chip lysis buffer Search Results


chip lysis buffer  (Boston BioProducts)
96
Boston BioProducts chip lysis buffer
Chip Lysis Buffer, supplied by Boston BioProducts, 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/product/chip+lysis+buffer/ChIP+Lysis+Buffer/custom%40chp-126%409406525
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chip lysis buffer  (Santa Cruz Biotechnology)
93
Santa Cruz Biotechnology chip lysis buffer
Chip Lysis Buffer, supplied by Santa Cruz Biotechnology, used in various techniques. Bioz Stars score: 93/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/chip+lysis+buffer/ChIP+Lysis+Buffer/pm37415159-99-6-9
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high salt chip buffer  (Santa Cruz Biotechnology)
93
Santa Cruz Biotechnology high salt chip buffer
(A and B), Nucleosome occupancy at a putative enhancer 10 kb upstream of the TSS of IL1A was determined in BMDMs prior to (blue bars and lines) and upon 1.5 h (yellow) or 3 h (red) induction with 1 μg/ml LPS as described in the legend of . ConSite predicted consensus sites for PU.1, C/EBP, IRF, AP1 and NFκB are indicated. (C and D), Nucleosome occupancy at the promoter of IL1A was determined as described in panel (A) in a region surrounding the TSS of IL1A. The TSS (black bar) and a putative TATA-box (blue bar) is indicated in panel (C). (E), Kinetics of nucleosome removal at IL1A and IL12B. BMDMs were induced with LPS for 15′, 30′, 60′ and 90′, and nucleosome occupancy was analyzed as described in (A). Nucleosome removal at three locations in the distal enhancer of IL12B (red lines) and in the enhancer of IL1A (blue lines) is shown. The data is displayed as the fold change in nucleosome occupancy over the levels found before induction at each location. The absence of changes in nucleosome occupancy at the TSS of IL12B (black line) and of IL1A (gray line) is shown for comparison. (F), <t>ChIP</t> experiments with antibodies against H3 (dark blue bars), H2A.Z (light blue), H3K4me1 (green), H3K4me3 (yellow) and H3K27ac (red) were performed as described in the . For these experiments <t>cross-linked</t> <t>chromatin</t> was lightly digested with MNase before incubation with the respective antibodies to increase resolution of the ChIP signal and the data was normalized to a region in the ORF of RPL4. Changes upon LPS induction in histone binding and histone modifications at the enhancers and promoters of IL12B and IL1A as well as at a control region in the GAPDH pseudo gene are shown as fold over levels found before induction. For H3K27ac the changes 1.5 h after LPS induction, and for all other histone variants and modifications the changes after 3 h of induction are shown. The error bars show the SEM of at least 3 independent experiments. Statistical significance of the changes in H3K4me3 and H3K27ac upon LPS induction compared to levels found prior to induction determined by Student's T-tests is indicated (*P<0.05; **P<0.01).
High Salt Chip Buffer, supplied by Santa Cruz Biotechnology, used in various techniques. Bioz Stars score: 93/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/chip+lysis+buffer/ChIP+Lysis+Buffer+High+Salt/pmc03976374-53-11-56
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chip lysis buffer  (DIAGENODE DIAGNOSTICS)
90
DIAGENODE DIAGNOSTICS chip lysis buffer
(A and B), Nucleosome occupancy at a putative enhancer 10 kb upstream of the TSS of IL1A was determined in BMDMs prior to (blue bars and lines) and upon 1.5 h (yellow) or 3 h (red) induction with 1 μg/ml LPS as described in the legend of . ConSite predicted consensus sites for PU.1, C/EBP, IRF, AP1 and NFκB are indicated. (C and D), Nucleosome occupancy at the promoter of IL1A was determined as described in panel (A) in a region surrounding the TSS of IL1A. The TSS (black bar) and a putative TATA-box (blue bar) is indicated in panel (C). (E), Kinetics of nucleosome removal at IL1A and IL12B. BMDMs were induced with LPS for 15′, 30′, 60′ and 90′, and nucleosome occupancy was analyzed as described in (A). Nucleosome removal at three locations in the distal enhancer of IL12B (red lines) and in the enhancer of IL1A (blue lines) is shown. The data is displayed as the fold change in nucleosome occupancy over the levels found before induction at each location. The absence of changes in nucleosome occupancy at the TSS of IL12B (black line) and of IL1A (gray line) is shown for comparison. (F), <t>ChIP</t> experiments with antibodies against H3 (dark blue bars), H2A.Z (light blue), H3K4me1 (green), H3K4me3 (yellow) and H3K27ac (red) were performed as described in the . For these experiments <t>cross-linked</t> <t>chromatin</t> was lightly digested with MNase before incubation with the respective antibodies to increase resolution of the ChIP signal and the data was normalized to a region in the ORF of RPL4. Changes upon LPS induction in histone binding and histone modifications at the enhancers and promoters of IL12B and IL1A as well as at a control region in the GAPDH pseudo gene are shown as fold over levels found before induction. For H3K27ac the changes 1.5 h after LPS induction, and for all other histone variants and modifications the changes after 3 h of induction are shown. The error bars show the SEM of at least 3 independent experiments. Statistical significance of the changes in H3K4me3 and H3K27ac upon LPS induction compared to levels found prior to induction determined by Student's T-tests is indicated (*P<0.05; **P<0.01).
Chip Lysis Buffer, supplied by DIAGENODE DIAGNOSTICS, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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magna chip cell lysis buffer  (Merck KGaA)
90
Merck KGaA magna chip cell lysis buffer
(A and B), Nucleosome occupancy at a putative enhancer 10 kb upstream of the TSS of IL1A was determined in BMDMs prior to (blue bars and lines) and upon 1.5 h (yellow) or 3 h (red) induction with 1 μg/ml LPS as described in the legend of . ConSite predicted consensus sites for PU.1, C/EBP, IRF, AP1 and NFκB are indicated. (C and D), Nucleosome occupancy at the promoter of IL1A was determined as described in panel (A) in a region surrounding the TSS of IL1A. The TSS (black bar) and a putative TATA-box (blue bar) is indicated in panel (C). (E), Kinetics of nucleosome removal at IL1A and IL12B. BMDMs were induced with LPS for 15′, 30′, 60′ and 90′, and nucleosome occupancy was analyzed as described in (A). Nucleosome removal at three locations in the distal enhancer of IL12B (red lines) and in the enhancer of IL1A (blue lines) is shown. The data is displayed as the fold change in nucleosome occupancy over the levels found before induction at each location. The absence of changes in nucleosome occupancy at the TSS of IL12B (black line) and of IL1A (gray line) is shown for comparison. (F), <t>ChIP</t> experiments with antibodies against H3 (dark blue bars), H2A.Z (light blue), H3K4me1 (green), H3K4me3 (yellow) and H3K27ac (red) were performed as described in the . For these experiments <t>cross-linked</t> <t>chromatin</t> was lightly digested with MNase before incubation with the respective antibodies to increase resolution of the ChIP signal and the data was normalized to a region in the ORF of RPL4. Changes upon LPS induction in histone binding and histone modifications at the enhancers and promoters of IL12B and IL1A as well as at a control region in the GAPDH pseudo gene are shown as fold over levels found before induction. For H3K27ac the changes 1.5 h after LPS induction, and for all other histone variants and modifications the changes after 3 h of induction are shown. The error bars show the SEM of at least 3 independent experiments. Statistical significance of the changes in H3K4me3 and H3K27ac upon LPS induction compared to levels found prior to induction determined by Student's T-tests is indicated (*P<0.05; **P<0.01).
Magna Chip Cell Lysis Buffer, supplied by Merck KGaA, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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cell lysis buffer red chip kittm  (DIAGENODE DIAGNOSTICS)
90
DIAGENODE DIAGNOSTICS cell lysis buffer red chip kittm
(A and B), Nucleosome occupancy at a putative enhancer 10 kb upstream of the TSS of IL1A was determined in BMDMs prior to (blue bars and lines) and upon 1.5 h (yellow) or 3 h (red) induction with 1 μg/ml LPS as described in the legend of . ConSite predicted consensus sites for PU.1, C/EBP, IRF, AP1 and NFκB are indicated. (C and D), Nucleosome occupancy at the promoter of IL1A was determined as described in panel (A) in a region surrounding the TSS of IL1A. The TSS (black bar) and a putative TATA-box (blue bar) is indicated in panel (C). (E), Kinetics of nucleosome removal at IL1A and IL12B. BMDMs were induced with LPS for 15′, 30′, 60′ and 90′, and nucleosome occupancy was analyzed as described in (A). Nucleosome removal at three locations in the distal enhancer of IL12B (red lines) and in the enhancer of IL1A (blue lines) is shown. The data is displayed as the fold change in nucleosome occupancy over the levels found