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Pol III co-occupies methylated SINEs with MBPs. ( a ) Semiquantitative ChIP assay in A31 fibroblasts showing specific binding of TFIIIB, TFIIIC and pol III to B1 and B2 loci, as well as 7SL , but not the Apo-E gene. Histone H3 and TAF I 48 provide positive and negative controls, respectively. ( b ) Semiquantitative ChIP assay in <t>HeLa</t> cells showing occupancy of pol III, TFIIIB and TFIIIC at Alu loci from chromosomes 6, 10, 19 and 22, as well as 7SL and Apo-E genes. ChIPs for histone H3 and TAF I 48 provide positive and negative controls, respectively. No antibody was used for the mock sample. ( c ) Mean±s.e.m. of the percentage input bound in three independent ChIP–quantitative PCR (qPCR) assays in HeLa cells, of the indicated proteins at individual Alu loci from chromosomes 6, 10, 19 and 22, as well as 7SL and Apo-E loci and Alu PV subfamily consensus. ChIPs for histone H3 and TAF I 48 provide positive and negative controls, respectively. No antibody was used for the mock samples. P values are calculated by t -test. ( d ) Mean±s.e.m. of four independent sequential ChIP–qPCR assays in which <t>DNA</t> immunoprecipitated from HeLa cells using pol III antibody was reprecipitated using antibodies against pol III, TFIIIB, TAF I 48 (negative control), MBD1, MBD2 and MeCP2, as indicated. No TAF I 48 signal was detected on Alu(c6).
Hela Input Dna, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 89/100, based on 10 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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1) Product Images from "SINE transcription by RNA polymerase III is suppressed by histone methylation but not by DNA methylation"

Article Title: SINE transcription by RNA polymerase III is suppressed by histone methylation but not by DNA methylation

Journal: Nature Communications

doi: 10.1038/ncomms7569

Pol III co-occupies methylated SINEs with MBPs. ( a ) Semiquantitative ChIP assay in A31 fibroblasts showing specific binding of TFIIIB, TFIIIC and pol III to B1 and B2 loci, as well as 7SL , but not the Apo-E gene. Histone H3 and TAF I 48 provide positive and negative controls, respectively. ( b ) Semiquantitative ChIP assay in HeLa cells showing occupancy of pol III, TFIIIB and TFIIIC at Alu loci from chromosomes 6, 10, 19 and 22, as well as 7SL and Apo-E genes. ChIPs for histone H3 and TAF I 48 provide positive and negative controls, respectively. No antibody was used for the mock sample. ( c ) Mean±s.e.m. of the percentage input bound in three independent ChIP–quantitative PCR (qPCR) assays in HeLa cells, of the indicated proteins at individual Alu loci from chromosomes 6, 10, 19 and 22, as well as 7SL and Apo-E loci and Alu PV subfamily consensus. ChIPs for histone H3 and TAF I 48 provide positive and negative controls, respectively. No antibody was used for the mock samples. P values are calculated by t -test. ( d ) Mean±s.e.m. of four independent sequential ChIP–qPCR assays in which DNA immunoprecipitated from HeLa cells using pol III antibody was reprecipitated using antibodies against pol III, TFIIIB, TAF I 48 (negative control), MBD1, MBD2 and MeCP2, as indicated. No TAF I 48 signal was detected on Alu(c6).
Figure Legend Snippet: Pol III co-occupies methylated SINEs with MBPs. ( a ) Semiquantitative ChIP assay in A31 fibroblasts showing specific binding of TFIIIB, TFIIIC and pol III to B1 and B2 loci, as well as 7SL , but not the Apo-E gene. Histone H3 and TAF I 48 provide positive and negative controls, respectively. ( b ) Semiquantitative ChIP assay in HeLa cells showing occupancy of pol III, TFIIIB and TFIIIC at Alu loci from chromosomes 6, 10, 19 and 22, as well as 7SL and Apo-E genes. ChIPs for histone H3 and TAF I 48 provide positive and negative controls, respectively. No antibody was used for the mock sample. ( c ) Mean±s.e.m. of the percentage input bound in three independent ChIP–quantitative PCR (qPCR) assays in HeLa cells, of the indicated proteins at individual Alu loci from chromosomes 6, 10, 19 and 22, as well as 7SL and Apo-E loci and Alu PV subfamily consensus. ChIPs for histone H3 and TAF I 48 provide positive and negative controls, respectively. No antibody was used for the mock samples. P values are calculated by t -test. ( d ) Mean±s.e.m. of four independent sequential ChIP–qPCR assays in which DNA immunoprecipitated from HeLa cells using pol III antibody was reprecipitated using antibodies against pol III, TFIIIB, TAF I 48 (negative control), MBD1, MBD2 and MeCP2, as indicated. No TAF I 48 signal was detected on Alu(c6).

