5 purification reagents t7 express lysy iq competent e coli/product/New England Biolabs
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    1) Product Images from "Dual detection of chromatin accessibility and DNA methylation using ATAC-Me"

    Article Title: Dual detection of chromatin accessibility and DNA methylation using ATAC-Me

    Journal: Nature protocols

    doi: 10.1038/s41596-021-00608-z

    ATAC-Me is appropriate for use on a variety of cell types and treatment conditions, including flow sorted samples and in vitro differentiation systems. 200,000 cells are recommended as a starting point (compared to 50,000 in standard ATAC-seq protocols) to compensate for DNA input loss resulting from added experimental steps and sodium bisulfite degradation. Cells are pelleted by centrifugation and resuspended in a gentle lysis buffer to isolate nuclei with intact chromatin (procedure steps 7–14). Nuclei are incubated in Tn5 transposition reaction buffer with Tn5 assembled with methylated adaptors, displayed here as a green circle (procedure step 15–20). Tn5 accessible DNA fragments (blue) undergo column-based purification (procedure steps 21–28) followed by oligo replacement (procedure step 29) and gap repair steps to incorporate asymmetric, sequencing-compatible adaptor ends and complete ligation of DNA bottom strands (procedure steps 30–34). Due to the subsequent bisulfite conversion, adaptor sequences and replacement oligonucleotides (green) are methylated to preserve the sequence of the Illumina compatible adaptor ends (sequences are included in Table 1). A small aliquot of the resulting fragment pool is reserved for a quality check PCR amplification prior to bisulfite conversion (procedure steps 35–37). Fragment distribution of high-quality libraries should reflect standard ATAC libraries with nucleosomal banding patterns (procedure step 38). Fragments undergo heat denaturation and sodium bisulfite conversion (procedure steps 39–58) followed by limited PCR amplification and indexing for next generation sequencing (procedure steps 59–68). Indexed primers are depicted as yellow and pink lines. Final libraries should display a fragment distribution between 200–600bp. Figure created with Biorender.com. This schematic is labeled with the corresponding procedure steps.
    Figure Legend Snippet: ATAC-Me is appropriate for use on a variety of cell types and treatment conditions, including flow sorted samples and in vitro differentiation systems. 200,000 cells are recommended as a starting point (compared to 50,000 in standard ATAC-seq protocols) to compensate for DNA input loss resulting from added experimental steps and sodium bisulfite degradation. Cells are pelleted by centrifugation and resuspended in a gentle lysis buffer to isolate nuclei with intact chromatin (procedure steps 7–14). Nuclei are incubated in Tn5 transposition reaction buffer with Tn5 assembled with methylated adaptors, displayed here as a green circle (procedure step 15–20). Tn5 accessible DNA fragments (blue) undergo column-based purification (procedure steps 21–28) followed by oligo replacement (procedure step 29) and gap repair steps to incorporate asymmetric, sequencing-compatible adaptor ends and complete ligation of DNA bottom strands (procedure steps 30–34). Due to the subsequent bisulfite conversion, adaptor sequences and replacement oligonucleotides (green) are methylated to preserve the sequence of the Illumina compatible adaptor ends (sequences are included in Table 1). A small aliquot of the resulting fragment pool is reserved for a quality check PCR amplification prior to bisulfite conversion (procedure steps 35–37). Fragment distribution of high-quality libraries should reflect standard ATAC libraries with nucleosomal banding patterns (procedure step 38). Fragments undergo heat denaturation and sodium bisulfite conversion (procedure steps 39–58) followed by limited PCR amplification and indexing for next generation sequencing (procedure steps 59–68). Indexed primers are depicted as yellow and pink lines. Final libraries should display a fragment distribution between 200–600bp. Figure created with Biorender.com. This schematic is labeled with the corresponding procedure steps.

    Techniques Used: In Vitro, Centrifugation, Gentle, Lysis, Incubation, Methylation, Purification, Sequencing, Ligation, Amplification, Next-Generation Sequencing, Labeling

    t7 express lysy iq competent e coli  (New England Biolabs)


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    New England Biolabs t7 express lysy iq competent e coli
    T7 Express Lysy Iq Competent E Coli, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    t7 express lysy iq cells  (New England Biolabs)


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    T7 Express Lysy Iq Cells, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 96/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    c3013 e coli  (New England Biolabs)


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    e coli bl21 t7 express lysy iq cells  (New England Biolabs)


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    E Coli Bl21 T7 Express Lysy Iq Cells, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 96/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    t7 express lysy iq competent e coli  (New England Biolabs)


