ctcf antibody Millipore Search Results


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  • 90
    Millipore rabbit anti ctcf
    <t>CSB</t> regulates a subset of <t>CTCF</t> occupancy sites upon oxidative stress. ( A ) CTCF ChIP-qPCR assays in CSB expressing (WT) and non-expressing (CS1AN) cells, with or without a 1-h menadione treatment (100 μM). Shown are means ± SEM ( n = 3). A paired t -test was used to determine if the difference in CTCF enrichment before and after menadione treatment was significant. Single asterisks indicate P values
    Rabbit Anti Ctcf, supplied by Millipore, used in various techniques. Bioz Stars score: 90/100, based on 58 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    90
    Merck KGaA ctcf antibody
    Characterization of DSCAM-AS1 SE in MCF-7 cells. ( a ) WashU genome browser view of the DSCAM-AS1 genomic locus, which is reported in association with apoERα ChIP-Seq and RNA-Seq reads enrichment in siCTR-(red) or siERα-(blue) transfected MCF-7 cells; and with GRO-Seq, ChIP-Seq profiles of histone modifications and DNase hypersensitivity signals (yellow), RNA-Pol II and eight TFs (teal-blue) obtained from vehicle treated MCF-7 cells (see the Materials and Methods section for detailed data source). <t>ERα</t> and <t>CTCF</t> ChIA-PET data performed in MCF-7 grown in full medium from ENCODE project are also included [ 26 ]. The coordinates of the predicted SE and aERBSs are reported at the top as black and orange boxes, respectively. ChIP-Seq genomic signal profiles are reported as read count per million sequenced reads. ( b , c ) Bar plots reporting ERα fold enrichment over IgG signal by ChIP-qPCR at DSCAM-AS1 promoter and E5-E6-enhancers, TFF1 promoter (positive control) and KCNQ1OT1 promoter (negative control), in MCF-7 cells grown in HD medium transfected with siERα or siCTR ( b ); treated for 45′ with 17β-estradiol (E2) or vehicle (veh) ( c ). Standard error of four biological replicates; p -value by unpaired t -test: ** p
    Ctcf Antibody, supplied by Merck KGaA, used in various techniques. Bioz Stars score: 90/100, based on 9 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    90
    Cell Signaling Technology Inc anti ctcf
    AR and <t>CTCF</t> do not colocalize, or interact in LNCaP cells. (A) Re-ChIP by CTCF, AR antibodies, or control IgG. Insulator1, 2 and, ARE1, 2, and 3 were tested. (B) Co-immunoprecipitation by CTCF antibody, and western blotting by AR, CTCF, or GAPDH. R-RWPE-1, L-LNCaP, <t>R1881-synthetic</t> androgen.
    Anti Ctcf, supplied by Cell Signaling Technology Inc, used in various techniques. Bioz Stars score: 90/100, based on 74 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    90
    Abcam anti ctcf
    AR and <t>CTCF</t> do not colocalize, or interact in LNCaP cells. (A) Re-ChIP by CTCF, AR antibodies, or control IgG. Insulator1, 2 and, ARE1, 2, and 3 were tested. (B) Co-immunoprecipitation by CTCF antibody, and western blotting by AR, CTCF, or GAPDH. R-RWPE-1, L-LNCaP, <t>R1881-synthetic</t> androgen.
    Anti Ctcf, supplied by Abcam, used in various techniques. Bioz Stars score: 90/100, based on 139 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    88
    Santa Cruz Biotechnology anti ctcf antibodies
    AR and <t>CTCF</t> do not colocalize, or interact in LNCaP cells. (A) Re-ChIP by CTCF, AR antibodies, or control IgG. Insulator1, 2 and, ARE1, 2, and 3 were tested. (B) Co-immunoprecipitation by CTCF antibody, and western blotting by AR, CTCF, or GAPDH. R-RWPE-1, L-LNCaP, <t>R1881-synthetic</t> androgen.
    Anti Ctcf Antibodies, supplied by Santa Cruz Biotechnology, used in various techniques. Bioz Stars score: 88/100, based on 8 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    79
    Millipore ctcf antibody 07 729
    AR and <t>CTCF</t> do not colocalize, or interact in LNCaP cells. (A) Re-ChIP by CTCF, AR antibodies, or control IgG. Insulator1, 2 and, ARE1, 2, and 3 were tested. (B) Co-immunoprecipitation by CTCF antibody, and western blotting by AR, CTCF, or GAPDH. R-RWPE-1, L-LNCaP, <t>R1881-synthetic</t> androgen.
    Ctcf Antibody 07 729, supplied by Millipore, used in various techniques. Bioz Stars score: 79/100, based on 9 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    82
    Millipore specific antibody
    AR and <t>CTCF</t> do not colocalize, or interact in LNCaP cells. (A) Re-ChIP by CTCF, AR antibodies, or control IgG. Insulator1, 2 and, ARE1, 2, and 3 were tested. (B) Co-immunoprecipitation by CTCF antibody, and western blotting by AR, CTCF, or GAPDH. R-RWPE-1, L-LNCaP, <t>R1881-synthetic</t> androgen.
    Specific Antibody, supplied by Millipore, used in various techniques. Bioz Stars score: 82/100, based on 20 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    75
    Millipore western blotting against anti ctcf antibody
    Knockdown of <t>CTCF</t> and schema of single cell sequencing. a . Western blot analysis of CTCF in luciferase control (shLuc) and CTCF-KD cells (shCTCF#1 and shCTCF#2). EL4 cells were infected with retroviral particles encoding GFP and an shRNA targeting CTCF or a control sequence for 5 days. b . Real-time quantitative PCR (RT-qPCR) analysis of CTCF expression in luciferase control (shLuc) and knockdown (shCTCF#1 and shCTCF#2) cells. The expression level of CTCF was normalized to <t>GAPDH.</t> c . Schema of single cell RNA sequencing using Fluidigm C1 system
    Western Blotting Against Anti Ctcf Antibody, supplied by Millipore, used in various techniques. Bioz Stars score: 75/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    90
    Millipore ctcf
    Validation of DNA binding protein occupancy. ChIP analysis of K562 chromatin for occupancy by the erythroid-specific transcription factors GATA1 and NF-E2; <t>RNA</t> Pol II; the chromatin architectural protein <t>CTCF;</t> and the barrier-associated proteins USF1,
    Ctcf, supplied by Millipore, used in various techniques. Bioz Stars score: 90/100, based on 36 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    88
    Becton Dickinson anti ctcf