Techniques Used: Methylation, Chromatin Immunoprecipitation, Binding Assay, Real-time Polymerase Chain Reaction, Immunoprecipitation, Negative Control

SINE expression is not stimulated by loss of DNA methylation. ( a ) Analysis by semiquantitative RT–PCR of expression levels of the indicated transcripts in matched Dnmt1 +/+ and Dnmt1 −/− fibroblasts. Duplicate samples are shown for both cell types. Apo-E and p53BP2 mRNAs provide controls that have been documented as being suppressed by DNA methylation. GAPDH mRNA provides a loading control. ( b ) Analysis by semiquantitative RT–PCR of expression levels of the indicated transcripts in mouse ES cells treated for 16 h with (+) or without (−) 5-azacytidine. Apo-E mRNA provides a control that has been documented as being inhibited by DNA methylation. ARPP P0 mRNA provides a loading control. ( c ) Analysis by semiquantitative RT–PCR of expression levels of the indicated transcripts in HeLa cells treated for 72 h with 5-azacytidine. Apo-E mRNA provides a control that has been documented as being inhibited by DNA methylation. ARPP P0 mRNA provides a loading control. ( d ) Analysis by primer extension of Alu transcripts in the RNA from Fig. 5c . Bracket indicates ~240 bp products that initiate at the principle pol III start site of Alu. Reverse transcriptase was omitted from the reactions in lanes 1 and 2. To confirm that the assay was not saturated, raising the amount of template RNA from 5 (lanes 5 and 6) to 10 μg (lanes 3 and 4) is shown to give a stronger signal. Alu, B1 and B2 RT–PCRs were performed with Alu, B1 and B2 consensus primers, respectively ( Supplementary Table 1 ).
Figure Legend Snippet: SINE expression is not stimulated by loss of DNA methylation. ( a ) Analysis by semiquantitative RT–PCR of expression levels of the indicated transcripts in matched Dnmt1 +/+ and Dnmt1 −/− fibroblasts. Duplicate samples are shown for both cell types. Apo-E and p53BP2 mRNAs provide controls that have been documented as being suppressed by DNA methylation. GAPDH mRNA provides a loading control. ( b ) Analysis by semiquantitative RT–PCR of expression levels of the indicated transcripts in mouse ES cells treated for 16 h with (+) or without (−) 5-azacytidine. Apo-E mRNA provides a control that has been documented as being inhibited by DNA methylation. ARPP P0 mRNA provides a loading control. ( c ) Analysis by semiquantitative RT–PCR of expression levels of the indicated transcripts in HeLa cells treated for 72 h with 5-azacytidine. Apo-E mRNA provides a control that has been documented as being inhibited by DNA methylation. ARPP P0 mRNA provides a loading control. ( d ) Analysis by primer extension of Alu transcripts in the RNA from Fig. 5c . Bracket indicates ~240 bp products that initiate at the principle pol III start site of Alu. Reverse transcriptase was omitted from the reactions in lanes 1 and 2. To confirm that the assay was not saturated, raising the amount of template RNA from 5 (lanes 5 and 6) to 10 μg (lanes 3 and 4) is shown to give a stronger signal. Alu, B1 and B2 RT–PCRs were performed with Alu, B1 and B2 consensus primers, respectively ( Supplementary Table 1 ).

Techniques Used: Expressing, DNA Methylation Assay, Reverse Transcription Polymerase Chain Reaction