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    T7 Express Lysy Iq Competent E Coli, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 96/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    c3013 cells  (New England Biolabs)


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    t7 expression competent e coli  (New England Biolabs)


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    New England Biolabs t7 express lysy iq cells
    T7 Express Lysy Iq Cells, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 96/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    New England Biolabs t7 express lysy iq competent e coli
    T7 Express Lysy Iq Competent E Coli, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    New England Biolabs tn5 purification reagents t7 express lysy iq competent e coli
    ATAC-Me is appropriate for use on a variety of cell types and treatment conditions, including flow sorted samples and in vitro differentiation systems. 200,000 cells are recommended as a starting point (compared to 50,000 in standard ATAC-seq protocols) to compensate for DNA input loss resulting from added experimental steps and sodium bisulfite degradation. Cells are pelleted by centrifugation and resuspended in a gentle lysis buffer to isolate nuclei with intact chromatin (procedure steps 7–14). Nuclei are incubated in <t>Tn5</t> transposition reaction buffer with Tn5 assembled with methylated adaptors, displayed here as a green circle (procedure step 15–20). Tn5 accessible DNA fragments (blue) undergo column-based <t>purification</t> (procedure steps 21–28) followed by oligo replacement (procedure step 29) and gap repair steps to incorporate asymmetric, sequencing-compatible adaptor ends and complete ligation of DNA bottom strands (procedure steps 30–34). Due to the subsequent bisulfite conversion, adaptor sequences and replacement oligonucleotides (green) are methylated to preserve the sequence of the Illumina compatible adaptor ends (sequences are included in Table 1). A small aliquot of the resulting fragment pool is reserved for a quality check PCR amplification prior to bisulfite conversion (procedure steps 35–37). Fragment distribution of high-quality libraries should reflect standard ATAC libraries with nucleosomal banding patterns (procedure step 38). Fragments undergo heat denaturation and sodium bisulfite conversion (procedure steps 39–58) followed by limited PCR amplification and indexing for next generation sequencing (procedure steps 59–68). Indexed primers are depicted as yellow and pink lines. Final libraries should display a fragment distribution between 200–600bp. Figure created with Biorender.com. This schematic is labeled with the corresponding procedure steps.
    Tn5 Purification Reagents T7 Express Lysy Iq Competent E Coli, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/tn5 purification reagents t7 express lysy iq competent e coli/product/New England Biolabs
    Average 86 stars, based on 1 article reviews
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    New England Biolabs c3013 e coli
    ATAC-Me is appropriate for use on a variety of cell types and treatment conditions, including flow sorted samples and in vitro differentiation systems. 200,000 cells are recommended as a starting point (compared to 50,000 in standard ATAC-seq protocols) to compensate for DNA input loss resulting from added experimental steps and sodium bisulfite degradation. Cells are pelleted by centrifugation and resuspended in a gentle lysis buffer to isolate nuclei with intact chromatin (procedure steps 7–14). Nuclei are incubated in <t>Tn5</t> transposition reaction buffer with Tn5 assembled with methylated adaptors, displayed here as a green circle (procedure step 15–20). Tn5 accessible DNA fragments (blue) undergo column-based <t>purification</t> (procedure steps 21–28) followed by oligo replacement (procedure step 29) and gap repair steps to incorporate asymmetric, sequencing-compatible adaptor ends and complete ligation of DNA bottom strands (procedure steps 30–34). Due to the subsequent bisulfite conversion, adaptor sequences and replacement oligonucleotides (green) are methylated to preserve the sequence of the Illumina compatible adaptor ends (sequences are included in Table 1). A small aliquot of the resulting fragment pool is reserved for a quality check PCR amplification prior to bisulfite conversion (procedure steps 35–37). Fragment distribution of high-quality libraries should reflect standard ATAC libraries with nucleosomal banding patterns (procedure step 38). Fragments undergo heat denaturation and sodium bisulfite conversion (procedure steps 39–58) followed by limited PCR amplification and indexing for next generation sequencing (procedure steps 59–68). Indexed primers are depicted as yellow and pink lines. Final libraries should display a fragment distribution between 200–600bp. Figure created with Biorender.com. This schematic is labeled with the corresponding procedure steps.
    C3013 E Coli, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 96/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/c3013 e coli/product/New England Biolabs
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    New England Biolabs e coli bl21 t7 express lysy iq cells
    ATAC-Me is appropriate for use on a variety of cell types and treatment conditions, including flow sorted samples and in vitro differentiation systems. 200,000 cells are recommended as a starting point (compared to 50,000 in standard ATAC-seq protocols) to compensate for DNA input loss resulting from added experimental steps and sodium bisulfite degradation. Cells are pelleted by centrifugation and resuspended in a gentle lysis buffer to isolate nuclei with intact chromatin (procedure steps 7–14). Nuclei are incubated in <t>Tn5</t> transposition reaction buffer with Tn5 assembled with methylated adaptors, displayed here as a green circle (procedure step 15–20). Tn5 accessible DNA fragments (blue) undergo column-based <t>purification</t> (procedure steps 21–28) followed by oligo replacement (procedure step 29) and gap repair steps to incorporate asymmetric, sequencing-compatible adaptor ends and complete ligation of DNA bottom strands (procedure steps 30–34). Due to the subsequent bisulfite conversion, adaptor sequences and replacement oligonucleotides (green) are methylated to preserve the sequence of the Illumina compatible adaptor ends (sequences are included in Table 1). A small aliquot of the resulting fragment pool is reserved for a quality check PCR amplification prior to bisulfite conversion (procedure steps 35–37). Fragment distribution of high-quality libraries should reflect standard ATAC libraries with nucleosomal banding patterns (procedure step 38). Fragments undergo heat denaturation and sodium bisulfite conversion (procedure steps 39–58) followed by limited PCR amplification and indexing for next generation sequencing (procedure steps 59–68). Indexed primers are depicted as yellow and pink lines. Final libraries should display a fragment distribution between 200–600bp. Figure created with Biorender.com. This schematic is labeled with the corresponding procedure steps.