    Validation of DNA binding protein occupancy. ChIP analysis of K562 chromatin for occupancy by the erythroid-specific transcription factors GATA1 and NF-E2; <t>RNA</t> Pol II; the chromatin architectural protein <t>CTCF;</t> and the barrier-associated proteins USF1,
    Anti Ctcf, supplied by Becton Dickinson, used in various techniques. Bioz Stars score: 88/100, based on 4 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    86
    Millipore ctcf monoclonal antibodies
    Validation of DNA binding protein occupancy. ChIP analysis of K562 chromatin for occupancy by the erythroid-specific transcription factors GATA1 and NF-E2; <t>RNA</t> Pol II; the chromatin architectural protein <t>CTCF;</t> and the barrier-associated proteins USF1,
    Ctcf Monoclonal Antibodies, supplied by Millipore, 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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    95
    Millipore rabbit polyclonal anti ctcf
    Validation of DNA binding protein occupancy. ChIP analysis of K562 chromatin for occupancy by the erythroid-specific transcription factors GATA1 and NF-E2; <t>RNA</t> Pol II; the chromatin architectural protein <t>CTCF;</t> and the barrier-associated proteins USF1,
    Rabbit Polyclonal Anti Ctcf, supplied by Millipore, used in various techniques. Bioz Stars score: 95/100, based on 25 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    79
    Millipore mouse anti ctcf
    Cohesin does not organize nucleosomes at <t>CTCF</t> sites. (A, B) ChIP seq for RAD21 was plotted with respect to CTCF sites following depletion of CTCF (A) or <t>SNF2H</t> (B). In each case enrichment for RAD21 is reduced following depletion (blue) in comparison to control depletions (red). (C) ChIP seq showing SNF2H enrichment at CTCF sites in RAD21 (blue) depleted and control (red) cells. SNF2H enrichment is not affected by depletion of RAD21. (D) Depletion of RAD21 (blue) has little effect on nucleosome organization at CTCF sites in comparison to a control depletion.
    Mouse Anti Ctcf, supplied by Millipore, used in various techniques. Bioz Stars score: 79/100, based on 4 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    81
    Millipore anti human ctcf
    Cohesin does not organize nucleosomes at <t>CTCF</t> sites. (A, B) ChIP seq for RAD21 was plotted with respect to CTCF sites following depletion of CTCF (A) or <t>SNF2H</t> (B). In each case enrichment for RAD21 is reduced following depletion (blue) in comparison to control depletions (red). (C) ChIP seq showing SNF2H enrichment at CTCF sites in RAD21 (blue) depleted and control (red) cells. SNF2H enrichment is not affected by depletion of RAD21. (D) Depletion of RAD21 (blue) has little effect on nucleosome organization at CTCF sites in comparison to a control depletion.
    Anti Human Ctcf, supplied by Millipore, used in various techniques. Bioz Stars score: 81/100, based on 5 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    79
    Millipore anti ccctc binding factor gene ctcf
    Cohesin does not organize nucleosomes at <t>CTCF</t> sites. (A, B) ChIP seq for RAD21 was plotted with respect to CTCF sites following depletion of CTCF (A) or <t>SNF2H</t> (B). In each case enrichment for RAD21 is reduced following depletion (blue) in comparison to control depletions (red). (C) ChIP seq showing SNF2H enrichment at CTCF sites in RAD21 (blue) depleted and control (red) cells. SNF2H enrichment is not affected by depletion of RAD21. (D) Depletion of RAD21 (blue) has little effect on nucleosome organization at CTCF sites in comparison to a control depletion.
    Anti Ccctc Binding Factor Gene Ctcf, supplied by Millipore, used in various techniques. Bioz Stars score: 79/100, based on 4 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Millipore polyclonal antibodies against ctcf
    Cohesin does not organize nucleosomes at <t>CTCF</t> sites. (A, B) ChIP seq for RAD21 was plotted with respect to CTCF sites following depletion of CTCF (A) or <t>SNF2H</t> (B). In each case enrichment for RAD21 is reduced following depletion (blue) in comparison to control depletions (red). (C) ChIP seq showing SNF2H enrichment at CTCF sites in RAD21 (blue) depleted and control (red) cells. SNF2H enrichment is not affected by depletion of RAD21. (D) Depletion of RAD21 (blue) has little effect on nucleosome organization at CTCF sites in comparison to a control depletion.
    Polyclonal Antibodies Against Ctcf, supplied by Millipore, used in various techniques. Bioz Stars score: 78/100, based on 5 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    88
    Millipore chip seq ctcf
    Cohesin does not organize nucleosomes at <t>CTCF</t> sites. (A, B) ChIP seq for RAD21 was plotted with respect to CTCF sites following depletion of CTCF (A) or <t>SNF2H</t> (B). In each case enrichment for RAD21 is reduced following depletion (blue) in comparison to control depletions (red). (C) ChIP seq showing SNF2H enrichment at CTCF sites in RAD21 (blue) depleted and control (red) cells. SNF2H enrichment is not affected by depletion of RAD21. (D) Depletion of RAD21 (blue) has little effect on nucleosome organization at CTCF sites in comparison to a control depletion.
    Chip Seq Ctcf, supplied by Millipore, used in various techniques. Bioz Stars score: 88/100, based on 8 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    91
    Merck KGaA immunoprecipitation ctcf
    Cohesin does not organize nucleosomes at <t>CTCF</t> sites. (A, B) ChIP seq for RAD21 was plotted with respect to CTCF sites following depletion of CTCF (A) or <t>SNF2H</t> (B). In each case enrichment for RAD21 is reduced following depletion (blue) in comparison to control depletions (red). (C) ChIP seq showing SNF2H enrichment at CTCF sites in RAD21 (blue) depleted and control (red) cells. SNF2H enrichment is not affected by depletion of RAD21. (D) Depletion of RAD21 (blue) has little effect on nucleosome organization at CTCF sites in comparison to a control depletion.
    Immunoprecipitation Ctcf, supplied by Merck KGaA, used in various techniques. Bioz Stars score: 91/100, based on 14 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Image Search Results