before induction at each location. The absence of changes in nucleosome occupancy at the TSS of IL12B (black line) and of IL1A (gray line) is shown for comparison. (F), <t>ChIP</t> experiments with antibodies against H3 (dark blue bars), H2A.Z (light blue), H3K4me1 (green), H3K4me3 (yellow) and H3K27ac (red) were performed as described in the . For these experiments <t>cross-linked</t> <t>chromatin</t> was lightly digested with MNase before incubation with the respective antibodies to increase resolution of the ChIP signal and the data was normalized to a region in the ORF of RPL4. Changes upon LPS induction in histone binding and histone modifications at the enhancers and promoters of IL12B and IL1A as well as at a control region in the GAPDH pseudo gene are shown as fold over levels found before induction. For H3K27ac the changes 1.5 h after LPS induction, and for all other histone variants and modifications the changes after 3 h of induction are shown. The error bars show the SEM of at least 3 independent experiments. Statistical significance of the changes in H3K4me3 and H3K27ac upon LPS induction compared to levels found prior to induction determined by Student's T-tests is indicated (*P<0.05; **P<0.01).
Cell Lysis Buffer Red Chip Kittm, supplied by DIAGENODE DIAGNOSTICS, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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cell lysis buffer lowcell# chip kit  (DIAGENODE DIAGNOSTICS)
90
DIAGENODE DIAGNOSTICS cell lysis buffer lowcell# chip kit
(A and B), Nucleosome occupancy at a putative enhancer 10 kb upstream of the TSS of IL1A was determined in BMDMs prior to (blue bars and lines) and upon 1.5 h (yellow) or 3 h (red) induction with 1 μg/ml LPS as described in the legend of . ConSite predicted consensus sites for PU.1, C/EBP, IRF, AP1 and NFκB are indicated. (C and D), Nucleosome occupancy at the promoter of IL1A was determined as described in panel (A) in a region surrounding the TSS of IL1A. The TSS (black bar) and a putative TATA-box (blue bar) is indicated in panel (C). (E), Kinetics of nucleosome removal at IL1A and IL12B. BMDMs were induced with LPS for 15′, 30′, 60′ and 90′, and nucleosome occupancy was analyzed as described in (A). Nucleosome removal at three locations in the distal enhancer of IL12B (red lines) and in the enhancer of IL1A (blue lines) is shown. The data is displayed as the fold change in nucleosome occupancy over the levels found before induction at each location. The absence of changes in nucleosome occupancy at the TSS of IL12B (black line) and of IL1A (gray line) is shown for comparison. (F), <t>ChIP</t> experiments with antibodies against H3 (dark blue bars), H2A.Z (light blue), H3K4me1 (green), H3K4me3 (yellow) and H3K27ac (red) were performed as described in the . For these experiments <t>cross-linked</t> <t>chromatin</t> was lightly digested with MNase before incubation with the respective antibodies to increase resolution of the ChIP signal and the data was normalized to a region in the ORF of RPL4. Changes upon LPS induction in histone binding and histone modifications at the enhancers and promoters of IL12B and IL1A as well as at a control region in the GAPDH pseudo gene are shown as fold over levels found before induction. For H3K27ac the changes 1.5 h after LPS induction, and for all other histone variants and modifications the changes after 3 h of induction are shown. The error bars show the SEM of at least 3 independent experiments. Statistical significance of the changes in H3K4me3 and H3K27ac upon LPS induction compared to levels found prior to induction determined by Student's T-tests is indicated (*P<0.05; **P<0.01).
Cell Lysis Buffer Lowcell# Chip Kit, supplied by DIAGENODE DIAGNOSTICS, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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chip lysis buffer + 1mm pmsf  (DIAGENODE DIAGNOSTICS)
90
DIAGENODE DIAGNOSTICS chip lysis buffer + 1mm pmsf