    E Coli Bl21 T7 Express Lysy Iq Cells, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 96/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    New England Biolabs c3013 cells
    ATAC-Me is appropriate for use on a variety of cell types and treatment conditions, including flow sorted samples and in vitro differentiation systems. 200,000 cells are recommended as a starting point (compared to 50,000 in standard ATAC-seq protocols) to compensate for DNA input loss resulting from added experimental steps and sodium bisulfite degradation. Cells are pelleted by centrifugation and resuspended in a gentle lysis buffer to isolate nuclei with intact chromatin (procedure steps 7–14). Nuclei are incubated in <t>Tn5</t> transposition reaction buffer with Tn5 assembled with methylated adaptors, displayed here as a green circle (procedure step 15–20). Tn5 accessible DNA fragments (blue) undergo column-based <t>purification</t> (procedure steps 21–28) followed by oligo replacement (procedure step 29) and gap repair steps to incorporate asymmetric, sequencing-compatible adaptor ends and complete ligation of DNA bottom strands (procedure steps 30–34). Due to the subsequent bisulfite conversion, adaptor sequences and replacement oligonucleotides (green) are methylated to preserve the sequence of the Illumina compatible adaptor ends (sequences are included in Table 1). A small aliquot of the resulting fragment pool is reserved for a quality check PCR amplification prior to bisulfite conversion (procedure steps 35–37). Fragment distribution of high-quality libraries should reflect standard ATAC libraries with nucleosomal banding patterns (procedure step 38). Fragments undergo heat denaturation and sodium bisulfite conversion (procedure steps 39–58) followed by limited PCR amplification and indexing for next generation sequencing (procedure steps 59–68). Indexed primers are depicted as yellow and pink lines. Final libraries should display a fragment distribution between 200–600bp. Figure created with Biorender.com. This schematic is labeled with the corresponding procedure steps.
    C3013 Cells, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 96/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    New England Biolabs t7 expression competent e coli
    ATAC-Me is appropriate for use on a variety of cell types and treatment conditions, including flow sorted samples and in vitro differentiation systems. 200,000 cells are recommended as a starting point (compared to 50,000 in standard ATAC-seq protocols) to compensate for DNA input loss resulting from added experimental steps and sodium bisulfite degradation. Cells are pelleted by centrifugation and resuspended in a gentle lysis buffer to isolate nuclei with intact chromatin (procedure steps 7–14). Nuclei are incubated in <t>Tn5</t> transposition reaction buffer with Tn5 assembled with methylated adaptors, displayed here as a green circle (procedure step 15–20). Tn5 accessible DNA fragments (blue) undergo column-based <t>purification</t> (procedure steps 21–28) followed by oligo replacement (procedure step 29) and gap repair steps to incorporate asymmetric, sequencing-compatible adaptor ends and complete ligation of DNA bottom strands (procedure steps 30–34). Due to the subsequent bisulfite conversion, adaptor sequences and replacement oligonucleotides (green) are methylated to preserve the sequence of the Illumina compatible adaptor ends (sequences are included in Table 1). A small aliquot of the resulting fragment pool is reserved for a quality check PCR amplification prior to bisulfite conversion (procedure steps 35–37). Fragment distribution of high-quality libraries should reflect standard ATAC libraries with nucleosomal banding patterns (procedure step 38). Fragments undergo heat denaturation and sodium bisulfite conversion (procedure steps 39–58) followed by limited PCR amplification and indexing for next generation sequencing (procedure steps 59–68). Indexed primers are depicted as yellow and pink lines. Final libraries should display a fragment distribution between 200–600bp. Figure created with Biorender.com. This schematic is labeled with the corresponding procedure steps.
    T7 Expression Competent E Coli, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 96/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    ATAC-Me is appropriate for use on a variety of cell types and treatment conditions, including flow sorted samples and in vitro differentiation systems. 200,000 cells are recommended as a starting point (compared to 50,000 in standard ATAC-seq protocols) to compensate for DNA input loss resulting from added experimental steps and sodium bisulfite degradation. Cells are pelleted by centrifugation and resuspended in a gentle lysis buffer to isolate nuclei with intact chromatin (procedure steps 7–14). Nuclei are incubated in Tn5 transposition reaction buffer with Tn5 assembled with methylated adaptors, displayed here as a green circle (procedure step 15–20). Tn5 accessible DNA fragments (blue) undergo column-based purification (procedure steps 21–28) followed by oligo replacement (procedure step 29) and gap repair steps to incorporate asymmetric, sequencing-compatible adaptor ends and complete ligation of DNA bottom strands (procedure steps 30–34). Due to the subsequent bisulfite conversion, adaptor sequences and replacement oligonucleotides (green) are methylated to preserve the sequence of the Illumina compatible adaptor ends (sequences are included in Table 1). A small aliquot of the resulting fragment pool is reserved for a quality check PCR amplification prior to bisulfite conversion (procedure steps 35–37). Fragment distribution of high-quality libraries should reflect standard ATAC libraries with nucleosomal banding patterns (procedure step 38). Fragments undergo heat denaturation and sodium bisulfite conversion (procedure steps 39–58) followed by limited PCR amplification and indexing for next generation sequencing (procedure steps 59–68). Indexed primers are depicted as yellow and pink lines. Final libraries should display a fragment distribution between 200–600bp. Figure created with Biorender.com. This schematic is labeled with the corresponding procedure steps.