    CSB regulates a subset of CTCF occupancy sites upon oxidative stress. ( A ) CTCF ChIP-qPCR assays in CSB expressing (WT) and non-expressing (CS1AN) cells, with or without a 1-h menadione treatment (100 μM). Shown are means ± SEM ( n = 3). A paired t -test was used to determine if the difference in CTCF enrichment before and after menadione treatment was significant. Single asterisks indicate P values

    Journal: Nucleic Acids Research

    Article Title: The CSB chromatin remodeler and CTCF architectural protein cooperate in response to oxidative stress

    doi: 10.1093/nar/gkv1219

    Figure Lengend Snippet: CSB regulates a subset of CTCF occupancy sites upon oxidative stress. ( A ) CTCF ChIP-qPCR assays in CSB expressing (WT) and non-expressing (CS1AN) cells, with or without a 1-h menadione treatment (100 μM). Shown are means ± SEM ( n = 3). A paired t -test was used to determine if the difference in CTCF enrichment before and after menadione treatment was significant. Single asterisks indicate P values

    Article Snippet: Antibodies Antibodies used for western blot analysis were rabbit anti-CSB (1:2000) , rabbit anti-CTCF (1:2000) (Millipore, 07-729), mouse anti-GAPDH (1:10 000) (Millipore, MAB374), rabbit anti-BRG1 (1:1000) , rabbit anti-acetylated histone H3 (1:1000) (Millipore, 06-599), HRP-conjugated goat anti-rabbit IgG (1:10 000) (Pierce, 31460) and HRP-conjugated goat anti-mouse (IgG+IgM) (1:10 000) (Jackson Laboratory, 115-035-044).

    Techniques: Chromatin Immunoprecipitation, Real-time Polymerase Chain Reaction, Expressing

    CTCF collaborates with CSB in response to oxidative stress. ( A ) Motif analysis of CSB ChIP-seq data. ( B ) Menadione sensitivity assays on CSB expressing and non-expressing (Vector) cells with decreased CTCF levels. Shown are means ± SEM ( n = 4). ( C ) Western blot showing a reduction in the CTCF protein level in cells expressing CTCF shRNA. Relative CTCF levels are shown below the CTCF blot. ( D ) CSB ChIP-qPCR assays in cells infected with lentivirus expressing control or CTCF shRNA, with or without with a 1-h menadione treatment (100 μM). Shown are means ± SEM ( n = 3). A paired t -test was used to determine if the difference in CSB enrichment with and without CTCF shRNA treatment was significant. Asterisks indicate P -values

    Journal: Nucleic Acids Research

    Article Title: The CSB chromatin remodeler and CTCF architectural protein cooperate in response to oxidative stress

    doi: 10.1093/nar/gkv1219

    Figure Lengend Snippet: CTCF collaborates with CSB in response to oxidative stress. ( A ) Motif analysis of CSB ChIP-seq data. ( B ) Menadione sensitivity assays on CSB expressing and non-expressing (Vector) cells with decreased CTCF levels. Shown are means ± SEM ( n = 4). ( C ) Western blot showing a reduction in the CTCF protein level in cells expressing CTCF shRNA. Relative CTCF levels are shown below the CTCF blot. ( D ) CSB ChIP-qPCR assays in cells infected with lentivirus expressing control or CTCF shRNA, with or without with a 1-h menadione treatment (100 μM). Shown are means ± SEM ( n = 3). A paired t -test was used to determine if the difference in CSB enrichment with and without CTCF shRNA treatment was significant. Asterisks indicate P -values

    Article Snippet: Antibodies Antibodies used for western blot analysis were rabbit anti-CSB (1:2000) , rabbit anti-CTCF (1:2000) (Millipore, 07-729), mouse anti-GAPDH (1:10 000) (Millipore, MAB374), rabbit anti-BRG1 (1:1000) , rabbit anti-acetylated histone H3 (1:1000) (Millipore, 06-599), HRP-conjugated goat anti-rabbit IgG (1:10 000) (Pierce, 31460) and HRP-conjugated goat anti-mouse (IgG+IgM) (1:10 000) (Jackson Laboratory, 115-035-044).

    Techniques: Chromatin Immunoprecipitation, Expressing, Plasmid Preparation, Western Blot, shRNA, Real-time Polymerase Chain Reaction, Infection

    CSB interacts with CTCF in cells and in vitro . ( A ) Co-immunoprecipitation of CSB and CTCF in 293T transiently transfected with Flag-tagged CTCF, with or without a 1-h treatment of 100 μM menadione. 3.3% of the lysates used for IP were loaded as input. ( B ) Schematics of recombinant proteins used in ( C – E ). All CSB derivatives were N-terminally tagged with the Flag epitope. (C) Coomassie-stained gel showing that CSB directly interacts with CTCF. CSB-C, but not CSB-N, is sufficient for the CTCF association. MBP was used as a negative control. (D and E) EMSA assays showing that CSB enhances CTCF association with DNA. (D) Varying amounts of purified MBP-CTCF (lane 2 in C) or MBP (lane 1 in C) were incubated with a 32 P-labeled, 200 bp DNA fragment containing a CTCF-binding motif (Supplementary Figure S4B). Protein–DNA complexes were resolved in a native 5% polyacrylamide gel. (E) Varying amounts of purified CSB were incubated with the radiolabeled DNA fragment in the presence or absence of MBP-CTCF. Reactions were subsequently resolved in a 5% native polyacrylamide gel. Protein–DNA complexes marked by ‘•’ and ‘••’ contain the MBP-CTCF protein, as they interacted with an anti-MBP antibody (Supplementary Figure S4A).