(A and B), Nucleosome occupancy at a putative enhancer 10 kb upstream of the TSS of IL1A was determined in BMDMs prior to (blue bars and lines) and upon 1.5 h (yellow) or 3 h (red) induction with 1 μg/ml LPS as described in the legend of . ConSite predicted consensus sites for PU.1, C/EBP, IRF, AP1 and NFκB are indicated. (C and D), Nucleosome occupancy at the promoter of IL1A was determined as described in panel (A) in a region surrounding the TSS of IL1A. The TSS (black bar) and a putative TATA-box (blue bar) is indicated in panel (C). (E), Kinetics of nucleosome removal at IL1A and IL12B. BMDMs were induced with LPS for 15′, 30′, 60′ and 90′, and nucleosome occupancy was analyzed as described in (A). Nucleosome removal at three locations in the distal enhancer of IL12B (red lines) and in the enhancer of IL1A (blue lines) is shown. The data is displayed as the fold change in nucleosome occupancy over the levels found before induction at each location. The absence of changes in nucleosome occupancy at the TSS of IL12B (black line) and of IL1A (gray line) is shown for comparison. (F), <t>ChIP</t> experiments with antibodies against H3 (dark blue bars), H2A.Z (light blue), H3K4me1 (green), H3K4me3 (yellow) and H3K27ac (red) were performed as described in the . For these experiments <t>cross-linked</t> <t>chromatin</t> was lightly digested with MNase before incubation with the respective antibodies to increase resolution of the ChIP signal and the data was normalized to a region in the ORF of RPL4. Changes upon LPS induction in histone binding and histone modifications at the enhancers and promoters of IL12B and IL1A as well as at a control region in the GAPDH pseudo gene are shown as fold over levels found before induction. For H3K27ac the changes 1.5 h after LPS induction, and for all other histone variants and modifications the changes after 3 h of induction are shown. The error bars show the SEM of at least 3 independent experiments. Statistical significance of the changes in H3K4me3 and H3K27ac upon LPS induction compared to levels found prior to induction determined by Student's T-tests is indicated (*P<0.05; **P<0.01).
Chip Lysis Buffer + 1mm Pmsf, supplied by DIAGENODE DIAGNOSTICS, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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lysis buffer lowcell# chip kit  (DIAGENODE DIAGNOSTICS)
90
DIAGENODE DIAGNOSTICS lysis buffer lowcell# chip kit
(A and B), Nucleosome occupancy at a putative enhancer 10 kb upstream of the TSS of IL1A was determined in BMDMs prior to (blue bars and lines) and upon 1.5 h (yellow) or 3 h (red) induction with 1 μg/ml LPS as described in the legend of . ConSite predicted consensus sites for PU.1, C/EBP, IRF, AP1 and NFκB are indicated. (C and D), Nucleosome occupancy at the promoter of IL1A was determined as described in panel (A) in a region surrounding the TSS of IL1A. The TSS (black bar) and a putative TATA-box (blue bar) is indicated in panel (C). (E), Kinetics of nucleosome removal at IL1A and IL12B. BMDMs were induced with LPS for 15′, 30′, 60′ and 90′, and nucleosome occupancy was analyzed as described in (A). Nucleosome removal at three locations in the distal enhancer of IL12B (red lines) and in the enhancer of IL1A (blue lines) is shown. The data is displayed as the fold change in nucleosome occupancy over the levels found before induction at each location. The absence of changes in nucleosome occupancy at the TSS of IL12B (black line) and of IL1A (gray line) is shown for comparison. (F), <t>ChIP</t> experiments with antibodies against H3 (dark blue bars), H2A.Z (light blue), H3K4me1 (green), H3K4me3 (yellow) and H3K27ac (red) were performed as described in the . For these experiments <t>cross-linked</t> <t>chromatin</t> was lightly digested with MNase before incubation with the respective antibodies to increase resolution of the ChIP signal and the data was normalized to a region in the ORF of RPL4. Changes upon LPS induction in histone binding and histone modifications at the enhancers and promoters of IL12B and IL1A as well as at a control region in the GAPDH pseudo gene are shown as fold over levels found before induction. For H3K27ac the changes 1.5 h after LPS induction, and for all other histone variants and modifications the changes after 3 h of induction are shown. The error bars show the SEM of at least 3 independent experiments. Statistical significance of the changes in H3K4me3 and H3K27ac upon LPS induction compared to levels found prior to induction determined by Student's T-tests is indicated (*P<0.05; **P<0.01).
Lysis Buffer Lowcell# Chip Kit, supplied by DIAGENODE DIAGNOSTICS, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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chip sonication nuclear lysis buffer  (Cosmo Bio USA)
90
Cosmo Bio USA chip sonication nuclear lysis buffer