DNA methylation does not prevent pol III occupancy of SINEs. ( a ) Percentage input bound in three independent ChIP–quantitative PCR (qPCR) assays with mouse ES cells treated for 16 h with (+) or without (−) 5-azacytidine, showing occupancy of MBD2, MeCP2 and pol III at 7SL, B1 and B2 loci, as well as an Alu inserted onto chromosomes 14 and 17. ChIPs for TAF I 48 and without antibody (mock) provide negative controls. ( b ) Percentage input bound in three independent ChIP–qPCR assays with HeLa cells treated for 72 h with (+) or without (−) 5-azacytidine, showing the binding of MBD2, TFIIIB, TFIIIC and pol III to DNA centred over the body of Alu(c22) or 200 bp downstream. The resolution of this assay is limited by the size of the genomic DNA fragments (~500 bp). ( c ) Percentage input bound in two independent ChIP–qPCR assays with matched Dnmt1 +/+ and Dnmt1 −/− fibroblasts showing occupancy of MBD2, TFIIIB, TFIIIC and pol III at B1 and B2 loci, as well as 7SL and Apo-E genes. ChIPs for TAF I 48 and without antibody (mock) provide negative controls. Error bars indicate s.e.m. and all P values are calculated by t -test.
Figure Legend Snippet: DNA methylation does not prevent pol III occupancy of SINEs. ( a ) Percentage input bound in three independent ChIP–quantitative PCR (qPCR) assays with mouse ES cells treated for 16 h with (+) or without (−) 5-azacytidine, showing occupancy of MBD2, MeCP2 and pol III at 7SL, B1 and B2 loci, as well as an Alu inserted onto chromosomes 14 and 17. ChIPs for TAF I 48 and without antibody (mock) provide negative controls. ( b ) Percentage input bound in three independent ChIP–qPCR assays with HeLa cells treated for 72 h with (+) or without (−) 5-azacytidine, showing the binding of MBD2, TFIIIB, TFIIIC and pol III to DNA centred over the body of Alu(c22) or 200 bp downstream. The resolution of this assay is limited by the size of the genomic DNA fragments (~500 bp). ( c ) Percentage input bound in two independent ChIP–qPCR assays with matched Dnmt1 +/+ and Dnmt1 −/− fibroblasts showing occupancy of MBD2, TFIIIB, TFIIIC and pol III at B1 and B2 loci, as well as 7SL and Apo-E genes. ChIPs for TAF I 48 and without antibody (mock) provide negative controls. Error bars indicate s.e.m. and all P values are calculated by t -test.

Techniques Used: DNA Methylation Assay, Chromatin Immunoprecipitation, Real-time Polymerase Chain Reaction, Binding Assay

Related Articles

Sequencing:

Article Title: SINE transcription by RNA polymerase III is suppressed by histone methylation but not by DNA methylation
Article Snippet: .. ChIP-BS-Seq library preparation and sequencing For HeLa input DNA, two libraries were prepared from the same input DNA: one with starting quantity of 10 ng, following the Illumina ChIP-Seq library protocol, with the addition of bisulfite conversion after addition of adaptors but before amplification; and one following the Illumina Bisulfite Sequencing protocol, including the recommended starting amount. .. All libraries included addition of 2% sheared lambda DNA to control for bisulfite conversion.

Methylation Sequencing:

Article Title: SINE transcription by RNA polymerase III is suppressed by histone methylation but not by DNA methylation
Article Snippet: .. ChIP-BS-Seq library preparation and sequencing For HeLa input DNA, two libraries were prepared from the same input DNA: one with starting quantity of 10 ng, following the Illumina ChIP-Seq library protocol, with the addition of bisulfite conversion after addition of adaptors but before amplification; and one following the Illumina Bisulfite Sequencing protocol, including the recommended starting amount. .. All libraries included addition of 2% sheared lambda DNA to control for bisulfite conversion.

Amplification:

Article Title: SINE transcription by RNA polymerase III is suppressed by histone methylation but not by DNA methylation
Article Snippet: .. ChIP-BS-Seq library preparation and sequencing For HeLa input DNA, two libraries were prepared from the same input DNA: one with starting quantity of 10 ng, following the Illumina ChIP-Seq library protocol, with the addition of bisulfite conversion after addition of adaptors but before amplification; and one following the Illumina Bisulfite Sequencing protocol, including the recommended starting amount. .. All libraries included addition of 2% sheared lambda DNA to control for bisulfite conversion.

Chromatin Immunoprecipitation:

Article Title: SINE transcription by RNA polymerase III is suppressed by histone methylation but not by DNA methylation
Article Snippet: .. ChIP-BS-Seq library preparation and sequencing For HeLa input DNA, two libraries were prepared from the same input DNA: one with starting quantity of 10 ng, following the Illumina ChIP-Seq library protocol, with the addition of bisulfite conversion after addition of adaptors but before amplification; and one following the Illumina Bisulfite Sequencing protocol, including the recommended starting amount. .. All libraries included addition of 2% sheared lambda DNA to control for bisulfite conversion.

ChIP-sequencing:

Article Title: SINE transcription by RNA polymerase III is suppressed by histone methylation but not by DNA methylation
Article Snippet: .. ChIP-BS-Seq library preparation and sequencing For HeLa input DNA, two libraries were prepared from the same input DNA: one with starting quantity of 10 ng, following the Illumina ChIP-Seq library protocol, with the addition of bisulfite conversion after addition of adaptors but before amplification; and one following the Illumina Bisulfite Sequencing protocol, including the recommended starting amount. .. All libraries included addition of 2% sheared lambda DNA to control for bisulfite conversion.

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    Illumina Inc hela input dna
    Pol III co-occupies methylated SINEs with MBPs. ( a ) Semiquantitative ChIP assay in A31 fibroblasts showing specific binding of TFIIIB, TFIIIC and pol III to B1 and B2 loci, as well as 7SL , but not the Apo-E gene. Histone H3 and TAF I 48 provide positive and negative controls, respectively. ( b ) Semiquantitative ChIP assay in <t>HeLa</t> cells showing occupancy of pol III, TFIIIB and TFIIIC at Alu loci from chromosomes 6, 10, 19 and 22, as well as 7SL and Apo-E genes. ChIPs for histone H3 and TAF I 48 provide positive and negative controls, respectively. No antibody was used for the mock sample. ( c ) Mean±s.e.m. of the percentage input bound in three independent ChIP–quantitative PCR (qPCR) assays in HeLa cells, of the indicated proteins at individual Alu loci from chromosomes 6, 10, 19 and 22, as well as 7SL and Apo-E loci and Alu PV subfamily consensus. ChIPs for histone H3 and TAF I 48 provide positive and negative controls, respectively. No antibody was used for the mock samples. P values are calculated by t -test. ( d ) Mean±s.e.m. of four independent sequential ChIP–qPCR assays in which <t>DNA</t> immunoprecipitated from HeLa cells using pol III antibody was reprecipitated using antibodies against pol III, TFIIIB, TAF I 48 (negative control), MBD1, MBD2 and MeCP2, as indicated. No TAF I 48 signal was detected on Alu(c6).
    Hela Input Dna, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 89/100, based on 10 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/hela input dna/product/Illumina Inc
    Average 89 stars, based on 10 article reviews
    Price from $9.99 to $1999.99
    hela input dna - by Bioz Stars, 2020-08
    89/100 stars
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    Pol III co-occupies methylated SINEs with MBPs. ( a ) Semiquantitative ChIP assay in A31 fibroblasts showing specific binding of TFIIIB, TFIIIC and pol III to B1 and B2 loci, as well as 7SL , but not the Apo-E gene. Histone H3 and TAF I 48 provide positive and negative controls, respectively. ( b ) Semiquantitative ChIP assay in HeLa cells showing occupancy of pol III, TFIIIB and TFIIIC at Alu loci from chromosomes 6, 10, 19 and 22, as well as 7SL and Apo-E genes. ChIPs for histone H3 and TAF I 48 provide positive and negative controls, respectively. No antibody was used for the mock sample. ( c ) Mean±s.e.m. of the percentage input bound in three independent ChIP–quantitative PCR (qPCR) assays in HeLa cells, of the indicated proteins at individual Alu loci from chromosomes 6, 10, 19 and 22, as well as 7SL and Apo-E loci and Alu PV subfamily consensus. ChIPs for histone H3 and TAF I 48 provide positive and negative controls, respectively. No antibody was used for the mock samples. P values are calculated by t -test. ( d ) Mean±s.e.m. of four independent sequential ChIP–qPCR assays in which DNA immunoprecipitated from HeLa cells using pol III antibody was reprecipitated using antibodies against pol III, TFIIIB, TAF I 48 (negative control), MBD1, MBD2 and MeCP2, as indicated. No TAF I 48 signal was detected on Alu(c6).