    Journal: Nucleic Acids Research

    Article Title: The CSB chromatin remodeler and CTCF architectural protein cooperate in response to oxidative stress

    doi: 10.1093/nar/gkv1219

    Figure Lengend Snippet: CSB interacts with CTCF in cells and in vitro . ( A ) Co-immunoprecipitation of CSB and CTCF in 293T transiently transfected with Flag-tagged CTCF, with or without a 1-h treatment of 100 μM menadione. 3.3% of the lysates used for IP were loaded as input. ( B ) Schematics of recombinant proteins used in ( C – E ). All CSB derivatives were N-terminally tagged with the Flag epitope. (C) Coomassie-stained gel showing that CSB directly interacts with CTCF. CSB-C, but not CSB-N, is sufficient for the CTCF association. MBP was used as a negative control. (D and E) EMSA assays showing that CSB enhances CTCF association with DNA. (D) Varying amounts of purified MBP-CTCF (lane 2 in C) or MBP (lane 1 in C) were incubated with a 32 P-labeled, 200 bp DNA fragment containing a CTCF-binding motif (Supplementary Figure S4B). Protein–DNA complexes were resolved in a native 5% polyacrylamide gel. (E) Varying amounts of purified CSB were incubated with the radiolabeled DNA fragment in the presence or absence of MBP-CTCF. Reactions were subsequently resolved in a 5% native polyacrylamide gel. Protein–DNA complexes marked by ‘•’ and ‘••’ contain the MBP-CTCF protein, as they interacted with an anti-MBP antibody (Supplementary Figure S4A).

    Article Snippet: Antibodies Antibodies used for western blot analysis were rabbit anti-CSB (1:2000) , rabbit anti-CTCF (1:2000) (Millipore, 07-729), mouse anti-GAPDH (1:10 000) (Millipore, MAB374), rabbit anti-BRG1 (1:1000) , rabbit anti-acetylated histone H3 (1:1000) (Millipore, 06-599), HRP-conjugated goat anti-rabbit IgG (1:10 000) (Pierce, 31460) and HRP-conjugated goat anti-mouse (IgG+IgM) (1:10 000) (Jackson Laboratory, 115-035-044).

    Techniques: In Vitro, Immunoprecipitation, Transfection, Recombinant, FLAG-tag, Staining, Negative Control, Purification, Incubation, Labeling, Binding Assay

    Characterization of DSCAM-AS1 SE in MCF-7 cells. ( a ) WashU genome browser view of the DSCAM-AS1 genomic locus, which is reported in association with apoERα ChIP-Seq and RNA-Seq reads enrichment in siCTR-(red) or siERα-(blue) transfected MCF-7 cells; and with GRO-Seq, ChIP-Seq profiles of histone modifications and DNase hypersensitivity signals (yellow), RNA-Pol II and eight TFs (teal-blue) obtained from vehicle treated MCF-7 cells (see the Materials and Methods section for detailed data source). ERα and CTCF ChIA-PET data performed in MCF-7 grown in full medium from ENCODE project are also included [ 26 ]. The coordinates of the predicted SE and aERBSs are reported at the top as black and orange boxes, respectively. ChIP-Seq genomic signal profiles are reported as read count per million sequenced reads. ( b , c ) Bar plots reporting ERα fold enrichment over IgG signal by ChIP-qPCR at DSCAM-AS1 promoter and E5-E6-enhancers, TFF1 promoter (positive control) and KCNQ1OT1 promoter (negative control), in MCF-7 cells grown in HD medium transfected with siERα or siCTR ( b ); treated for 45′ with 17β-estradiol (E2) or vehicle (veh) ( c ). Standard error of four biological replicates; p -value by unpaired t -test: ** p

    Journal: International Journal of Molecular Sciences

    Article Title: Luminal lncRNAs Regulation by ERα-Controlled Enhancers in a Ligand-Independent Manner in Breast Cancer Cells

    doi: 10.3390/ijms19020593

    Figure Lengend Snippet: Characterization of DSCAM-AS1 SE in MCF-7 cells. ( a ) WashU genome browser view of the DSCAM-AS1 genomic locus, which is reported in association with apoERα ChIP-Seq and RNA-Seq reads enrichment in siCTR-(red) or siERα-(blue) transfected MCF-7 cells; and with GRO-Seq, ChIP-Seq profiles of histone modifications and DNase hypersensitivity signals (yellow), RNA-Pol II and eight TFs (teal-blue) obtained from vehicle treated MCF-7 cells (see the Materials and Methods section for detailed data source). ERα and CTCF ChIA-PET data performed in MCF-7 grown in full medium from ENCODE project are also included [ 26 ]. The coordinates of the predicted SE and aERBSs are reported at the top as black and orange boxes, respectively. ChIP-Seq genomic signal profiles are reported as read count per million sequenced reads. ( b , c ) Bar plots reporting ERα fold enrichment over IgG signal by ChIP-qPCR at DSCAM-AS1 promoter and E5-E6-enhancers, TFF1 promoter (positive control) and KCNQ1OT1 promoter (negative control), in MCF-7 cells grown in HD medium transfected with siERα or siCTR ( b ); treated for 45′ with 17β-estradiol (E2) or vehicle (veh) ( c ). Standard error of four biological replicates; p -value by unpaired t -test: ** p

    Article Snippet: Antibodies used were designed against ERα (Santa Cruz Biotechnology, Dallas, TX, USA; sc543 and sc-7207), CTCF (Merck-Millipore, Burlington, MA, USA; 07-729), GATA3 (Santa Cruz Biotechnology, Dallas, TX, USA; sc-268), p300 (Santa Cruz Biotechnology Dallas, TX, USA sc-585), FOXM1 (Santa Cruz Biotechnology Dallas, TX, USA sc-376471) and Hsp90 (Cell Signaling Technology, Danvers, MA, USA; 4874) proteins.