    Journal: Nature protocols

    Article Title: Dual detection of chromatin accessibility and DNA methylation using ATAC-Me

    doi: 10.1038/s41596-021-00608-z

    Figure Lengend Snippet: ATAC-Me is appropriate for use on a variety of cell types and treatment conditions, including flow sorted samples and in vitro differentiation systems. 200,000 cells are recommended as a starting point (compared to 50,000 in standard ATAC-seq protocols) to compensate for DNA input loss resulting from added experimental steps and sodium bisulfite degradation. Cells are pelleted by centrifugation and resuspended in a gentle lysis buffer to isolate nuclei with intact chromatin (procedure steps 7–14). Nuclei are incubated in Tn5 transposition reaction buffer with Tn5 assembled with methylated adaptors, displayed here as a green circle (procedure step 15–20). Tn5 accessible DNA fragments (blue) undergo column-based purification (procedure steps 21–28) followed by oligo replacement (procedure step 29) and gap repair steps to incorporate asymmetric, sequencing-compatible adaptor ends and complete ligation of DNA bottom strands (procedure steps 30–34). Due to the subsequent bisulfite conversion, adaptor sequences and replacement oligonucleotides (green) are methylated to preserve the sequence of the Illumina compatible adaptor ends (sequences are included in Table 1). A small aliquot of the resulting fragment pool is reserved for a quality check PCR amplification prior to bisulfite conversion (procedure steps 35–37). Fragment distribution of high-quality libraries should reflect standard ATAC libraries with nucleosomal banding patterns (procedure step 38). Fragments undergo heat denaturation and sodium bisulfite conversion (procedure steps 39–58) followed by limited PCR amplification and indexing for next generation sequencing (procedure steps 59–68). Indexed primers are depicted as yellow and pink lines. Final libraries should display a fragment distribution between 200–600bp. Figure created with Biorender.com. This schematic is labeled with the corresponding procedure steps.

    Article Snippet: Nuclease free water. . Tn5 purification reagents T7 Express lysY/Iq Competent E. coli (NEB, cat. no. C3013l).

    Techniques: In Vitro, Centrifugation, Gentle, Lysis, Incubation, Methylation, Purification, Sequencing, Ligation, Amplification, Next-Generation Sequencing, Labeling