(A and B), Nucleosome occupancy at a putative enhancer 10 kb upstream of the TSS of IL1A was determined in BMDMs prior to (blue bars and lines) and upon 1.5 h (yellow) or 3 h (red) induction with 1 μg/ml LPS as described in the legend of . ConSite predicted consensus sites for PU.1, C/EBP, IRF, AP1 and NFκB are indicated. (C and D), Nucleosome occupancy at the promoter of IL1A was determined as described in panel (A) in a region surrounding the TSS of IL1A. The TSS (black bar) and a putative TATA-box (blue bar) is indicated in panel (C). (E), Kinetics of nucleosome removal at IL1A and IL12B. BMDMs were induced with LPS for 15′, 30′, 60′ and 90′, and nucleosome occupancy was analyzed as described in (A). Nucleosome removal at three locations in the distal enhancer of IL12B (red lines) and in the enhancer of IL1A (blue lines) is shown. The data is displayed as the fold change in nucleosome occupancy over the levels found before induction at each location. The absence of changes in nucleosome occupancy at the TSS of IL12B (black line) and of IL1A (gray line) is shown for comparison. (F), <t>ChIP</t> experiments with antibodies against H3 (dark blue bars), H2A.Z (light blue), H3K4me1 (green), H3K4me3 (yellow) and H3K27ac (red) were performed as described in the . For these experiments <t>cross-linked</t> <t>chromatin</t> was lightly digested with MNase before incubation with the respective antibodies to increase resolution of the ChIP signal and the data was normalized to a region in the ORF of RPL4. Changes upon LPS induction in histone binding and histone modifications at the enhancers and promoters of IL12B and IL1A as well as at a control region in the GAPDH pseudo gene are shown as fold over levels found before induction. For H3K27ac the changes 1.5 h after LPS induction, and for all other histone variants and modifications the changes after 3 h of induction are shown. The error bars show the SEM of at least 3 independent experiments. Statistical significance of the changes in H3K4me3 and H3K27ac upon LPS induction compared to levels found prior to induction determined by Student's T-tests is indicated (*P<0.05; **P<0.01).
Chip Sonication Nuclear Lysis Buffer, supplied by Cosmo Bio USA, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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lysis buffer b low cell chip kit  (DIAGENODE DIAGNOSTICS)
90
DIAGENODE DIAGNOSTICS lysis buffer b low cell chip kit
(A and B), Nucleosome occupancy at a putative enhancer 10 kb upstream of the TSS of IL1A was determined in BMDMs prior to (blue bars and lines) and upon 1.5 h (yellow) or 3 h (red) induction with 1 μg/ml LPS as described in the legend of . ConSite predicted consensus sites for PU.1, C/EBP, IRF, AP1 and NFκB are indicated. (C and D), Nucleosome occupancy at the promoter of IL1A was determined as described in panel (A) in a region surrounding the TSS of IL1A. The TSS (black bar) and a putative TATA-box (blue bar) is indicated in panel (C). (E), Kinetics of nucleosome removal at IL1A and IL12B. BMDMs were induced with LPS for 15′, 30′, 60′ and 90′, and nucleosome occupancy was analyzed as described in (A). Nucleosome removal at three locations in the distal enhancer of IL12B (red lines) and in the enhancer of IL1A (blue lines) is shown. The data is displayed as the fold change in nucleosome occupancy over the levels found before induction at each location. The absence of changes in nucleosome occupancy at the TSS of IL12B (black line) and of IL1A (gray line) is shown for comparison. (F), <t>ChIP</t> experiments with antibodies against H3 (dark blue bars), H2A.Z (light blue), H3K4me1 (green), H3K4me3 (yellow) and H3K27ac (red) were performed as described in the . For these experiments <t>cross-linked</t> <t>chromatin</t> was lightly digested with MNase before incubation with the respective antibodies to increase resolution of the ChIP signal and the data was normalized to a region in the ORF of RPL4. Changes upon LPS induction in histone binding and histone modifications at the enhancers and promoters of IL12B and IL1A as well as at a control region in the GAPDH pseudo gene are shown as fold over levels found before induction. For H3K27ac the changes 1.5 h after LPS induction, and for all other histone variants and modifications the changes after 3 h of induction are shown. The error bars show the SEM of at least 3 independent experiments. Statistical significance of the changes in H3K4me3 and H3K27ac upon LPS induction compared to levels found prior to induction determined by Student's T-tests is indicated (*P<0.05; **P<0.01).
Lysis Buffer B Low Cell Chip Kit, supplied by DIAGENODE DIAGNOSTICS, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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Image Search Results