    Journal: Nature Communications

    Article Title: SINE transcription by RNA polymerase III is suppressed by histone methylation but not by DNA methylation

    doi: 10.1038/ncomms7569

    Figure Lengend Snippet: Pol III co-occupies methylated SINEs with MBPs. ( a ) Semiquantitative ChIP assay in A31 fibroblasts showing specific binding of TFIIIB, TFIIIC and pol III to B1 and B2 loci, as well as 7SL , but not the Apo-E gene. Histone H3 and TAF I 48 provide positive and negative controls, respectively. ( b ) Semiquantitative ChIP assay in HeLa cells showing occupancy of pol III, TFIIIB and TFIIIC at Alu loci from chromosomes 6, 10, 19 and 22, as well as 7SL and Apo-E genes. ChIPs for histone H3 and TAF I 48 provide positive and negative controls, respectively. No antibody was used for the mock sample. ( c ) Mean±s.e.m. of the percentage input bound in three independent ChIP–quantitative PCR (qPCR) assays in HeLa cells, of the indicated proteins at individual Alu loci from chromosomes 6, 10, 19 and 22, as well as 7SL and Apo-E loci and Alu PV subfamily consensus. ChIPs for histone H3 and TAF I 48 provide positive and negative controls, respectively. No antibody was used for the mock samples. P values are calculated by t -test. ( d ) Mean±s.e.m. of four independent sequential ChIP–qPCR assays in which DNA immunoprecipitated from HeLa cells using pol III antibody was reprecipitated using antibodies against pol III, TFIIIB, TAF I 48 (negative control), MBD1, MBD2 and MeCP2, as indicated. No TAF I 48 signal was detected on Alu(c6).

    Article Snippet: ChIP-BS-Seq library preparation and sequencing For HeLa input DNA, two libraries were prepared from the same input DNA: one with starting quantity of 10 ng, following the Illumina ChIP-Seq library protocol, with the addition of bisulfite conversion after addition of adaptors but before amplification; and one following the Illumina Bisulfite Sequencing protocol, including the recommended starting amount.

    Techniques: Methylation, Chromatin Immunoprecipitation, Binding Assay, Real-time Polymerase Chain Reaction, Immunoprecipitation, Negative Control

    SINE expression is not stimulated by loss of DNA methylation. ( a ) Analysis by semiquantitative RT–PCR of expression levels of the indicated transcripts in matched Dnmt1 +/+ and Dnmt1 −/− fibroblasts. Duplicate samples are shown for both cell types. Apo-E and p53BP2 mRNAs provide controls that have been documented as being suppressed by DNA methylation. GAPDH mRNA provides a loading control. ( b ) Analysis by semiquantitative RT–PCR of expression levels of the indicated transcripts in mouse ES cells treated for 16 h with (+) or without (−) 5-azacytidine. Apo-E mRNA provides a control that has been documented as being inhibited by DNA methylation. ARPP P0 mRNA provides a loading control. ( c ) Analysis by semiquantitative RT–PCR of expression levels of the indicated transcripts in HeLa cells treated for 72 h with 5-azacytidine. Apo-E mRNA provides a control that has been documented as being inhibited by DNA methylation. ARPP P0 mRNA provides a loading control. ( d ) Analysis by primer extension of Alu transcripts in the RNA from Fig. 5c . Bracket indicates ~240 bp products that initiate at the principle pol III start site of Alu. Reverse transcriptase was omitted from the reactions in lanes 1 and 2. To confirm that the assay was not saturated, raising the amount of template RNA from 5 (lanes 5 and 6) to 10 μg (lanes 3 and 4) is shown to give a stronger signal. Alu, B1 and B2 RT–PCRs were performed with Alu, B1 and B2 consensus primers, respectively ( Supplementary Table 1 ).

    Journal: Nature Communications

    Article Title: SINE transcription by RNA polymerase III is suppressed by histone methylation but not by DNA methylation

    doi: 10.1038/ncomms7569

    Figure Lengend Snippet: SINE expression is not stimulated by loss of DNA methylation. ( a ) Analysis by semiquantitative RT–PCR of expression levels of the indicated transcripts in matched Dnmt1 +/+ and Dnmt1 −/− fibroblasts. Duplicate samples are shown for both cell types. Apo-E and p53BP2 mRNAs provide controls that have been documented as being suppressed by DNA methylation. GAPDH mRNA provides a loading control. ( b ) Analysis by semiquantitative RT–PCR of expression levels of the indicated transcripts in mouse ES cells treated for 16 h with (+) or without (−) 5-azacytidine. Apo-E mRNA provides a control that has been documented as being inhibited by DNA methylation. ARPP P0 mRNA provides a loading control. ( c ) Analysis by semiquantitative RT–PCR of expression levels of the indicated transcripts in HeLa cells treated for 72 h with 5-azacytidine. Apo-E mRNA provides a control that has been documented as being inhibited by DNA methylation. ARPP P0 mRNA provides a loading control. ( d ) Analysis by primer extension of Alu transcripts in the RNA from Fig. 5c . Bracket indicates ~240 bp products that initiate at the principle pol III start site of Alu. Reverse transcriptase was omitted from the reactions in lanes 1 and 2. To confirm that the assay was not saturated, raising the amount of template RNA from 5 (lanes 5 and 6) to 10 μg (lanes 3 and 4) is shown to give a stronger signal. Alu, B1 and B2 RT–PCRs were performed with Alu, B1 and B2 consensus primers, respectively ( Supplementary Table 1 ).

    Article Snippet: ChIP-BS-Seq library preparation and sequencing For HeLa input DNA, two libraries were prepared from the same input DNA: one with starting quantity of 10 ng, following the Illumina ChIP-Seq library protocol, with the addition of bisulfite conversion after addition of adaptors but before amplification; and one following the Illumina Bisulfite Sequencing protocol, including the recommended starting amount.

    Techniques: Expressing, DNA Methylation Assay, Reverse Transcription Polymerase Chain Reaction

    DNA methylation does not prevent pol III occupancy of SINEs. ( a ) Percentage input bound in three independent ChIP–quantitative PCR (qPCR) assays with mouse ES cells treated for 16 h with (+) or without (−) 5-azacytidine, showing occupancy of MBD2, MeCP2 and pol III at 7SL, B1 and B2 loci, as well as an Alu inserted onto chromosomes 14 and 17. ChIPs for TAF I 48 and without antibody (mock) provide negative controls. ( b ) Percentage input bound in three independent ChIP–qPCR assays with HeLa cells treated for 72 h with (+) or without (−) 5-azacytidine, showing the binding of MBD2, TFIIIB, TFIIIC and pol III to DNA centred over the body of Alu(c22) or 200 bp downstream. The resolution of this assay is limited by the size of the genomic DNA fragments (~500 bp). ( c ) Percentage input bound in two independent ChIP–qPCR assays with matched Dnmt1 +/+ and Dnmt1 −/− fibroblasts showing occupancy of MBD2, TFIIIB, TFIIIC and pol III at B1 and B2 loci, as well as 7SL and Apo-E genes. ChIPs for TAF I 48 and without antibody (mock) provide negative controls. Error bars indicate s.e.m. and all P values are calculated by t -test.

    Journal: Nature Communications

    Article Title: SINE transcription by RNA polymerase III is suppressed by histone methylation but not by DNA methylation

    doi: 10.1038/ncomms7569

    Figure Lengend Snippet: DNA methylation does not prevent pol III occupancy of SINEs. ( a ) Percentage input bound in three independent ChIP–quantitative PCR (qPCR) assays with mouse ES cells treated for 16 h with (+) or without (−) 5-azacytidine, showing occupancy of MBD2, MeCP2 and pol III at 7SL, B1 and B2 loci, as well as an Alu inserted onto chromosomes 14 and 17. ChIPs for TAF I 48 and without antibody (mock) provide negative controls. ( b ) Percentage input bound in three independent ChIP–qPCR assays with HeLa cells treated for 72 h with (+) or without (−) 5-azacytidine, showing the binding of MBD2, TFIIIB, TFIIIC and pol III to DNA centred over the body of Alu(c22) or 200 bp downstream. The resolution of this assay is limited by the size of the genomic DNA fragments (~500 bp). ( c ) Percentage input bound in two independent ChIP–qPCR assays with matched Dnmt1 +/+ and Dnmt1 −/− fibroblasts showing occupancy of MBD2, TFIIIB, TFIIIC and pol III at B1 and B2 loci, as well as 7SL and Apo-E genes. ChIPs for TAF I 48 and without antibody (mock) provide negative controls. Error bars indicate s.e.m. and all P values are calculated by t -test.

    Article Snippet: ChIP-BS-Seq library preparation and sequencing For HeLa input DNA, two libraries were prepared from the same input DNA: one with starting quantity of 10 ng, following the Illumina ChIP-Seq library protocol, with the addition of bisulfite conversion after addition of adaptors but before amplification; and one following the Illumina Bisulfite Sequencing protocol, including the recommended starting amount.

    Techniques: DNA Methylation Assay, Chromatin Immunoprecipitation, Real-time Polymerase Chain Reaction, Binding Assay