    Techniques: Chromatin Immunoprecipitation, RNA Sequencing Assay, Transfection, ChIA Pet Assay, Real-time Polymerase Chain Reaction, Positive Control, Negative Control

    AR and CTCF do not colocalize, or interact in LNCaP cells. (A) Re-ChIP by CTCF, AR antibodies, or control IgG. Insulator1, 2 and, ARE1, 2, and 3 were tested. (B) Co-immunoprecipitation by CTCF antibody, and western blotting by AR, CTCF, or GAPDH. R-RWPE-1, L-LNCaP, R1881-synthetic androgen.

    Journal: PLoS ONE

    Article Title: Role of CTCF in Regulating SLC45A3-ELK4 Chimeric RNA

    doi: 10.1371/journal.pone.0150382

    Figure Lengend Snippet: AR and CTCF do not colocalize, or interact in LNCaP cells. (A) Re-ChIP by CTCF, AR antibodies, or control IgG. Insulator1, 2 and, ARE1, 2, and 3 were tested. (B) Co-immunoprecipitation by CTCF antibody, and western blotting by AR, CTCF, or GAPDH. R-RWPE-1, L-LNCaP, R1881-synthetic androgen.

    Article Snippet: For androgen treatment, cells were hormone starved for 2–3 days in RPMI 1640 (Phenol free) media, supplemented with 5% charcoal-striped FBS, and treated with 1 nM R1881 for 24 h. Antibodies including anti-AR (06–680) from Millipore and anti-CTCF (3418) from Cell Signaling were used in this study.

    Techniques: Chromatin Immunoprecipitation, Immunoprecipitation, Western Blot

    Knockdown of CTCF and schema of single cell sequencing. a . Western blot analysis of CTCF in luciferase control (shLuc) and CTCF-KD cells (shCTCF#1 and shCTCF#2). EL4 cells were infected with retroviral particles encoding GFP and an shRNA targeting CTCF or a control sequence for 5 days. b . Real-time quantitative PCR (RT-qPCR) analysis of CTCF expression in luciferase control (shLuc) and knockdown (shCTCF#1 and shCTCF#2) cells. The expression level of CTCF was normalized to GAPDH. c . Schema of single cell RNA sequencing using Fluidigm C1 system

    Journal: BMC Genomics

    Article Title: Exploring the changing landscape of cell-to-cell variation after CTCF knockdown via single cell RNA-seq

    doi: 10.1186/s12864-019-6379-5

    Figure Lengend Snippet: Knockdown of CTCF and schema of single cell sequencing. a . Western blot analysis of CTCF in luciferase control (shLuc) and CTCF-KD cells (shCTCF#1 and shCTCF#2). EL4 cells were infected with retroviral particles encoding GFP and an shRNA targeting CTCF or a control sequence for 5 days. b . Real-time quantitative PCR (RT-qPCR) analysis of CTCF expression in luciferase control (shLuc) and knockdown (shCTCF#1 and shCTCF#2) cells. The expression level of CTCF was normalized to GAPDH. c . Schema of single cell RNA sequencing using Fluidigm C1 system

    Article Snippet: Protein samples (40 μg/lane) were applied to SDS-PAGE followed by Western blotting against anti-CTCF antibody (07–729, Millipore), and anti-GAPDH antibody (sc-1616, Santa Cruz Biotechnology).

    Techniques: Sequencing, Western Blot, Luciferase, Infection, shRNA, Real-time Polymerase Chain Reaction, Quantitative RT-PCR, Expressing, RNA Sequencing Assay

    Validation of DNA binding protein occupancy. ChIP analysis of K562 chromatin for occupancy by the erythroid-specific transcription factors GATA1 and NF-E2; RNA Pol II; the chromatin architectural protein CTCF; and the barrier-associated proteins USF1,

    Journal: Blood

    Article Title: A tissue-specific chromatin loop activates the erythroid ankyrin-1 promoter

    doi: 10.1182/blood-2012-08-450262

    Figure Lengend Snippet: Validation of DNA binding protein occupancy. ChIP analysis of K562 chromatin for occupancy by the erythroid-specific transcription factors GATA1 and NF-E2; RNA Pol II; the chromatin architectural protein CTCF; and the barrier-associated proteins USF1,

    Article Snippet: ChIP was performed using the Magna ChIP A assay kit (17-610; Millipore), with anti-GATA1 (sc-265), –NF-E2 (sc-22 827), -USF2 (sc-862), -USF1 (sc-8983), -PRMT1, and -RNA polymerase II (sc-130851; all from Santa Cruz Biotechnology), -CTCF (07-729; Millipore), or -CARM1 (PRMT4, ab84370; Abcam) antibodies.

    Techniques: Binding Assay, Chromatin Immunoprecipitation

    Expression and occupancy of a set of transcription factors corresponding to the identified motifs at FAIRE peaks Expression levels of AR, CTCF, FOXA1, ERG, ETV1, and NKX3-1 relative to TBP in four independent primary tumors. Error bars indicate SD from triplicate analysis. FAIRE-seq snapshots of accessible chromatin regions containing a CTCF motif in four primary tumors (green) and CTCF binding as assessed through ChIP-seq in LNCaP cells (red track, GSE33213). Heatmap, illustrating ChIP–qPCR-based enrichment of CTCF binding at accessible chromatin sites depicted in (B). FAIRE-seq snapshots of accessible chromatin regions containing an ERG motif in four primary tumors (green) and ERG binding as assessed through ChIP-seq in LNCaP cells (blue track, GSM1193658). Heatmap, illustrating ChIP–qPCR-based enrichment of ERG binding at accessible chromatin sites depicted in (D).

    Journal: EMBO Molecular Medicine

    Article Title: Androgen receptor profiling predicts prostate cancer outcome

    doi: 10.15252/emmm.201505424

    Figure Lengend Snippet: Expression and occupancy of a set of transcription factors corresponding to the identified motifs at FAIRE peaks Expression levels of AR, CTCF, FOXA1, ERG, ETV1, and NKX3-1 relative to TBP in four independent primary tumors. Error bars indicate SD from triplicate analysis. FAIRE-seq snapshots of accessible chromatin regions containing a CTCF motif in four primary tumors (green) and CTCF binding as assessed through ChIP-seq in LNCaP cells (red track, GSE33213). Heatmap, illustrating ChIP–qPCR-based enrichment of CTCF binding at accessible chromatin sites depicted in (B). FAIRE-seq snapshots of accessible chromatin regions containing an ERG motif in four primary tumors (green) and ERG binding as assessed through ChIP-seq in LNCaP cells (blue track, GSM1193658). Heatmap, illustrating ChIP–qPCR-based enrichment of ERG binding at accessible chromatin sites depicted in (D).

    Article Snippet: Antibodies used were AR-N20 (sc-618; Santa Cruz), CTCF (07-729; Millipore), and ERG (sc-353; Santa Cruz).

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

    Epigenome map of the Kallikrein locus in prostate cells. RNA-seq and ChIP-seq (H3K27me3, H3K9ac, H3K4me3 and CTCF) profiles of adjacent, transcriptionally active (green highlight) and silenced (red highlight) regions in LNCaP cancer cell line and normal PrEC cells. CTCF ChIP-seq shows CTCF binding throughout the locus. Two CTCF sites are located at the boundary between the active and silenced regions.

    Journal: Nature Communications

    Article Title: Constitutively bound CTCF sites maintain 3D chromatin architecture and long-range epigenetically regulated domains

    doi: 10.1038/s41467-019-13753-7

    Figure Lengend Snippet: Epigenome map of the Kallikrein locus in prostate cells. RNA-seq and ChIP-seq (H3K27me3, H3K9ac, H3K4me3 and CTCF) profiles of adjacent, transcriptionally active (green highlight) and silenced (red highlight) regions in LNCaP cancer cell line and normal PrEC cells. CTCF ChIP-seq shows CTCF binding throughout the locus. Two CTCF sites are located at the boundary between the active and silenced regions.

    Article Snippet: 10 μg of the following antibodies were added per ChIP and incubated overnight—CTCF (#07-729, Millipore), RAD21 (#ab992, Abcam), H3K4me3 (#39159, Active Motif), H3K27ac (#39133, Active Motif).

    Techniques: RNA Sequencing Assay, Chromatin Immunoprecipitation, Binding Assay

    A subset of CTCF binding sites is more resistant to CTCF depletion. a Bar plot quantifying ‘lost’, ‘persistent’ and ‘gained’ CTCF sites in LNCaP cells. b UCSC genome browser screenshot demonstrating maintenance of CTCF binding at some sites (box) following CTCF knockdown. c CTCF ChIP-seq illustrates CTCF binding at the boundary of the active and silenced regions at the KLK locus is retained following 144 h of CTCF RNAi. All other binding in the region is lost. RAD21 ChIP-qPCR performed after 144 h of control and CTCF RNAi demonstrates that cohesin binding is maintained where CTCF binding is persistent at the KLK locus (* indicates where two-tailed t -test, p

    Journal: Nature Communications

    Article Title: Constitutively bound CTCF sites maintain 3D chromatin architecture and long-range epigenetically regulated domains

    doi: 10.1038/s41467-019-13753-7

    Figure Lengend Snippet: A subset of CTCF binding sites is more resistant to CTCF depletion. a Bar plot quantifying ‘lost’, ‘persistent’ and ‘gained’ CTCF sites in LNCaP cells. b UCSC genome browser screenshot demonstrating maintenance of CTCF binding at some sites (box) following CTCF knockdown. c CTCF ChIP-seq illustrates CTCF binding at the boundary of the active and silenced regions at the KLK locus is retained following 144 h of CTCF RNAi. All other binding in the region is lost. RAD21 ChIP-qPCR performed after 144 h of control and CTCF RNAi demonstrates that cohesin binding is maintained where CTCF binding is persistent at the KLK locus (* indicates where two-tailed t -test, p

    Article Snippet: 10 μg of the following antibodies were added per ChIP and incubated overnight—CTCF (#07-729, Millipore), RAD21 (#ab992, Abcam), H3K4me3 (#39159, Active Motif), H3K27ac (#39133, Active Motif).

    Techniques: Binding Assay, Chromatin Immunoprecipitation, Real-time Polymerase Chain Reaction, Two Tailed Test

    Cohesin does not organize nucleosomes at CTCF sites. (A, B) ChIP seq for RAD21 was plotted with respect to CTCF sites following depletion of CTCF (A) or SNF2H (B). In each case enrichment for RAD21 is reduced following depletion (blue) in comparison to control depletions (red). (C) ChIP seq showing SNF2H enrichment at CTCF sites in RAD21 (blue) depleted and control (red) cells. SNF2H enrichment is not affected by depletion of RAD21. (D) Depletion of RAD21 (blue) has little effect on nucleosome organization at CTCF sites in comparison to a control depletion.

    Journal: PLoS Genetics

    Article Title: The Chromatin Remodelling Enzymes SNF2H and SNF2L Position Nucleosomes adjacent to CTCF and Other Transcription Factors

    doi: 10.1371/journal.pgen.1005940

    Figure Lengend Snippet: Cohesin does not organize nucleosomes at CTCF sites. (A, B) ChIP seq for RAD21 was plotted with respect to CTCF sites following depletion of CTCF (A) or SNF2H (B). In each case enrichment for RAD21 is reduced following depletion (blue) in comparison to control depletions (red). (C) ChIP seq showing SNF2H enrichment at CTCF sites in RAD21 (blue) depleted and control (red) cells. SNF2H enrichment is not affected by depletion of RAD21. (D) Depletion of RAD21 (blue) has little effect on nucleosome organization at CTCF sites in comparison to a control depletion.

    Article Snippet: Primary antibodies for ChIP used were rabbit anti-human SNF2H (Abcam, ab72499), mouse anti-CTCF (Millipore, 17–10044), rabbit anti-RAD21 (Abcam, ab992), rabbit anti-BPTF (Millipore, Abe24), and rat anti-SNF2L (2C4, [ ] which has been kindly provided by P. Becker).

    Techniques: Chromatin Immunoprecipitation

    SNF2L and SNF2H contribute to the nucleosome phasing at transcription factor binding sites. (A-D) Nucleosome density plots of sequenced mono nucleosomal DNA after depletion of SNF2L and SNF2H proteins mapped to the JUN (A, B) or RFX5 (C, D) transcription factor binding sites. Depleting SNF2L (A, C green) shows an effect on the factor proximal nucleosomes at majority of transcription factor binding sites while the effect of SNF2H knock down (B, D blue) affects distal nucleosomes at the binding sites for factors such as JUN (see main text). Transcription factors such as E2H2 (E, F) and GTF3C2 (G, H) that have no well organised nucleosomes are less affected by the depletion of SNF2H (F, H blue) or SNF2L (E, G green). In all plots data was only taken from factor binding sites that do not have adjacent CTCF sites.

    Journal: PLoS Genetics

    Article Title: The Chromatin Remodelling Enzymes SNF2H and SNF2L Position Nucleosomes adjacent to CTCF and Other Transcription Factors

    doi: 10.1371/journal.pgen.1005940

    Figure Lengend Snippet: SNF2L and SNF2H contribute to the nucleosome phasing at transcription factor binding sites. (A-D) Nucleosome density plots of sequenced mono nucleosomal DNA after depletion of SNF2L and SNF2H proteins mapped to the JUN (A, B) or RFX5 (C, D) transcription factor binding sites. Depleting SNF2L (A, C green) shows an effect on the factor proximal nucleosomes at majority of transcription factor binding sites while the effect of SNF2H knock down (B, D blue) affects distal nucleosomes at the binding sites for factors such as JUN (see main text). Transcription factors such as E2H2 (E, F) and GTF3C2 (G, H) that have no well organised nucleosomes are less affected by the depletion of SNF2H (F, H blue) or SNF2L (E, G green). In all plots data was only taken from factor binding sites that do not have adjacent CTCF sites.

    Article Snippet: Primary antibodies for ChIP used were rabbit anti-human SNF2H (Abcam, ab72499), mouse anti-CTCF (Millipore, 17–10044), rabbit anti-RAD21 (Abcam, ab992), rabbit anti-BPTF (Millipore, Abe24), and rat anti-SNF2L (2C4, [ ] which has been kindly provided by P. Becker).

    Techniques: Binding Assay

    Interdependence of SNF2H and CTCF binding. (A) Chromatin of control cells (red) and CTCF depleted (blue) HeLa cells was immuno-precipitated using an anti-SNF2H antibody and the resulting DNA fragments sequenced. SNF2H is enriched at CTCF sites in comparison to the surrounding DNA, and this enrichment is reduced following depletion of CTCF. (B) ChIP seq experiment for CTCF showing enrichment at CTCF sites (red). Following depletion of SNF2H CTCF occupancy is reduced (blue). (C) Protein levels of SNF2H (green bands) and CTCF (top red bands) in cells depleted for SNF2H, control cells or CTCF depleted cells. Two different quantities (lane 1 and 2) of whole cell extracts of the respective cells were immuno-blotted for SNF2H, CTCF and beta-actin as a loading control. Depletion of SNF2H does not result in any global change in CTCF protein levels.

    Journal: PLoS Genetics

    Article Title: The Chromatin Remodelling Enzymes SNF2H and SNF2L Position Nucleosomes adjacent to CTCF and Other Transcription Factors

    doi: 10.1371/journal.pgen.1005940

    Figure Lengend Snippet: Interdependence of SNF2H and CTCF binding. (A) Chromatin of control cells (red) and CTCF depleted (blue) HeLa cells was immuno-precipitated using an anti-SNF2H antibody and the resulting DNA fragments sequenced. SNF2H is enriched at CTCF sites in comparison to the surrounding DNA, and this enrichment is reduced following depletion of CTCF. (B) ChIP seq experiment for CTCF showing enrichment at CTCF sites (red). Following depletion of SNF2H CTCF occupancy is reduced (blue). (C) Protein levels of SNF2H (green bands) and CTCF (top red bands) in cells depleted for SNF2H, control cells or CTCF depleted cells. Two different quantities (lane 1 and 2) of whole cell extracts of the respective cells were immuno-blotted for SNF2H, CTCF and beta-actin as a loading control. Depletion of SNF2H does not result in any global change in CTCF protein levels.

    Article Snippet: Primary antibodies for ChIP used were rabbit anti-human SNF2H (Abcam, ab72499), mouse anti-CTCF (Millipore, 17–10044), rabbit anti-RAD21 (Abcam, ab992), rabbit anti-BPTF (Millipore, Abe24), and rat anti-SNF2L (2C4, [ ] which has been kindly provided by P. Becker).

    Techniques: Binding Assay, Chromatin Immunoprecipitation

    SNF2H organizes nucleosomes at CTCF binding sites. (A-C) Mono nucleosomes were isolated from cell lines following siRNA depletion of proteins indicated. Sequencing of the nucleosomal DNA enabled reads to be mapped with respect to CTCF sites. The strong nucleosome organization flanking the CTCF binding sites is disrupted following depletion of either CTCF (A) or SNF2H (B). The depletion of SNF2L (C) shows only a small effect. The same control depletion data is plotted in (B) and (C).

    Journal: PLoS Genetics

    Article Title: The Chromatin Remodelling Enzymes SNF2H and SNF2L Position Nucleosomes adjacent to CTCF and Other Transcription Factors

    doi: 10.1371/journal.pgen.1005940

    Figure Lengend Snippet: SNF2H organizes nucleosomes at CTCF binding sites. (A-C) Mono nucleosomes were isolated from cell lines following siRNA depletion of proteins indicated. Sequencing of the nucleosomal DNA enabled reads to be mapped with respect to CTCF sites. The strong nucleosome organization flanking the CTCF binding sites is disrupted following depletion of either CTCF (A) or SNF2H (B). The depletion of SNF2L (C) shows only a small effect. The same control depletion data is plotted in (B) and (C).

    Article Snippet: Primary antibodies for ChIP used were rabbit anti-human SNF2H (Abcam, ab72499), mouse anti-CTCF (Millipore, 17–10044), rabbit anti-RAD21 (Abcam, ab992), rabbit anti-BPTF (Millipore, Abe24), and rat anti-SNF2L (2C4, [ ] which has been kindly provided by P. Becker).

    Techniques: Binding Assay, Isolation, Sequencing

    Depletion of SNF2H affects the transcription of many genes regulated by CTCF. (A) RNA seq was performed for cells depleted of CTCF and SNF2H. Expression of 3294 genes could be significantly (p

    Journal: PLoS Genetics

    Article Title: The Chromatin Remodelling Enzymes SNF2H and SNF2L Position Nucleosomes adjacent to CTCF and Other Transcription Factors

    doi: 10.1371/journal.pgen.1005940

    Figure Lengend Snippet: Depletion of SNF2H affects the transcription of many genes regulated by CTCF. (A) RNA seq was performed for cells depleted of CTCF and SNF2H. Expression of 3294 genes could be significantly (p

    Article Snippet: Primary antibodies for ChIP used were rabbit anti-human SNF2H (Abcam, ab72499), mouse anti-CTCF (Millipore, 17–10044), rabbit anti-RAD21 (Abcam, ab992), rabbit anti-BPTF (Millipore, Abe24), and rat anti-SNF2L (2C4, [ ] which has been kindly provided by P. Becker).

    Techniques: RNA Sequencing Assay, Expressing

    Constructive and destructive interference between nucleosomes organized by CTCF and other transcription factors. (A, B) ChIP seq enrichment for CTCF at sites bound by RFX5 (A) and JUN (B). For each transcription factor, data for subsets of sites that either include (red) or do not include (blue) CTCF bound sites within 500 bp was plotted. The removal of coincident CTCF sites greatly reduces CTCF ChIP at both RFX5 and JUN sites (A, B). Nucleosome density plots for RFX5 sites (C) that include CTCF sites within 500 bp (red) and that do not include CTCF sites (blue) 500 bp show that nucleosomes are better organised at RFX5 binding sites that do have adjacent CTCF sites (C, red). In contrast, at JUN binding sites nucleosomes are better organised at the subset of sites not flanked by CTCF sites (D, blue). Nucleosome density plots for RFX5 (E) and JUN (F, G) after CTCF depletion (blue) and control cells (red). CTCF removal disrupts nucleosome organisation at RFX5 sites (E, blue) and improves it slightly at JUN sites if CTCF sites are adjacent (F, blue). Removing JUN sites where CTCF sites are within 500 bp shows a much more prominent nucleosomal pattern with or without CTCF depletion (G). ChIP seq enrichment for RAD21 at RFX5 (H) and JUN (I) binding sites. RAD21 is enriched at factor binding sites with CTCF sites within 500 bp (red). Depletion of CTCF has limited effect on RAD21 enrichment (blue) at RFX5 and JUN sites, indicateingthat RAD21 enrichment is only partially CTCF dependent at these sites.

    Journal: PLoS Genetics

    Article Title: The Chromatin Remodelling Enzymes SNF2H and SNF2L Position Nucleosomes adjacent to CTCF and Other Transcription Factors

    doi: 10.1371/journal.pgen.1005940

    Figure Lengend Snippet: Constructive and destructive interference between nucleosomes organized by CTCF and other transcription factors. (A, B) ChIP seq enrichment for CTCF at sites bound by RFX5 (A) and JUN (B). For each transcription factor, data for subsets of sites that either include (red) or do not include (blue) CTCF bound sites within 500 bp was plotted. The removal of coincident CTCF sites greatly reduces CTCF ChIP at both RFX5 and JUN sites (A, B). Nucleosome density plots for RFX5 sites (C) that include CTCF sites within 500 bp (red) and that do not include CTCF sites (blue) 500 bp show that nucleosomes are better organised at RFX5 binding sites that do have adjacent CTCF sites (C, red). In contrast, at JUN binding sites nucleosomes are better organised at the subset of sites not flanked by CTCF sites (D, blue). Nucleosome density plots for RFX5 (E) and JUN (F, G) after CTCF depletion (blue) and control cells (red). CTCF removal disrupts nucleosome organisation at RFX5 sites (E, blue) and improves it slightly at JUN sites if CTCF sites are adjacent (F, blue). Removing JUN sites where CTCF sites are within 500 bp shows a much more prominent nucleosomal pattern with or without CTCF depletion (G). ChIP seq enrichment for RAD21 at RFX5 (H) and JUN (I) binding sites. RAD21 is enriched at factor binding sites with CTCF sites within 500 bp (red). Depletion of CTCF has limited effect on RAD21 enrichment (blue) at RFX5 and JUN sites, indicateingthat RAD21 enrichment is only partially CTCF dependent at these sites.

    Article Snippet: Primary antibodies for ChIP used were rabbit anti-human SNF2H (Abcam, ab72499), mouse anti-CTCF (Millipore, 17–10044), rabbit anti-RAD21 (Abcam, ab992), rabbit anti-BPTF (Millipore, Abe24), and rat anti-SNF2L (2C4, [ ] which has been kindly provided by P. Becker).

    Techniques: Chromatin Immunoprecipitation, Binding Assay