(A and B), Nucleosome occupancy at a putative enhancer 10 kb upstream of the TSS of IL1A was determined in BMDMs prior to (blue bars and lines) and upon 1.5 h (yellow) or 3 h (red) induction with 1 μg/ml LPS as described in the legend of . ConSite predicted consensus sites for PU.1, C/EBP, IRF, AP1 and NFκB are indicated. (C and D), Nucleosome occupancy at the promoter of IL1A was determined as described in panel (A) in a region surrounding the TSS of IL1A. The TSS (black bar) and a putative TATA-box (blue bar) is indicated in panel (C). (E), Kinetics of nucleosome removal at IL1A and IL12B. BMDMs were induced with LPS for 15′, 30′, 60′ and 90′, and nucleosome occupancy was analyzed as described in (A). Nucleosome removal at three locations in the distal enhancer of IL12B (red lines) and in the enhancer of IL1A (blue lines) is shown. The data is displayed as the fold change in nucleosome occupancy over the levels found before induction at each location. The absence of changes in nucleosome occupancy at the TSS of IL12B (black line) and of IL1A (gray line) is shown for comparison. (F), ChIP experiments with antibodies against H3 (dark blue bars), H2A.Z (light blue), H3K4me1 (green), H3K4me3 (yellow) and H3K27ac (red) were performed as described in the . For these experiments cross-linked chromatin was lightly digested with MNase before incubation with the respective antibodies to increase resolution of the ChIP signal and the data was normalized to a region in the ORF of RPL4. Changes upon LPS induction in histone binding and histone modifications at the enhancers and promoters of IL12B and IL1A as well as at a control region in the GAPDH pseudo gene are shown as fold over levels found before induction. For H3K27ac the changes 1.5 h after LPS induction, and for all other histone variants and modifications the changes after 3 h of induction are shown. The error bars show the SEM of at least 3 independent experiments. Statistical significance of the changes in H3K4me3 and H3K27ac upon LPS induction compared to levels found prior to induction determined by Student's T-tests is indicated (*P<0.05; **P<0.01).

Journal: PLoS ONE

Article Title: Nucleosomes Are Stably Evicted from Enhancers but Not Promoters upon Induction of Certain Pro-Inflammatory Genes in Mouse Macrophages

doi: 10.1371/journal.pone.0093971

Figure Lengend Snippet: (A and B), Nucleosome occupancy at a putative enhancer 10 kb upstream of the TSS of IL1A was determined in BMDMs prior to (blue bars and lines) and upon 1.5 h (yellow) or 3 h (red) induction with 1 μg/ml LPS as described in the legend of . ConSite predicted consensus sites for PU.1, C/EBP, IRF, AP1 and NFκB are indicated. (C and D), Nucleosome occupancy at the promoter of IL1A was determined as described in panel (A) in a region surrounding the TSS of IL1A. The TSS (black bar) and a putative TATA-box (blue bar) is indicated in panel (C). (E), Kinetics of nucleosome removal at IL1A and IL12B. BMDMs were induced with LPS for 15′, 30′, 60′ and 90′, and nucleosome occupancy was analyzed as described in (A). Nucleosome removal at three locations in the distal enhancer of IL12B (red lines) and in the enhancer of IL1A (blue lines) is shown. The data is displayed as the fold change in nucleosome occupancy over the levels found before induction at each location. The absence of changes in nucleosome occupancy at the TSS of IL12B (black line) and of IL1A (gray line) is shown for comparison. (F), ChIP experiments with antibodies against H3 (dark blue bars), H2A.Z (light blue), H3K4me1 (green), H3K4me3 (yellow) and H3K27ac (red) were performed as described in the . For these experiments cross-linked chromatin was lightly digested with MNase before incubation with the respective antibodies to increase resolution of the ChIP signal and the data was normalized to a region in the ORF of RPL4. Changes upon LPS induction in histone binding and histone modifications at the enhancers and promoters of IL12B and IL1A as well as at a control region in the GAPDH pseudo gene are shown as fold over levels found before induction. For H3K27ac the changes 1.5 h after LPS induction, and for all other histone variants and modifications the changes after 3 h of induction are shown. The error bars show the SEM of at least 3 independent experiments. Statistical significance of the changes in H3K4me3 and H3K27ac upon LPS induction compared to levels found prior to induction determined by Student's T-tests is indicated (*P<0.05; **P<0.01).

Article Snippet: For all other ChIP experiments isolated chromatin was directly diluted with High Salt ChIP buffer and incubated with either 1 μg of anti-PolI antibody (sc-56767), 6 μg anti-TBP (sc-204), 4 μg anti-PU.1 (sc-352), 4 μg anti-C/EBPβ (sc-150), 6 μg anti-NFκB (sc-372), 5 μg anti-c-Jun (sc-45), 6 μg anti-p300 (sc-585) or 10 μg anti-IRF3 (sc-9082) all from Santa Cruz Biotechnologies.

Techniques: Comparison, Incubation, Binding Assay, Control

(A and B), ChIP experiments were performed as described in the legend of with antibodies that detect (A) PolII or (B) TBP in BMDMs before (dark blue bars), and upon 1.5 h (yellow) or 3 h (red) LPS induction. Cross-linked chromatin was either untreated (solid bars), or lightly digested with MNase (hatched bars) as described in the . The data was normalized to a region in the KIT promoter and genomic locations are indicated. The experiment was performed twice and error bars indicating the SEM are shown.

Journal: PLoS ONE

Article Title: Nucleosomes Are Stably Evicted from Enhancers but Not Promoters upon Induction of Certain Pro-Inflammatory Genes in Mouse Macrophages

doi: 10.1371/journal.pone.0093971

Figure Lengend Snippet: (A and B), ChIP experiments were performed as described in the legend of with antibodies that detect (A) PolII or (B) TBP in BMDMs before (dark blue bars), and upon 1.5 h (yellow) or 3 h (red) LPS induction. Cross-linked chromatin was either untreated (solid bars), or lightly digested with MNase (hatched bars) as described in the . The data was normalized to a region in the KIT promoter and genomic locations are indicated. The experiment was performed twice and error bars indicating the SEM are shown.

Article Snippet: For all other ChIP experiments isolated chromatin was directly diluted with High Salt ChIP buffer and incubated with either 1 μg of anti-PolI antibody (sc-56767), 6 μg anti-TBP (sc-204), 4 μg anti-PU.1 (sc-352), 4 μg anti-C/EBPβ (sc-150), 6 μg anti-NFκB (sc-372), 5 μg anti-c-Jun (sc-45), 6 μg anti-p300 (sc-585) or 10 μg anti-IRF3 (sc-9082) all from Santa Cruz Biotechnologies.

Techniques: