Structured Review

Santa Cruz Biotechnology anti pol ii
Anti Pol Ii, supplied by Santa Cruz Biotechnology, used in various techniques. Bioz Stars score: 99/100, based on 12 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/result/anti pol ii/product/Santa Cruz Biotechnology
Average 99 stars, based on 12 article reviews
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anti pol ii - by Bioz Stars, 2019-10
99/100 stars

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Clone Assay:

Article Title: Telomerase reverse transcriptase promotes cancer cell proliferation by augmenting tRNA expression
Article Snippet: The following Abs were used for Western blot analysis: anti-TERT (Abcam; ab32020, lot YI021602CR); anti-RPC32 (Santa Cruz Biotechnology Inc.; sc-28712); anti-MYC (Santa Cruz Biotechnology Inc.; sc-764); anti–pol II (Santa Cruz Biotechnology Inc.; sc-899); anti-GTF3C2 (Abcam; ab89113); anti-POLR3B (Abcam; ab86143); anti–TATA-box–binding protein (anti-TBP) (Santa Cruz Biotechnology Inc.; sc-273); anti-FLAG (Sigma-Aldrich; F7425); anti–proliferating cell nuclear antigen (anti-PCNA) (Cell Signaling Technology; CST2586); and anti-nucleolin (Santa Cruz Biotechnology Inc.; sc-13057). .. The following Abs were used for Western blot analysis: anti-TERT (Abcam; ab32020, lot YI021602CR); anti-RPC32 (Santa Cruz Biotechnology Inc.; sc-28712); anti-MYC (Santa Cruz Biotechnology Inc.; sc-764); anti–pol II (Santa Cruz Biotechnology Inc.; sc-899); anti-GTF3C2 (Abcam; ab89113); anti-POLR3B (Abcam; ab86143); anti–TATA-box–binding protein (anti-TBP) (Santa Cruz Biotechnology Inc.; sc-273); anti-FLAG (Sigma-Aldrich; F7425); anti–proliferating cell nuclear antigen (anti-PCNA) (Cell Signaling Technology; CST2586); and anti-nucleolin (Santa Cruz Biotechnology Inc.; sc-13057).

Centrifugation:

Article Title: The comprehensive epigenome map of piRNA clusters
Article Snippet: Lysate was then pre-incubated with protein A-Sepharose (GE Healthcare) and then cleared by 1500 rpm centrifugation 30 s at room temperature. .. Pre-cleared lysate (Input) was incubated with anti-pol II (Santa Cruz), anti-Mouse IgG (IgG-M; Santa Cruz), anti-H3K9me2 (Millipore), anti-H3K9me3 (Millipore or Abcam), anti-H3K9ac (Millipore), anti-H3K4me2 (Millipore), anti-H3K4me3 (Millipore or Abcam) and anti-rabbit IgG (IgG-R; Millipore) (1:1000) at 4°C for overnight.

Amplification:

Article Title: A Pitx2-MicroRNA Pathway Modulates Cell Proliferation in Myoblasts and Skeletal-Muscle Satellite Cells and Promotes Their Commitment to a Myogenic Cell Fate
Article Snippet: For chromatin immunoprecipitation, the antibodies used were anti-V5 (clone V5-10; Sigma) or anti-polymerase II (anti-Pol II) (8WG16) (Santa Cruz); antibody against mouse dystrophin was used as a mouse IgG control. .. As controls, normal rabbit IgG replaced the anti-V5 antibody to reveal nonspecific immunoprecipitation of chromatin.

Expressing:

Article Title: Transcriptional Control of Brown Fat Determination by PRDM16
Article Snippet: As a point of reference, the Ct values for both PRDM16 and TBP mRNA expression in BAT were typically 24–26. .. Lysates were resolved by SDS-PAGE, transferred to PVDF membrane (Millipore) and probed with anti-UCP1 (Chemicon), anti-Flag M2 (Sigma), anti-PRDM16 (rabbit polyclonal), and anti-pol-II (Santa-Cruz biotechnology).

Article Title: Telomerase reverse transcriptase promotes cancer cell proliferation by augmenting tRNA expression
Article Snippet: The following Abs were used for Western blot analysis: anti-TERT (Abcam; ab32020, lot YI021602CR); anti-RPC32 (Santa Cruz Biotechnology Inc.; sc-28712); anti-MYC (Santa Cruz Biotechnology Inc.; sc-764); anti–pol II (Santa Cruz Biotechnology Inc.; sc-899); anti-GTF3C2 (Abcam; ab89113); anti-POLR3B (Abcam; ab86143); anti–TATA-box–binding protein (anti-TBP) (Santa Cruz Biotechnology Inc.; sc-273); anti-FLAG (Sigma-Aldrich; F7425); anti–proliferating cell nuclear antigen (anti-PCNA) (Cell Signaling Technology; CST2586); and anti-nucleolin (Santa Cruz Biotechnology Inc.; sc-13057). .. The following Abs were used for Western blot analysis: anti-TERT (Abcam; ab32020, lot YI021602CR); anti-RPC32 (Santa Cruz Biotechnology Inc.; sc-28712); anti-MYC (Santa Cruz Biotechnology Inc.; sc-764); anti–pol II (Santa Cruz Biotechnology Inc.; sc-899); anti-GTF3C2 (Abcam; ab89113); anti-POLR3B (Abcam; ab86143); anti–TATA-box–binding protein (anti-TBP) (Santa Cruz Biotechnology Inc.; sc-273); anti-FLAG (Sigma-Aldrich; F7425); anti–proliferating cell nuclear antigen (anti-PCNA) (Cell Signaling Technology; CST2586); and anti-nucleolin (Santa Cruz Biotechnology Inc.; sc-13057).

Positive Control:

Article Title: SP1 and RARα regulate AGAP2 expression in cancer
Article Snippet: Afterwards, crosslinked proteins of interest were immunoprecipitated with 2 μg of either anti-RARα (C-20), anti-RXRα (D-20) (both from Santa Cruz Biotechnology), anti-PCAF (C14G9, Cell Signaling), or 1 μg of anti-SP1 (D4C3, Cell Signalling). .. Anti-Pol II (N-20, Santa Cruz Biotechnology) was used as positive control and rabbit IgG (Invitrogen) as negative control. .. Immunoprecipitated DNA was purified and used for qPCR amplifications. (Primer sequences for qPCR analysis can be found in Supplementary Table ).

Polymerase Chain Reaction:

Article Title: In Vivo and in Vitro Evidence That PPAR? Ligands Are Antagonists of Leptin Signaling in Breast Cancer
Article Snippet: The precleared chromatin was immunoprecipitated with specific anti-GR (E-20), PPARγ (H-100), or anti-polymerase II (RNA-PoII H-224) antibodies (Santa Cruz Biotechnology) and were reimmunoprecipitated with anti-PPARγ, anti-NCoR (NB120-2781), or anti-SMRT (NB300-732) antibodies (Novus Biologicals). .. Pellets were washed as reported, eluted with elution buffer (1% SDS, 0.1 mol/L NaHCO3 ), and digested with proteinase K. DNA was obtained by phenol/chloroform/isoamyl alcohol extractions and were precipitated with ethanol; 5 μL of each sample and input were used for real-time PCR with the primers flanking GRE sequence present in the leptin promoter region: 5′-GCCCAGGCTGTAGTGCAAT-3′ and 5′-TAGCCAGGTGTGGTGG-3′.

Article Title: Transcriptional Control of Brown Fat Determination by PRDM16
Article Snippet: Q-PCR was performed using the ABI-9300 PCR machine. .. Lysates were resolved by SDS-PAGE, transferred to PVDF membrane (Millipore) and probed with anti-UCP1 (Chemicon), anti-Flag M2 (Sigma), anti-PRDM16 (rabbit polyclonal), and anti-pol-II (Santa-Cruz biotechnology).

Article Title: BRCA1 Expression Is Epigenetically Repressed in Sporadic Ovarian Cancer Cells by Overexpression of C-Terminal Binding Protein 2
Article Snippet: The anti-polymerase II (Pol II) (N-20)X antibody was from Santa Cruz Biotechnology (Dallas, TX). .. The DNA-protein cross-links were reversed in the ChIP and input samples by adding 100 µl of reverse buffer (1% SDS and 0.1 M NaHCO3 ) and heating to 65°C for 6 hours.

Immunostaining:

Article Title: Essential role of the TFIID subunit TAF4 in murine embryogenesis and embryonic stem cell differentiation
Article Snippet: The following antibodies were used: anti-OCT4 (sc-9081; Santa Cruz), anti-NANOG (RCAB001P; Reprocell), SOX2 (L1D6A2; Cell Signaling), previously described or recently developed in house antibodies against TBP (3G3), TAF1, TAF3 (ref. ), TAF4 (32TA and also sc-136093; Santa Cruz), TAF4B (ref. ), TAF5 (1TA), TAF6 (25TA), TAF7 (19TA), TAF12 (22TA), and TAF13 (16TA), TAF10 (sc-102125; Santa Cruz) and in house 6TA2B11 (ref. ), anti-Pol II (sc-9001x; Santa Cruz), anti-Tnnt2 (MS-295-P1; Thermo scientific). .. The following antibodies were used: anti-OCT4 (sc-9081; Santa Cruz), anti-NANOG (RCAB001P; Reprocell), SOX2 (L1D6A2; Cell Signaling), previously described or recently developed in house antibodies against TBP (3G3), TAF1, TAF3 (ref. ), TAF4 (32TA and also sc-136093; Santa Cruz), TAF4B (ref. ), TAF5 (1TA), TAF6 (25TA), TAF7 (19TA), TAF12 (22TA), and TAF13 (16TA), TAF10 (sc-102125; Santa Cruz) and in house 6TA2B11 (ref. ), anti-Pol II (sc-9001x; Santa Cruz), anti-Tnnt2 (MS-295-P1; Thermo scientific).

Real-time Polymerase Chain Reaction:

Article Title: Repurposing Pan-HDAC Inhibitors for ARID1A-Mutated Ovarian Cancer
Article Snippet: The following antibodies were used to perform ChIP: anti-HDAC2 (Abcam), anti-H3K27ac (Millipore), anti-Pol II (Santa Cruz), and anti-EZH2 (Cell Signaling). .. Isotype-matched immunoglobulin G was used as a negative control.

Article Title: Identification of linc-NeD125, a novel long non coding RNA that hosts miR-125b-1 and negatively controls proliferation of human neuroblastoma cells
Article Snippet: Sheared chromatin was immunoprecipitated with anti-Egr2 or anti-Pol II (Santa Cruz Biotechnology, sc-899). .. Normal rabbit IgG, provided by the kit, was used as negative control.

Article Title: In Vivo and in Vitro Evidence That PPAR? Ligands Are Antagonists of Leptin Signaling in Breast Cancer
Article Snippet: The precleared chromatin was immunoprecipitated with specific anti-GR (E-20), PPARγ (H-100), or anti-polymerase II (RNA-PoII H-224) antibodies (Santa Cruz Biotechnology) and were reimmunoprecipitated with anti-PPARγ, anti-NCoR (NB120-2781), or anti-SMRT (NB300-732) antibodies (Novus Biologicals). .. Normal mouse serum IgG was used as negative control.

Article Title: Transcriptional Control of Brown Fat Determination by PRDM16
Article Snippet: Paragraph title: Real-time PCR analysis and Western blotting ... Lysates were resolved by SDS-PAGE, transferred to PVDF membrane (Millipore) and probed with anti-UCP1 (Chemicon), anti-Flag M2 (Sigma), anti-PRDM16 (rabbit polyclonal), and anti-pol-II (Santa-Cruz biotechnology).

Incubation:

Article Title: Mediator MED23 cooperates with RUNX2 to drive osteoblast differentiation and bone development
Article Snippet: Cell lysates were then sonicated to shear chromatin. .. After that, cell lysates were centrifuged and 100 μl supernatant was diluted with 900 μl dilution buffer (16.7 mM Tris-HCl, pH 8.0, 0.01% SDS, 1.1% Triton X-100, 1.2 mM EDTA, 167 mM NaCl) and then incubated with 2 μg anti-RUNX2 or 2 μg anti-Pol II (Santa Cruz) or non-immune Rabbit IgG overnight at 4° C. About 20 μl Protein G magnetic beads (Life technologies) were added for another 4 h on a rotating wheel. .. Chromatin then was immunoprecipitated, decrosslinked at 65 °C and treated with Proteinase K. Precipitated DNA was extracted and quantified by real-time PCR.

Article Title: The comprehensive epigenome map of piRNA clusters
Article Snippet: Lysate was then pre-incubated with protein A-Sepharose (GE Healthcare) and then cleared by 1500 rpm centrifugation 30 s at room temperature. .. Pre-cleared lysate (Input) was incubated with anti-pol II (Santa Cruz), anti-Mouse IgG (IgG-M; Santa Cruz), anti-H3K9me2 (Millipore), anti-H3K9me3 (Millipore or Abcam), anti-H3K9ac (Millipore), anti-H3K4me2 (Millipore), anti-H3K4me3 (Millipore or Abcam) and anti-rabbit IgG (IgG-R; Millipore) (1:1000) at 4°C for overnight. .. Lysate was then incubated with equilibrated Protein-A-Sepharose beads for 1 h at 4°C.

Article Title: BRCA1 Expression Is Epigenetically Repressed in Sporadic Ovarian Cancer Cells by Overexpression of C-Terminal Binding Protein 2
Article Snippet: The remainder of the lysates were diluted with 10 volumes of ChIP dilution buffer [20 mM Tris-HCl (pH 8.0), 150 mM NaCl, 2 mM EDTA, and 1% Triton X-100] and incubated overnight at 4°C with various selected antibodies prebound to Dynal magnetic beads (Invitrogen Corp). .. The anti-polymerase II (Pol II) (N-20)X antibody was from Santa Cruz Biotechnology (Dallas, TX).

Formalin-fixed Paraffin-Embedded:

Article Title: Epigenetic regulation of the extrinsic oncosuppressor PTX3 gene in inflammation and cancer
Article Snippet: ChIP and PAT-ChIP assays were performed as described. .. Briefly, the chromatin obtained from 12 × 106 cells or 5 × 10-µm-thick FFPE tissue sections was sonicated to obtain 200−400 bp chromatin fragments, then immunoprecipitated at 4°C overnight with the following antibodies: anti-H3, anti-H3K27ac and anti-H3K4me1 (Abcam), anti-H3K4me3 (Active Motif), anti-H3K27me3, anti-NF-κB p65 (RelA), anti-EZH2 and anti-SUZ12 (Millipore-Upstate), anti-Pol II (N-20), anti TAF II p250, and anti STAT3 (C-20) (Santa Cruz biochemistry). .. Rabbit IgG (Millipore) was used as negative control.

Mass Spectrometry:

Article Title: Essential role of the TFIID subunit TAF4 in murine embryogenesis and embryonic stem cell differentiation
Article Snippet: 500 μl fractions were collected and analysed by western blot. .. The following antibodies were used: anti-OCT4 (sc-9081; Santa Cruz), anti-NANOG (RCAB001P; Reprocell), SOX2 (L1D6A2; Cell Signaling), previously described or recently developed in house antibodies against TBP (3G3), TAF1, TAF3 (ref. ), TAF4 (32TA and also sc-136093; Santa Cruz), TAF4B (ref. ), TAF5 (1TA), TAF6 (25TA), TAF7 (19TA), TAF12 (22TA), and TAF13 (16TA), TAF10 (sc-102125; Santa Cruz) and in house 6TA2B11 (ref. ), anti-Pol II (sc-9001x; Santa Cruz), anti-Tnnt2 (MS-295-P1; Thermo scientific). .. We also used a polyclonal TAF4B antibody (2057) raised against a peptide corresponding to amino acids 692–710 of human TAF4B that is 100% conserved in mouse Taf4b.

Modification:

Article Title: Silencing of IFN-stimulated gene transcription is regulated by histone H1 and its chaperone TAF-I
Article Snippet: HeLa S3 and HEK293 cells were grown in Dulbecco's modified essential medium supplemented with 10% fetal calf serum. .. Antibodies used in this study are as follows: Anti-STAT1α/β (sc-346; Santa Cruz Biotechnology), anti-STAT2 (sc-476; Santa Cruz Biotechnology), anti-IRF9 (sc-10793; Santa Cruz Biotechnology), anti-phospho-(Tyr701) STAT1 (#9171; Cell Signaling Technology), anti-phospho-(Tyr689) STAT2 (#07-224; Upstate Biotechnology), anti-phospho-(Ser727) STAT1 (#06-802; Upstate Biotechnology), anti-Pol II (sc-899; Santa Cruz Biotechnology), anti-β-Actin (A5441; SIGMA), anti-Histone H3 (ab1791; Abcam), anti-acetyl-Histone H3 (06-599; Millipore), anti-Histone H1.2 (ab4086; Abcam), anti-Flag (F3165; SIGMA) and anti-TAF-Iα/β (monoclonal antibody KM1725) ( ) antibodies.

Western Blot:

Article Title: Targeting STAT5 in Hematological Malignancies through Inhibition of the Bromodomain and Extra-Terminal (BET) Bromodomain Protein BRD2
Article Snippet: Paragraph title: Immunoblots and chromatin immunoprecipitation (ChIP) ... Briefly, leukemia cells were formaldehyde fixed and sonicated, and lysates were immunoprecipitated with anti-STAT5 or anti-polymerase II (sc-9001, Santa Cruz Biotechnology) antibodies.

Article Title: Regulation of nucleosome architecture and factor binding revealed by nuclease footprinting of the ESC genome
Article Snippet: Paragraph title: Western blotting ... The antibodies used to detect proteins were: anti-Brg1 (1:1000, Bethyl A300-813A), anti-Mbd3 (1:1000, Bethyl A302-529A), anti-Klf4 (1:1000, Millipore AB4138), anti-Pol II (1:1000, Santa Cruz sc-899), anti-GAPDH (1:5000, Cell Signaling 2118), and anti-actin (1:50,000, Sigma A1978).

Article Title: Transcriptional Control of Brown Fat Determination by PRDM16
Article Snippet: Paragraph title: Real-time PCR analysis and Western blotting ... Lysates were resolved by SDS-PAGE, transferred to PVDF membrane (Millipore) and probed with anti-UCP1 (Chemicon), anti-Flag M2 (Sigma), anti-PRDM16 (rabbit polyclonal), and anti-pol-II (Santa-Cruz biotechnology).

Article Title: Telomerase reverse transcriptase promotes cancer cell proliferation by augmenting tRNA expression
Article Snippet: IgG was obtained from Santa Cruz Biotechnology Inc. .. The following Abs were used for Western blot analysis: anti-TERT (Abcam; ab32020, lot YI021602CR); anti-RPC32 (Santa Cruz Biotechnology Inc.; sc-28712); anti-MYC (Santa Cruz Biotechnology Inc.; sc-764); anti–pol II (Santa Cruz Biotechnology Inc.; sc-899); anti-GTF3C2 (Abcam; ab89113); anti-POLR3B (Abcam; ab86143); anti–TATA-box–binding protein (anti-TBP) (Santa Cruz Biotechnology Inc.; sc-273); anti-FLAG (Sigma-Aldrich; F7425); anti–proliferating cell nuclear antigen (anti-PCNA) (Cell Signaling Technology; CST2586); and anti-nucleolin (Santa Cruz Biotechnology Inc.; sc-13057). .. Human TERT and TERT DN vectors (D712A and V713I) were described previously ( ).

Transfection:

Article Title: A Pitx2-MicroRNA Pathway Modulates Cell Proliferation in Myoblasts and Skeletal-Muscle Satellite Cells and Promotes Their Commitment to a Myogenic Cell Fate
Article Snippet: After 24 h of Pitx2c transfection, the cells were cross-linked with 1% formaldehyde for 10 min at 37°C. .. For chromatin immunoprecipitation, the antibodies used were anti-V5 (clone V5-10; Sigma) or anti-polymerase II (anti-Pol II) (8WG16) (Santa Cruz); antibody against mouse dystrophin was used as a mouse IgG control.

Activation Assay:

Article Title: Epigenetic Modulation of Microglial Inflammatory Gene Loci in Helminth-Induced Immune Suppression
Article Snippet: The following antibodies were used to analyze microglia activation and maturation: M1/70 (anti-Mac1), 1D3 (anti-MHC-II), as well as purified anti-mouse TNF-α, IL-6, and NOS2 (BD Biosciences, San Diego, CA). .. Antibodies used in ChIP assays included anti-Pol-II (Santa Cruz Biotechnology [Dallas, Texas, USA]) at 2 mg/IP, anti-H3K4Me3 (Millipore [Billerica, Massachusetts, USA]) at 1 mg/IP, anti-H3K9/14Ac (cell signaling technology [Danvers, Massachusetts, USA]) at 2 mg/IP, or normal rabbit IgGs.

Protease Inhibitor:

Article Title: The comprehensive epigenome map of piRNA clusters
Article Snippet: Ten micrograms per microliters of cleared lysate was 10-fold diluted by ChIP dilution buffer (1% Triton X-100, 2 mM EDTA, 150 mM NaCl, 20 mM Tris–HCl (pH 8.1) and protease inhibitor cocktail). .. Pre-cleared lysate (Input) was incubated with anti-pol II (Santa Cruz), anti-Mouse IgG (IgG-M; Santa Cruz), anti-H3K9me2 (Millipore), anti-H3K9me3 (Millipore or Abcam), anti-H3K9ac (Millipore), anti-H3K4me2 (Millipore), anti-H3K4me3 (Millipore or Abcam) and anti-rabbit IgG (IgG-R; Millipore) (1:1000) at 4°C for overnight.

Cell Culture:

Article Title: Androgen receptor-mediated downregulation of microRNA-221 and -222 in castration-resistant prostate cancer
Article Snippet: Paragraph title: Cell culture and materials ... Antibodies are: anti-AR (Abcam, ab74272), anti-FOXA1 (Abcam, ab23738), anti-acetylated H3K9/14 (Millipore, #06–599), anti-acetylated H3K27 (Abcam, ab4729), ant-dimethyl-H3K4 (Millipore, #07–030), ant-trimethyl-H3K4 (Millipore, #07–473), anti-trimethyl-H3K27 (Millipore, #07–449), anti-Pol II (Santa Cruz Technology, sc-899), and anti-β-tubulin (Santa Cruz Technology, sc-80011).

Article Title: Silencing of IFN-stimulated gene transcription is regulated by histone H1 and its chaperone TAF-I
Article Snippet: Paragraph title: Cell culture and antibodies ... Antibodies used in this study are as follows: Anti-STAT1α/β (sc-346; Santa Cruz Biotechnology), anti-STAT2 (sc-476; Santa Cruz Biotechnology), anti-IRF9 (sc-10793; Santa Cruz Biotechnology), anti-phospho-(Tyr701) STAT1 (#9171; Cell Signaling Technology), anti-phospho-(Tyr689) STAT2 (#07-224; Upstate Biotechnology), anti-phospho-(Ser727) STAT1 (#06-802; Upstate Biotechnology), anti-Pol II (sc-899; Santa Cruz Biotechnology), anti-β-Actin (A5441; SIGMA), anti-Histone H3 (ab1791; Abcam), anti-acetyl-Histone H3 (06-599; Millipore), anti-Histone H1.2 (ab4086; Abcam), anti-Flag (F3165; SIGMA) and anti-TAF-Iα/β (monoclonal antibody KM1725) ( ) antibodies.

Generated:

Article Title: Identification of linc-NeD125, a novel long non coding RNA that hosts miR-125b-1 and negatively controls proliferation of human neuroblastoma cells
Article Snippet: Sheared chromatin was immunoprecipitated with anti-Egr2 or anti-Pol II (Santa Cruz Biotechnology, sc-899). .. Normal rabbit IgG, provided by the kit, was used as negative control.

Article Title: Transcriptional activators enhance polyadenylation of mRNA precursors
Article Snippet: Anti-CPSF100 and anti-CstF64 antibodies were generated in our lab ( ). .. Anti-His and anti-Pol II (N20) were purchased from Santa Cruz.

other:

Article Title: Non-coding RNA derived from the region adjacent to the human HO-1 E2 enhancer selectively regulates HO-1 gene induction by modulating Pol II binding
Article Snippet: Anti-NRF2 (sc-13032), anti-Lamin B (sc-6217), anti-Pol II (sc-899), anti-HSP90 (sc-59577) and anti-BACH1 (sc-14700) antibodies were purchased from Santa Cruz Biotechnology, Inc. Anti-β-Actin antibody (A1978) was obtained from Sigma-Aldrich.

Sequencing:

Article Title: In Vivo and in Vitro Evidence That PPAR? Ligands Are Antagonists of Leptin Signaling in Breast Cancer
Article Snippet: The precleared chromatin was immunoprecipitated with specific anti-GR (E-20), PPARγ (H-100), or anti-polymerase II (RNA-PoII H-224) antibodies (Santa Cruz Biotechnology) and were reimmunoprecipitated with anti-PPARγ, anti-NCoR (NB120-2781), or anti-SMRT (NB300-732) antibodies (Novus Biologicals). .. Normal mouse serum IgG was used as negative control.

Sonication:

Article Title: SP1 and RARα regulate AGAP2 expression in cancer
Article Snippet: The chromatin was sheared to 100–600 bp by sonication using an AFA Focused-Ultrasonicator (S220- Series from CovarisTM ) at 6 × 60 second on-off pulses at 4 °C. .. Anti-Pol II (N-20, Santa Cruz Biotechnology) was used as positive control and rabbit IgG (Invitrogen) as negative control.

Article Title: Mediator MED23 cooperates with RUNX2 to drive osteoblast differentiation and bone development
Article Snippet: Cell lysates were then sonicated to shear chromatin. .. After that, cell lysates were centrifuged and 100 μl supernatant was diluted with 900 μl dilution buffer (16.7 mM Tris-HCl, pH 8.0, 0.01% SDS, 1.1% Triton X-100, 1.2 mM EDTA, 167 mM NaCl) and then incubated with 2 μg anti-RUNX2 or 2 μg anti-Pol II (Santa Cruz) or non-immune Rabbit IgG overnight at 4° C. About 20 μl Protein G magnetic beads (Life technologies) were added for another 4 h on a rotating wheel.

Article Title: Targeting STAT5 in Hematological Malignancies through Inhibition of the Bromodomain and Extra-Terminal (BET) Bromodomain Protein BRD2
Article Snippet: Band intensity was quantitated using Image J software (NIH). .. Briefly, leukemia cells were formaldehyde fixed and sonicated, and lysates were immunoprecipitated with anti-STAT5 or anti-polymerase II (sc-9001, Santa Cruz Biotechnology) antibodies. .. Quantitative PCR was performed in triplicate on ChIP product or input using SYBR Green PCR Master Mix (Applied Biosystems, Foster City, CA) and region-specific primers ( ).

Article Title: In Vivo and in Vitro Evidence That PPAR? Ligands Are Antagonists of Leptin Signaling in Breast Cancer
Article Snippet: MCF-7 cells were cross-linked with 1% formaldehyde and sonicated. .. The precleared chromatin was immunoprecipitated with specific anti-GR (E-20), PPARγ (H-100), or anti-polymerase II (RNA-PoII H-224) antibodies (Santa Cruz Biotechnology) and were reimmunoprecipitated with anti-PPARγ, anti-NCoR (NB120-2781), or anti-SMRT (NB300-732) antibodies (Novus Biologicals).

Article Title: Epigenetic regulation of the extrinsic oncosuppressor PTX3 gene in inflammation and cancer
Article Snippet: ChIP and PAT-ChIP assays were performed as described. .. Briefly, the chromatin obtained from 12 × 106 cells or 5 × 10-µm-thick FFPE tissue sections was sonicated to obtain 200−400 bp chromatin fragments, then immunoprecipitated at 4°C overnight with the following antibodies: anti-H3, anti-H3K27ac and anti-H3K4me1 (Abcam), anti-H3K4me3 (Active Motif), anti-H3K27me3, anti-NF-κB p65 (RelA), anti-EZH2 and anti-SUZ12 (Millipore-Upstate), anti-Pol II (N-20), anti TAF II p250, and anti STAT3 (C-20) (Santa Cruz biochemistry). .. Rabbit IgG (Millipore) was used as negative control.

Article Title: The comprehensive epigenome map of piRNA clusters
Article Snippet: After incubation on ice, homogenates were sonicated with Sonifier 250 (BRANSON) 10 s followed by incubation on ice 10 s (duty cycle = 50 and out put control = 7). .. Pre-cleared lysate (Input) was incubated with anti-pol II (Santa Cruz), anti-Mouse IgG (IgG-M; Santa Cruz), anti-H3K9me2 (Millipore), anti-H3K9me3 (Millipore or Abcam), anti-H3K9ac (Millipore), anti-H3K4me2 (Millipore), anti-H3K4me3 (Millipore or Abcam) and anti-rabbit IgG (IgG-R; Millipore) (1:1000) at 4°C for overnight.

Article Title: BRCA1 Expression Is Epigenetically Repressed in Sporadic Ovarian Cancer Cells by Overexpression of C-Terminal Binding Protein 2
Article Snippet: The cells were then sonicated on a Vibra-Cell VCX 130 (Sonics, Newtown, CT) using a 3-mm tip with four 30-second pulses at 12% amplitude. .. The anti-polymerase II (Pol II) (N-20)X antibody was from Santa Cruz Biotechnology (Dallas, TX).

Binding Assay:

Article Title: Identification of linc-NeD125, a novel long non coding RNA that hosts miR-125b-1 and negatively controls proliferation of human neuroblastoma cells
Article Snippet: For the analysis of H3K4me3 levels, REST and EGR1 binding on linc-NeD125 promoter, chromatin extracts from proliferating or 6 days RA-treated BE(2)-C cells were immunoprecipitated with anti-trimethyl Histone H3 (Lys4) (Millipore 07–473), anti-REST , or anti-EGR1 according to Laneve et al., 2010 with minor modifications. .. Sheared chromatin was immunoprecipitated with anti-Egr2 or anti-Pol II (Santa Cruz Biotechnology, sc-899).

Article Title: Targeting STAT5 in Hematological Malignancies through Inhibition of the Bromodomain and Extra-Terminal (BET) Bromodomain Protein BRD2
Article Snippet: Briefly, leukemia cells were formaldehyde fixed and sonicated, and lysates were immunoprecipitated with anti-STAT5 or anti-polymerase II (sc-9001, Santa Cruz Biotechnology) antibodies. .. Quantitative PCR was performed in triplicate on ChIP product or input using SYBR Green PCR Master Mix (Applied Biosystems, Foster City, CA) and region-specific primers ( ).

Article Title: A Pitx2-MicroRNA Pathway Modulates Cell Proliferation in Myoblasts and Skeletal-Muscle Satellite Cells and Promotes Their Commitment to a Myogenic Cell Fate
Article Snippet: For chromatin immunoprecipitation, the antibodies used were anti-V5 (clone V5-10; Sigma) or anti-polymerase II (anti-Pol II) (8WG16) (Santa Cruz); antibody against mouse dystrophin was used as a mouse IgG control. .. For chromatin immunoprecipitation, the antibodies used were anti-V5 (clone V5-10; Sigma) or anti-polymerase II (anti-Pol II) (8WG16) (Santa Cruz); antibody against mouse dystrophin was used as a mouse IgG control.

Immunofluorescence:

Article Title: Epigenetic Modulation of Microglial Inflammatory Gene Loci in Helminth-Induced Immune Suppression
Article Snippet: For immunofluorescence (IF) staining, fluorescent-conjugated secondary antibodies and isotype control antibodies (Jackson Immuno Research Laboratories, West Grove, PA) were used. .. Antibodies used in ChIP assays included anti-Pol-II (Santa Cruz Biotechnology [Dallas, Texas, USA]) at 2 mg/IP, anti-H3K4Me3 (Millipore [Billerica, Massachusetts, USA]) at 1 mg/IP, anti-H3K9/14Ac (cell signaling technology [Danvers, Massachusetts, USA]) at 2 mg/IP, or normal rabbit IgGs.

ChIP-sequencing:

Article Title: The comprehensive epigenome map of piRNA clusters
Article Snippet: Paragraph title: ChIP and ChIP-seq ... Pre-cleared lysate (Input) was incubated with anti-pol II (Santa Cruz), anti-Mouse IgG (IgG-M; Santa Cruz), anti-H3K9me2 (Millipore), anti-H3K9me3 (Millipore or Abcam), anti-H3K9ac (Millipore), anti-H3K4me2 (Millipore), anti-H3K4me3 (Millipore or Abcam) and anti-rabbit IgG (IgG-R; Millipore) (1:1000) at 4°C for overnight.

Magnetic Beads:

Article Title: Mediator MED23 cooperates with RUNX2 to drive osteoblast differentiation and bone development
Article Snippet: Cell lysates were then sonicated to shear chromatin. .. After that, cell lysates were centrifuged and 100 μl supernatant was diluted with 900 μl dilution buffer (16.7 mM Tris-HCl, pH 8.0, 0.01% SDS, 1.1% Triton X-100, 1.2 mM EDTA, 167 mM NaCl) and then incubated with 2 μg anti-RUNX2 or 2 μg anti-Pol II (Santa Cruz) or non-immune Rabbit IgG overnight at 4° C. About 20 μl Protein G magnetic beads (Life technologies) were added for another 4 h on a rotating wheel. .. Chromatin then was immunoprecipitated, decrosslinked at 65 °C and treated with Proteinase K. Precipitated DNA was extracted and quantified by real-time PCR.

Article Title: BRCA1 Expression Is Epigenetically Repressed in Sporadic Ovarian Cancer Cells by Overexpression of C-Terminal Binding Protein 2
Article Snippet: The remainder of the lysates were diluted with 10 volumes of ChIP dilution buffer [20 mM Tris-HCl (pH 8.0), 150 mM NaCl, 2 mM EDTA, and 1% Triton X-100] and incubated overnight at 4°C with various selected antibodies prebound to Dynal magnetic beads (Invitrogen Corp). .. The anti-polymerase II (Pol II) (N-20)X antibody was from Santa Cruz Biotechnology (Dallas, TX).

Isolation:

Article Title: Regulation of nucleosome architecture and factor binding revealed by nuclease footprinting of the ESC genome
Article Snippet: Nuclear and cytoplasmic fractions were isolated using the NE-PER extraction kit (Thermo Scientific) following the manufacturers instructions. .. The antibodies used to detect proteins were: anti-Brg1 (1:1000, Bethyl A300-813A), anti-Mbd3 (1:1000, Bethyl A302-529A), anti-Klf4 (1:1000, Millipore AB4138), anti-Pol II (1:1000, Santa Cruz sc-899), anti-GAPDH (1:5000, Cell Signaling 2118), and anti-actin (1:50,000, Sigma A1978).

Purification:

Article Title: Epigenetic Modulation of Microglial Inflammatory Gene Loci in Helminth-Induced Immune Suppression
Article Snippet: The following antibodies were used to analyze microglia activation and maturation: M1/70 (anti-Mac1), 1D3 (anti-MHC-II), as well as purified anti-mouse TNF-α, IL-6, and NOS2 (BD Biosciences, San Diego, CA). .. Antibodies used in ChIP assays included anti-Pol-II (Santa Cruz Biotechnology [Dallas, Texas, USA]) at 2 mg/IP, anti-H3K4Me3 (Millipore [Billerica, Massachusetts, USA]) at 1 mg/IP, anti-H3K9/14Ac (cell signaling technology [Danvers, Massachusetts, USA]) at 2 mg/IP, or normal rabbit IgGs.

Article Title: BRCA1 Expression Is Epigenetically Repressed in Sporadic Ovarian Cancer Cells by Overexpression of C-Terminal Binding Protein 2
Article Snippet: The anti-polymerase II (Pol II) (N-20)X antibody was from Santa Cruz Biotechnology (Dallas, TX). .. The DNA-protein cross-links were reversed in the ChIP and input samples by adding 100 µl of reverse buffer (1% SDS and 0.1 M NaHCO3 ) and heating to 65°C for 6 hours.

Reverse Transcription Polymerase Chain Reaction:

Article Title: Epigenetic regulation of the extrinsic oncosuppressor PTX3 gene in inflammation and cancer
Article Snippet: Briefly, the chromatin obtained from 12 × 106 cells or 5 × 10-µm-thick FFPE tissue sections was sonicated to obtain 200−400 bp chromatin fragments, then immunoprecipitated at 4°C overnight with the following antibodies: anti-H3, anti-H3K27ac and anti-H3K4me1 (Abcam), anti-H3K4me3 (Active Motif), anti-H3K27me3, anti-NF-κB p65 (RelA), anti-EZH2 and anti-SUZ12 (Millipore-Upstate), anti-Pol II (N-20), anti TAF II p250, and anti STAT3 (C-20) (Santa Cruz biochemistry). .. Rabbit IgG (Millipore) was used as negative control.

Staining:

Article Title: Epigenetic Modulation of Microglial Inflammatory Gene Loci in Helminth-Induced Immune Suppression
Article Snippet: For immunofluorescence (IF) staining, fluorescent-conjugated secondary antibodies and isotype control antibodies (Jackson Immuno Research Laboratories, West Grove, PA) were used. .. Antibodies used in ChIP assays included anti-Pol-II (Santa Cruz Biotechnology [Dallas, Texas, USA]) at 2 mg/IP, anti-H3K4Me3 (Millipore [Billerica, Massachusetts, USA]) at 1 mg/IP, anti-H3K9/14Ac (cell signaling technology [Danvers, Massachusetts, USA]) at 2 mg/IP, or normal rabbit IgGs.

Chromatin Immunoprecipitation:

Article Title: SP1 and RARα regulate AGAP2 expression in cancer
Article Snippet: Paragraph title: Chromatin immunoprecipitation ... Anti-Pol II (N-20, Santa Cruz Biotechnology) was used as positive control and rabbit IgG (Invitrogen) as negative control.

Article Title: Repurposing Pan-HDAC Inhibitors for ARID1A-Mutated Ovarian Cancer
Article Snippet: Given that mutation and loss of expression of ARID1A and genetic alterations in other subunits of ATP-dependent chromatin remodeling complexes are observed in ~20% of all human cancers , our findings may have far-reaching implications for improving therapy for an array of cancer types. .. The following antibodies were used to perform ChIP: anti-HDAC2 (Abcam), anti-H3K27ac (Millipore), anti-Pol II (Santa Cruz), and anti-EZH2 (Cell Signaling). .. Isotype-matched immunoglobulin G was used as a negative control.

Article Title: Mediator MED23 cooperates with RUNX2 to drive osteoblast differentiation and bone development
Article Snippet: Paragraph title: ChIP assay ... After that, cell lysates were centrifuged and 100 μl supernatant was diluted with 900 μl dilution buffer (16.7 mM Tris-HCl, pH 8.0, 0.01% SDS, 1.1% Triton X-100, 1.2 mM EDTA, 167 mM NaCl) and then incubated with 2 μg anti-RUNX2 or 2 μg anti-Pol II (Santa Cruz) or non-immune Rabbit IgG overnight at 4° C. About 20 μl Protein G magnetic beads (Life technologies) were added for another 4 h on a rotating wheel.

Article Title: Identification of linc-NeD125, a novel long non coding RNA that hosts miR-125b-1 and negatively controls proliferation of human neuroblastoma cells
Article Snippet: Paragraph title: Chromatin Immunoprecipitation (ChIP) Assays ... Sheared chromatin was immunoprecipitated with anti-Egr2 or anti-Pol II (Santa Cruz Biotechnology, sc-899).

Article Title: Wnt/?-Catenin Signaling Enhances Cyclooxygenase-2 (COX2) Transcriptional Activity in Gastric Cancer Cells
Article Snippet: Paragraph title: Chromatin immunoprecipitation (ChIP) assays ... Additionally, the fraction of the RNA polymerase II (Pol-II) and acetylated histones H3 and H4 (H3ac and H4ac) bound either to the TBE-II region (−793/−594) or the proximal region (−118/+62) of the COX2 promoter was similarly assessed (anti-Pol-II, Santa Cruz; H3ac and H4ac, Upstate).

Article Title: Targeting STAT5 in Hematological Malignancies through Inhibition of the Bromodomain and Extra-Terminal (BET) Bromodomain Protein BRD2
Article Snippet: Paragraph title: Immunoblots and chromatin immunoprecipitation (ChIP) ... Briefly, leukemia cells were formaldehyde fixed and sonicated, and lysates were immunoprecipitated with anti-STAT5 or anti-polymerase II (sc-9001, Santa Cruz Biotechnology) antibodies.

Article Title: Epigenetic Modulation of Microglial Inflammatory Gene Loci in Helminth-Induced Immune Suppression
Article Snippet: For immunofluorescence (IF) staining, fluorescent-conjugated secondary antibodies and isotype control antibodies (Jackson Immuno Research Laboratories, West Grove, PA) were used. .. Antibodies used in ChIP assays included anti-Pol-II (Santa Cruz Biotechnology [Dallas, Texas, USA]) at 2 mg/IP, anti-H3K4Me3 (Millipore [Billerica, Massachusetts, USA]) at 1 mg/IP, anti-H3K9/14Ac (cell signaling technology [Danvers, Massachusetts, USA]) at 2 mg/IP, or normal rabbit IgGs. .. Murine NCC was induced by i.c. injection of 50 μl of HBSS (Hank's balance salt solution) containing approximately ∼40 M. corti metacestodes into 5-week old C57BL/6 mice under short-term anesthesia ( ; ; , ; ).

Article Title: In Vivo and in Vitro Evidence That PPAR? Ligands Are Antagonists of Leptin Signaling in Breast Cancer
Article Snippet: Paragraph title: Chromatin Immunoprecipitation and Re–Chromatin Immunoprecipitation Assays ... The precleared chromatin was immunoprecipitated with specific anti-GR (E-20), PPARγ (H-100), or anti-polymerase II (RNA-PoII H-224) antibodies (Santa Cruz Biotechnology) and were reimmunoprecipitated with anti-PPARγ, anti-NCoR (NB120-2781), or anti-SMRT (NB300-732) antibodies (Novus Biologicals).

Article Title: Epigenetic regulation of the extrinsic oncosuppressor PTX3 gene in inflammation and cancer
Article Snippet: Paragraph title: ChIP, PAT-ChIP and MIRA assays ... Briefly, the chromatin obtained from 12 × 106 cells or 5 × 10-µm-thick FFPE tissue sections was sonicated to obtain 200−400 bp chromatin fragments, then immunoprecipitated at 4°C overnight with the following antibodies: anti-H3, anti-H3K27ac and anti-H3K4me1 (Abcam), anti-H3K4me3 (Active Motif), anti-H3K27me3, anti-NF-κB p65 (RelA), anti-EZH2 and anti-SUZ12 (Millipore-Upstate), anti-Pol II (N-20), anti TAF II p250, and anti STAT3 (C-20) (Santa Cruz biochemistry).

Article Title: The comprehensive epigenome map of piRNA clusters
Article Snippet: Paragraph title: ChIP and ChIP-seq ... Pre-cleared lysate (Input) was incubated with anti-pol II (Santa Cruz), anti-Mouse IgG (IgG-M; Santa Cruz), anti-H3K9me2 (Millipore), anti-H3K9me3 (Millipore or Abcam), anti-H3K9ac (Millipore), anti-H3K4me2 (Millipore), anti-H3K4me3 (Millipore or Abcam) and anti-rabbit IgG (IgG-R; Millipore) (1:1000) at 4°C for overnight.

Article Title: BRCA1 Expression Is Epigenetically Repressed in Sporadic Ovarian Cancer Cells by Overexpression of C-Terminal Binding Protein 2
Article Snippet: Paragraph title: Chromatin Immunoprecipitation Assay ... The anti-polymerase II (Pol II) (N-20)X antibody was from Santa Cruz Biotechnology (Dallas, TX).

Article Title: A Pitx2-MicroRNA Pathway Modulates Cell Proliferation in Myoblasts and Skeletal-Muscle Satellite Cells and Promotes Their Commitment to a Myogenic Cell Fate
Article Snippet: After 24 h of Pitx2c transfection, the cells were cross-linked with 1% formaldehyde for 10 min at 37°C. .. For chromatin immunoprecipitation, the antibodies used were anti-V5 (clone V5-10; Sigma) or anti-polymerase II (anti-Pol II) (8WG16) (Santa Cruz); antibody against mouse dystrophin was used as a mouse IgG control. .. All PCRs were performed at an annealing temperature of 60°C.

Article Title: Telomerase reverse transcriptase promotes cancer cell proliferation by augmenting tRNA expression
Article Snippet: The anti-FLAG mAb (F1804) used for ChIP experiments was obtained from Sigma-Aldrich. .. The following Abs were used for Western blot analysis: anti-TERT (Abcam; ab32020, lot YI021602CR); anti-RPC32 (Santa Cruz Biotechnology Inc.; sc-28712); anti-MYC (Santa Cruz Biotechnology Inc.; sc-764); anti–pol II (Santa Cruz Biotechnology Inc.; sc-899); anti-GTF3C2 (Abcam; ab89113); anti-POLR3B (Abcam; ab86143); anti–TATA-box–binding protein (anti-TBP) (Santa Cruz Biotechnology Inc.; sc-273); anti-FLAG (Sigma-Aldrich; F7425); anti–proliferating cell nuclear antigen (anti-PCNA) (Cell Signaling Technology; CST2586); and anti-nucleolin (Santa Cruz Biotechnology Inc.; sc-13057).

SDS Page:

Article Title: Regulation of nucleosome architecture and factor binding revealed by nuclease footprinting of the ESC genome
Article Snippet: 30 μg of lysate were separated by SDS-PAGE, transferred to nitrocellulose (Life Sciences), and assayed by immunoblotting. .. The antibodies used to detect proteins were: anti-Brg1 (1:1000, Bethyl A300-813A), anti-Mbd3 (1:1000, Bethyl A302-529A), anti-Klf4 (1:1000, Millipore AB4138), anti-Pol II (1:1000, Santa Cruz sc-899), anti-GAPDH (1:5000, Cell Signaling 2118), and anti-actin (1:50,000, Sigma A1978).

Article Title: Transcriptional Control of Brown Fat Determination by PRDM16
Article Snippet: For western blot analysis, cells or tissues were lysed in RIPA buffer (0.5% NP-40, 0.1% sodium deoxycholate, 150 mM NaCl, 50 mM Tris-Cl, pH 7.5). .. Lysates were resolved by SDS-PAGE, transferred to PVDF membrane (Millipore) and probed with anti-UCP1 (Chemicon), anti-Flag M2 (Sigma), anti-PRDM16 (rabbit polyclonal), and anti-pol-II (Santa-Cruz biotechnology). .. All animal experiments were performed according to procedures approved by the Dana-Farber Cancer Institute’s Institutional Animal Care and Use Committee.

Plasmid Preparation:

Article Title: A Pitx2-MicroRNA Pathway Modulates Cell Proliferation in Myoblasts and Skeletal-Muscle Satellite Cells and Promotes Their Commitment to a Myogenic Cell Fate
Article Snippet: Sol8 cells were transfected with 8 μg of the pcDNA-V5-Pitx2c plasmid in 100-mm dishes. .. For chromatin immunoprecipitation, the antibodies used were anti-V5 (clone V5-10; Sigma) or anti-polymerase II (anti-Pol II) (8WG16) (Santa Cruz); antibody against mouse dystrophin was used as a mouse IgG control.

Article Title: Telomerase reverse transcriptase promotes cancer cell proliferation by augmenting tRNA expression
Article Snippet: The following Abs were used for Western blot analysis: anti-TERT (Abcam; ab32020, lot YI021602CR); anti-RPC32 (Santa Cruz Biotechnology Inc.; sc-28712); anti-MYC (Santa Cruz Biotechnology Inc.; sc-764); anti–pol II (Santa Cruz Biotechnology Inc.; sc-899); anti-GTF3C2 (Abcam; ab89113); anti-POLR3B (Abcam; ab86143); anti–TATA-box–binding protein (anti-TBP) (Santa Cruz Biotechnology Inc.; sc-273); anti-FLAG (Sigma-Aldrich; F7425); anti–proliferating cell nuclear antigen (anti-PCNA) (Cell Signaling Technology; CST2586); and anti-nucleolin (Santa Cruz Biotechnology Inc.; sc-13057). .. The following Abs were used for Western blot analysis: anti-TERT (Abcam; ab32020, lot YI021602CR); anti-RPC32 (Santa Cruz Biotechnology Inc.; sc-28712); anti-MYC (Santa Cruz Biotechnology Inc.; sc-764); anti–pol II (Santa Cruz Biotechnology Inc.; sc-899); anti-GTF3C2 (Abcam; ab89113); anti-POLR3B (Abcam; ab86143); anti–TATA-box–binding protein (anti-TBP) (Santa Cruz Biotechnology Inc.; sc-273); anti-FLAG (Sigma-Aldrich; F7425); anti–proliferating cell nuclear antigen (anti-PCNA) (Cell Signaling Technology; CST2586); and anti-nucleolin (Santa Cruz Biotechnology Inc.; sc-13057).

Software:

Article Title: Targeting STAT5 in Hematological Malignancies through Inhibition of the Bromodomain and Extra-Terminal (BET) Bromodomain Protein BRD2
Article Snippet: Band intensity was quantitated using Image J software (NIH). .. Briefly, leukemia cells were formaldehyde fixed and sonicated, and lysates were immunoprecipitated with anti-STAT5 or anti-polymerase II (sc-9001, Santa Cruz Biotechnology) antibodies.

Negative Control:

Article Title: SP1 and RARα regulate AGAP2 expression in cancer
Article Snippet: Afterwards, crosslinked proteins of interest were immunoprecipitated with 2 μg of either anti-RARα (C-20), anti-RXRα (D-20) (both from Santa Cruz Biotechnology), anti-PCAF (C14G9, Cell Signaling), or 1 μg of anti-SP1 (D4C3, Cell Signalling). .. Anti-Pol II (N-20, Santa Cruz Biotechnology) was used as positive control and rabbit IgG (Invitrogen) as negative control. .. Immunoprecipitated DNA was purified and used for qPCR amplifications. (Primer sequences for qPCR analysis can be found in Supplementary Table ).

Immunoprecipitation:

Article Title: SP1 and RARα regulate AGAP2 expression in cancer
Article Snippet: Afterwards, crosslinked proteins of interest were immunoprecipitated with 2 μg of either anti-RARα (C-20), anti-RXRα (D-20) (both from Santa Cruz Biotechnology), anti-PCAF (C14G9, Cell Signaling), or 1 μg of anti-SP1 (D4C3, Cell Signalling). .. Anti-Pol II (N-20, Santa Cruz Biotechnology) was used as positive control and rabbit IgG (Invitrogen) as negative control.

Article Title: Identification of linc-NeD125, a novel long non coding RNA that hosts miR-125b-1 and negatively controls proliferation of human neuroblastoma cells
Article Snippet: For EGR2 transcription factor and RNA Pol II, ChIP analyses were performed on chromatin extracts from proliferating or 6 days RA-treated BE(2)-C cells according to manufacturer's specifications of MAGnify Chromatin Immunoprecipitation System kit (Invitrogen). .. Sheared chromatin was immunoprecipitated with anti-Egr2 or anti-Pol II (Santa Cruz Biotechnology, sc-899). .. Normal rabbit IgG, provided by the kit, was used as negative control.

Article Title: Wnt/?-Catenin Signaling Enhances Cyclooxygenase-2 (COX2) Transcriptional Activity in Gastric Cancer Cells
Article Snippet: The fraction of nuclear β-catenin bound either to TBE Sites I, II, III or IV in the human COX2 promoter was immunoprecipitated with anti β-catenin antibodies (Santa Cruz) and assessed by real time-PCR using specific primers ( ). .. Additionally, the fraction of the RNA polymerase II (Pol-II) and acetylated histones H3 and H4 (H3ac and H4ac) bound either to the TBE-II region (−793/−594) or the proximal region (−118/+62) of the COX2 promoter was similarly assessed (anti-Pol-II, Santa Cruz; H3ac and H4ac, Upstate).

Article Title: Targeting STAT5 in Hematological Malignancies through Inhibition of the Bromodomain and Extra-Terminal (BET) Bromodomain Protein BRD2
Article Snippet: Band intensity was quantitated using Image J software (NIH). .. Briefly, leukemia cells were formaldehyde fixed and sonicated, and lysates were immunoprecipitated with anti-STAT5 or anti-polymerase II (sc-9001, Santa Cruz Biotechnology) antibodies. .. Quantitative PCR was performed in triplicate on ChIP product or input using SYBR Green PCR Master Mix (Applied Biosystems, Foster City, CA) and region-specific primers ( ).

Article Title: In Vivo and in Vitro Evidence That PPAR? Ligands Are Antagonists of Leptin Signaling in Breast Cancer
Article Snippet: Supernatants were immunocleared with salmon sperm DNA/protein A agarose for 1 hour at 4°C. .. The precleared chromatin was immunoprecipitated with specific anti-GR (E-20), PPARγ (H-100), or anti-polymerase II (RNA-PoII H-224) antibodies (Santa Cruz Biotechnology) and were reimmunoprecipitated with anti-PPARγ, anti-NCoR (NB120-2781), or anti-SMRT (NB300-732) antibodies (Novus Biologicals). .. Normal mouse serum IgG was used as negative control.

Article Title: Epigenetic regulation of the extrinsic oncosuppressor PTX3 gene in inflammation and cancer
Article Snippet: ChIP and PAT-ChIP assays were performed as described. .. Briefly, the chromatin obtained from 12 × 106 cells or 5 × 10-µm-thick FFPE tissue sections was sonicated to obtain 200−400 bp chromatin fragments, then immunoprecipitated at 4°C overnight with the following antibodies: anti-H3, anti-H3K27ac and anti-H3K4me1 (Abcam), anti-H3K4me3 (Active Motif), anti-H3K27me3, anti-NF-κB p65 (RelA), anti-EZH2 and anti-SUZ12 (Millipore-Upstate), anti-Pol II (N-20), anti TAF II p250, and anti STAT3 (C-20) (Santa Cruz biochemistry). .. Rabbit IgG (Millipore) was used as negative control.

Article Title: A Pitx2-MicroRNA Pathway Modulates Cell Proliferation in Myoblasts and Skeletal-Muscle Satellite Cells and Promotes Their Commitment to a Myogenic Cell Fate
Article Snippet: For chromatin immunoprecipitation, the antibodies used were anti-V5 (clone V5-10; Sigma) or anti-polymerase II (anti-Pol II) (8WG16) (Santa Cruz); antibody against mouse dystrophin was used as a mouse IgG control. .. Different primers were used to amplify the DNA regions containing the Pitx2 binding site 6 kb upstream of the coding sequences for miR-15b, miR-106b, miR-503, and miR-23b ( ).

Lysis:

Article Title: Mediator MED23 cooperates with RUNX2 to drive osteoblast differentiation and bone development
Article Snippet: Cells were washed and scraped in cold PBS and harvested in ChIP lysis buffer (50 mM Tris-HCl, pH 7.4, 1% SDS, 10 mM EDTA). .. After that, cell lysates were centrifuged and 100 μl supernatant was diluted with 900 μl dilution buffer (16.7 mM Tris-HCl, pH 8.0, 0.01% SDS, 1.1% Triton X-100, 1.2 mM EDTA, 167 mM NaCl) and then incubated with 2 μg anti-RUNX2 or 2 μg anti-Pol II (Santa Cruz) or non-immune Rabbit IgG overnight at 4° C. About 20 μl Protein G magnetic beads (Life technologies) were added for another 4 h on a rotating wheel.

Article Title: BRCA1 Expression Is Epigenetically Repressed in Sporadic Ovarian Cancer Cells by Overexpression of C-Terminal Binding Protein 2
Article Snippet: They were lysed with lysis buffer [50 mM Tris-HCl (pH 8.0), 10 mM EDTA, and 1% sodium dodecyl sulfate (SDS)] supplemented with Complete protease inhibitors (Roche) for 10 minutes. .. The anti-polymerase II (Pol II) (N-20)X antibody was from Santa Cruz Biotechnology (Dallas, TX).

T-Test:

Article Title: Transcriptional Control of Brown Fat Determination by PRDM16
Article Snippet: Lysates were resolved by SDS-PAGE, transferred to PVDF membrane (Millipore) and probed with anti-UCP1 (Chemicon), anti-Flag M2 (Sigma), anti-PRDM16 (rabbit polyclonal), and anti-pol-II (Santa-Cruz biotechnology). .. Lysates were resolved by SDS-PAGE, transferred to PVDF membrane (Millipore) and probed with anti-UCP1 (Chemicon), anti-Flag M2 (Sigma), anti-PRDM16 (rabbit polyclonal), and anti-pol-II (Santa-Cruz biotechnology).

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    Santa Cruz Biotechnology rna polymerase ii antibody
    DNA methylation downstream of <t>SALL4</t> TSS interferes with <t>RNA</t> polymerase II elongation ( a ) Diagram of SALL4 gene. TSS and exon1–4 are shown. ChIP assays with RNA polymerase II antibody, employing HepAD38 cells grown −/+ HBV replication by tetracycline removal for D0–D10, and SALL4 primers spanning different exons, as indicated. ( b ) RIP assays with RNA polymerase II antibody, employing HepAD38 cells grown −/+ HBV replication by tetracycline removal for D0 and D10, and SALL4 primers spanning exons 1 and 4, as indicated in (a).
    Rna Polymerase Ii Antibody, supplied by Santa Cruz Biotechnology, used in various techniques. Bioz Stars score: 84/100, based on 4 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/rna polymerase ii antibody/product/Santa Cruz Biotechnology
    Average 84 stars, based on 4 article reviews
    Price from $9.99 to $1999.99
    rna polymerase ii antibody - by Bioz Stars, 2019-10
    84/100 stars
      Buy from Supplier

    84
    Santa Cruz Biotechnology primary antibodies against med1
    <t>Med1</t> ablation extended Sox2 and stem cell signatures. (A) Stem cell marker Sox2 expression in dental epithelia at three different stages; the CL (left panels), the Sec (second left), and the Mat stage (third left) in Med1 KO and CON at 4 wk (green Sox2, red Notch1, blue DAPI). The location of the 3 stages is shown in the upper diagram. Enlarged images of the boxed area of the Mat stage are also shown (far right panels), and papillary structures are indicated by dotted lines. The lower diagram shows the location of Sox2 (green) in the papillary layer. (B) The mRNA expression of Sox2 and Vwa2 at three stages (CL, Sec, and Mat) in KO (closed bars) compared to CON (open bars) at 4 wk. The SD of relative expression (% of GAPDH) and the statistical significance (n = 3, * p
    Primary Antibodies Against Med1, supplied by Santa Cruz Biotechnology, used in various techniques. Bioz Stars score: 84/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/primary antibodies against med1/product/Santa Cruz Biotechnology
    Average 84 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    primary antibodies against med1 - by Bioz Stars, 2019-10
    84/100 stars
      Buy from Supplier

    Image Search Results


    DNA methylation downstream of SALL4 TSS interferes with RNA polymerase II elongation ( a ) Diagram of SALL4 gene. TSS and exon1–4 are shown. ChIP assays with RNA polymerase II antibody, employing HepAD38 cells grown −/+ HBV replication by tetracycline removal for D0–D10, and SALL4 primers spanning different exons, as indicated. ( b ) RIP assays with RNA polymerase II antibody, employing HepAD38 cells grown −/+ HBV replication by tetracycline removal for D0 and D10, and SALL4 primers spanning exons 1 and 4, as indicated in (a).

    Journal: Oncogene

    Article Title: DNA demethylation induces SALL4 gene re-expression in subgroups of hepatocellular carcinoma associated with Hepatitis B or C virus infection

    doi: 10.1038/onc.2016.399

    Figure Lengend Snippet: DNA methylation downstream of SALL4 TSS interferes with RNA polymerase II elongation ( a ) Diagram of SALL4 gene. TSS and exon1–4 are shown. ChIP assays with RNA polymerase II antibody, employing HepAD38 cells grown −/+ HBV replication by tetracycline removal for D0–D10, and SALL4 primers spanning different exons, as indicated. ( b ) RIP assays with RNA polymerase II antibody, employing HepAD38 cells grown −/+ HBV replication by tetracycline removal for D0 and D10, and SALL4 primers spanning exons 1 and 4, as indicated in (a).

    Article Snippet: The following antibodies were used in this study: SALL4 antibody (Abcam, Cambridge, MA); HBc antibody (Dako, Carpinteria, CA); RNA polymerase II antibody (Santa cruz biotechnology, Dallas, Texas); BRG1 antibody (Abcam, Cambridge, MA); STAT3 antibody (Santa Cruz biotechnology, Dallas, Texas); OCT4 antibody (Abcam, Cambridge, MA); H3K27me3 antibody (Abcam, Cambridge, MA); Histone 3 antibody (Active Motif, Carlsbad, CA).

    Techniques: DNA Methylation Assay, Chromatin Immunoprecipitation

    BRG1/BAF complex is involved in SALL4 re-expression in HBV replicating hepatocytes ( a, b ) PCR quantification of SALL4 mRNA (Left panel), and immunoblots of SALL4 (Right panel), following transfection of BRG1 siRNA (siBRG1) ( a ), and BRG1 plasmid ( b ), in HepAD38 cells grown with HBV replication by tetracycline removal for 10 days. Results are from three independent RNA isolations performed in identical triplicates. Error bars represent S.D. * P

    Journal: Oncogene

    Article Title: DNA demethylation induces SALL4 gene re-expression in subgroups of hepatocellular carcinoma associated with Hepatitis B or C virus infection

    doi: 10.1038/onc.2016.399

    Figure Lengend Snippet: BRG1/BAF complex is involved in SALL4 re-expression in HBV replicating hepatocytes ( a, b ) PCR quantification of SALL4 mRNA (Left panel), and immunoblots of SALL4 (Right panel), following transfection of BRG1 siRNA (siBRG1) ( a ), and BRG1 plasmid ( b ), in HepAD38 cells grown with HBV replication by tetracycline removal for 10 days. Results are from three independent RNA isolations performed in identical triplicates. Error bars represent S.D. * P

    Article Snippet: The following antibodies were used in this study: SALL4 antibody (Abcam, Cambridge, MA); HBc antibody (Dako, Carpinteria, CA); RNA polymerase II antibody (Santa cruz biotechnology, Dallas, Texas); BRG1 antibody (Abcam, Cambridge, MA); STAT3 antibody (Santa Cruz biotechnology, Dallas, Texas); OCT4 antibody (Abcam, Cambridge, MA); H3K27me3 antibody (Abcam, Cambridge, MA); Histone 3 antibody (Active Motif, Carlsbad, CA).

    Techniques: Expressing, Polymerase Chain Reaction, Western Blot, Transfection, Plasmid Preparation

    HBV infection induces DNA demethylation of SALL4 in HepG2 hNTCP cell line ( a ) Quantification of secreted HBeAg by ELISA (Left panel), and quantification of pregenomic RNA by QPCR (Right panel) after HBV infection for 6 days. ( b ) Quantification of SALL4 gene expression (SALL4A and SALL4B slicing variants) by QPCR after HBV infection for 4 and 6 days (D4, D6). ( c ) Bisulfite sequencing PCR results of SALL4 clones, using DNA from HepG2 hNTCP cells without (−) HBV infection (D0) or with (+) HBV infection at 4 and 6 days (D4 and D6). Open and closed circles denote unmethylated and methylated states, respectively. Error bars denote S.D. * P

    Journal: Oncogene

    Article Title: DNA demethylation induces SALL4 gene re-expression in subgroups of hepatocellular carcinoma associated with Hepatitis B or C virus infection

    doi: 10.1038/onc.2016.399

    Figure Lengend Snippet: HBV infection induces DNA demethylation of SALL4 in HepG2 hNTCP cell line ( a ) Quantification of secreted HBeAg by ELISA (Left panel), and quantification of pregenomic RNA by QPCR (Right panel) after HBV infection for 6 days. ( b ) Quantification of SALL4 gene expression (SALL4A and SALL4B slicing variants) by QPCR after HBV infection for 4 and 6 days (D4, D6). ( c ) Bisulfite sequencing PCR results of SALL4 clones, using DNA from HepG2 hNTCP cells without (−) HBV infection (D0) or with (+) HBV infection at 4 and 6 days (D4 and D6). Open and closed circles denote unmethylated and methylated states, respectively. Error bars denote S.D. * P

    Article Snippet: The following antibodies were used in this study: SALL4 antibody (Abcam, Cambridge, MA); HBc antibody (Dako, Carpinteria, CA); RNA polymerase II antibody (Santa cruz biotechnology, Dallas, Texas); BRG1 antibody (Abcam, Cambridge, MA); STAT3 antibody (Santa Cruz biotechnology, Dallas, Texas); OCT4 antibody (Abcam, Cambridge, MA); H3K27me3 antibody (Abcam, Cambridge, MA); Histone 3 antibody (Active Motif, Carlsbad, CA).

    Techniques: Infection, Enzyme-linked Immunosorbent Assay, Real-time Polymerase Chain Reaction, Expressing, Methylation Sequencing, Polymerase Chain Reaction, Clone Assay, Methylation

    HBV replication induces DNA demethylation of SALL4 in HepAD38 cell line ( a ) PCR quantification of SALL4 mRNA in HepAD38 cells grown without (−) HBV replication (D0) or with (+) HBV replication by tetracycline removal for 5, 10, 20 days (D5–D20). Results are from three independent RNA isolations performed in identical triplicates. Error bars denote S.D. * P

    Journal: Oncogene

    Article Title: DNA demethylation induces SALL4 gene re-expression in subgroups of hepatocellular carcinoma associated with Hepatitis B or C virus infection

    doi: 10.1038/onc.2016.399

    Figure Lengend Snippet: HBV replication induces DNA demethylation of SALL4 in HepAD38 cell line ( a ) PCR quantification of SALL4 mRNA in HepAD38 cells grown without (−) HBV replication (D0) or with (+) HBV replication by tetracycline removal for 5, 10, 20 days (D5–D20). Results are from three independent RNA isolations performed in identical triplicates. Error bars denote S.D. * P

    Article Snippet: The following antibodies were used in this study: SALL4 antibody (Abcam, Cambridge, MA); HBc antibody (Dako, Carpinteria, CA); RNA polymerase II antibody (Santa cruz biotechnology, Dallas, Texas); BRG1 antibody (Abcam, Cambridge, MA); STAT3 antibody (Santa Cruz biotechnology, Dallas, Texas); OCT4 antibody (Abcam, Cambridge, MA); H3K27me3 antibody (Abcam, Cambridge, MA); Histone 3 antibody (Active Motif, Carlsbad, CA).

    Techniques: Polymerase Chain Reaction

    SALL4 re-expression in liver cancer cell lines and HCV-related HCCs via DNA demethylation ( a ) Methylation-specific PCR (MSP) assay for SALL4 CpG site 13 and CpG sites 24–26, employing genomic DNA from HepAD38 cells grown without (−) and with (+) HBV replication for 10 days, analyzed 2% agarose gel electrophoresis. Relative intensity quantified by ImageJ software is ratio of +/− HBV replication. ( b ) QRT-PCR of SALL4 mRNA expression employing RNA from HepAD38 cells grown in the absence of HBV replication, Huh7 and Hep3B cell lines. Data normalized to GAPDH. −ΔCt values are shown. ( c ) MSP assay for CpG site 13 and CpG24–26 using genomic DNA from HepAD38 (without HBV replication), Huh7 and Hep3B cells, analyzed by 2% agarose gel electrophoresis. Relative intensity quantified by ImageJ software is ratio of signal from Huh7 or Hep3B to HepAD38 cells. ( d ) and ( f ) QRT-PCR of SALL4 mRNA expression in HBV- and HCV- related liver tumors (T) vs. peritumoral tissue (PT); ( e ) and ( h ) MSP assay for methylation of CpG13 and CpG24–26 sites using genomic DNA of HBV- and HCV- related HCCs; relative intensity is ratio of T/PT. ( g ) Statistical analysis for methylation status of SALL4 CpG13 and CpG24–26 sites in patient samples with SALL4 High and SALL4 low mRNA expression, using unpaired t test; P

    Journal: Oncogene

    Article Title: DNA demethylation induces SALL4 gene re-expression in subgroups of hepatocellular carcinoma associated with Hepatitis B or C virus infection

    doi: 10.1038/onc.2016.399

    Figure Lengend Snippet: SALL4 re-expression in liver cancer cell lines and HCV-related HCCs via DNA demethylation ( a ) Methylation-specific PCR (MSP) assay for SALL4 CpG site 13 and CpG sites 24–26, employing genomic DNA from HepAD38 cells grown without (−) and with (+) HBV replication for 10 days, analyzed 2% agarose gel electrophoresis. Relative intensity quantified by ImageJ software is ratio of +/− HBV replication. ( b ) QRT-PCR of SALL4 mRNA expression employing RNA from HepAD38 cells grown in the absence of HBV replication, Huh7 and Hep3B cell lines. Data normalized to GAPDH. −ΔCt values are shown. ( c ) MSP assay for CpG site 13 and CpG24–26 using genomic DNA from HepAD38 (without HBV replication), Huh7 and Hep3B cells, analyzed by 2% agarose gel electrophoresis. Relative intensity quantified by ImageJ software is ratio of signal from Huh7 or Hep3B to HepAD38 cells. ( d ) and ( f ) QRT-PCR of SALL4 mRNA expression in HBV- and HCV- related liver tumors (T) vs. peritumoral tissue (PT); ( e ) and ( h ) MSP assay for methylation of CpG13 and CpG24–26 sites using genomic DNA of HBV- and HCV- related HCCs; relative intensity is ratio of T/PT. ( g ) Statistical analysis for methylation status of SALL4 CpG13 and CpG24–26 sites in patient samples with SALL4 High and SALL4 low mRNA expression, using unpaired t test; P

    Article Snippet: The following antibodies were used in this study: SALL4 antibody (Abcam, Cambridge, MA); HBc antibody (Dako, Carpinteria, CA); RNA polymerase II antibody (Santa cruz biotechnology, Dallas, Texas); BRG1 antibody (Abcam, Cambridge, MA); STAT3 antibody (Santa Cruz biotechnology, Dallas, Texas); OCT4 antibody (Abcam, Cambridge, MA); H3K27me3 antibody (Abcam, Cambridge, MA); Histone 3 antibody (Active Motif, Carlsbad, CA).

    Techniques: Expressing, Methylation, Polymerase Chain Reaction, MSP Assay, Agarose Gel Electrophoresis, Software, Quantitative RT-PCR

    TSA blocks PMA-induced c-Jun but not c-Fos expression in HeLa cells . A and C . HeLa cells were pretreated with TSA (0-1 μM) for 1 h followed by treatment with PMA (50 ng/ml) for 2 h. Cell lysates (50 μg) containing equal amount of total proteins were analyzed by western blot using either anti-c-Jun or anti-c-Fos antibody. B and D . HeLa cells were pretreated with TSA and then with PMA under similar conditions as described above. Total RNA was isolated and the levels of c-jun and c-fos mRNAs were detected by semiquantitative RT-PCR. Actin was used as control.

    Journal: Molecular Cancer

    Article Title: Transcriptional regulation of human osteopontin promoter by histone deacetylase inhibitor, trichostatin A in cervical cancer cells

    doi: 10.1186/1476-4598-9-178

    Figure Lengend Snippet: TSA blocks PMA-induced c-Jun but not c-Fos expression in HeLa cells . A and C . HeLa cells were pretreated with TSA (0-1 μM) for 1 h followed by treatment with PMA (50 ng/ml) for 2 h. Cell lysates (50 μg) containing equal amount of total proteins were analyzed by western blot using either anti-c-Jun or anti-c-Fos antibody. B and D . HeLa cells were pretreated with TSA and then with PMA under similar conditions as described above. Total RNA was isolated and the levels of c-jun and c-fos mRNAs were detected by semiquantitative RT-PCR. Actin was used as control.

    Article Snippet: The anti-HDAC4, anti-c-Jun, anti-c-Fos, anti-acetyl-H3, anti-acetyl-H4, anti-RNA pol II, anti-TFIIB, anti-cyclin D1, anti-uPA, anti-OPN and anti-actin antibodies were purchased from Santa Cruz Biotechnology.

    Techniques: Expressing, Western Blot, Isolation, Reverse Transcription Polymerase Chain Reaction

    TSA inhibits PMA-induced hyperacetylation of histones H3 and H4 and recruitment of RNA pol II and TFIIB to OPN promoter in HeLa cells . A-D . HeLa cells were pretreated with TSA for 1 h and then with PMA for 2 h. Cross-linked DNA-protein complexes were immunoprecipitated with anti-acetyl H3, anti-acetyl H4, anti-RNA pol II or anti-TFIIB antibody and PCR amplified using specific primers derived from the region of OPN promoter containing AP-1 binding site. For negative controls, normal mouse IgG was used. The data represents three experiments exhibiting similar results.

    Journal: Molecular Cancer

    Article Title: Transcriptional regulation of human osteopontin promoter by histone deacetylase inhibitor, trichostatin A in cervical cancer cells

    doi: 10.1186/1476-4598-9-178

    Figure Lengend Snippet: TSA inhibits PMA-induced hyperacetylation of histones H3 and H4 and recruitment of RNA pol II and TFIIB to OPN promoter in HeLa cells . A-D . HeLa cells were pretreated with TSA for 1 h and then with PMA for 2 h. Cross-linked DNA-protein complexes were immunoprecipitated with anti-acetyl H3, anti-acetyl H4, anti-RNA pol II or anti-TFIIB antibody and PCR amplified using specific primers derived from the region of OPN promoter containing AP-1 binding site. For negative controls, normal mouse IgG was used. The data represents three experiments exhibiting similar results.

    Article Snippet: The anti-HDAC4, anti-c-Jun, anti-c-Fos, anti-acetyl-H3, anti-acetyl-H4, anti-RNA pol II, anti-TFIIB, anti-cyclin D1, anti-uPA, anti-OPN and anti-actin antibodies were purchased from Santa Cruz Biotechnology.

    Techniques: Immunoprecipitation, Polymerase Chain Reaction, Amplification, Derivative Assay, Binding Assay

    Effect of TSA on cyclin D1 and uPA expression at protein and RNA levels in HeLa cells . A and C . HeLa cells were pretreated with TSA (0-1 μM) for 1 h followed by treatment with PMA (50 ng/ml) for 6 h. Cell lysates were analyzed by western blot using anti-cyclin D1 or anti-uPA antibody. B and D . Total RNA was isolated from HeLa cells treated under similar conditions and cyclin D1 and uPA mRNA levels were detected by semi-quantitative RT-PCR. Actin was used as loading control for both western blot and RT-PCR.

    Journal: Molecular Cancer

    Article Title: Transcriptional regulation of human osteopontin promoter by histone deacetylase inhibitor, trichostatin A in cervical cancer cells

    doi: 10.1186/1476-4598-9-178

    Figure Lengend Snippet: Effect of TSA on cyclin D1 and uPA expression at protein and RNA levels in HeLa cells . A and C . HeLa cells were pretreated with TSA (0-1 μM) for 1 h followed by treatment with PMA (50 ng/ml) for 6 h. Cell lysates were analyzed by western blot using anti-cyclin D1 or anti-uPA antibody. B and D . Total RNA was isolated from HeLa cells treated under similar conditions and cyclin D1 and uPA mRNA levels were detected by semi-quantitative RT-PCR. Actin was used as loading control for both western blot and RT-PCR.

    Article Snippet: The anti-HDAC4, anti-c-Jun, anti-c-Fos, anti-acetyl-H3, anti-acetyl-H4, anti-RNA pol II, anti-TFIIB, anti-cyclin D1, anti-uPA, anti-OPN and anti-actin antibodies were purchased from Santa Cruz Biotechnology.

    Techniques: Expressing, Western Blot, Isolation, Quantitative RT-PCR, Reverse Transcription Polymerase Chain Reaction

    TSA suppresses PMA-induced OPN transcription in HeLa cells . A . HeLa cells were preincubated with 0-1 μM TSA for 1 h followed by treatment with PMA (50 ng/ml) for 6 h. Whole cell lysates were analyzed by western blot using anti-OPN antibody. B . HeLa cells were pretreated with TSA followed by PMA under similar conditions as described above. Total RNA was isolated and OPN mRNA levels were detected by semiquantitative RT-PCR and analyzed by agarose gel electrophoresis. Actin was used as control. The data represents three experiments exhibiting similar results. C . HeLa cells were cotransfected with hOPN promoter deletion constructs (-500/+20, -267/+20, -127/+20, -70/+20 and -20/+20) containing luciferase reporter gene along with renilla luciferase vector, pRL followed by stimulation with PMA. The luciferase activity was measured in cell lysates and normalized to Renilla luciferase activity. Fold-changes in luciferase activity with respect to control were calculated. Columns, mean of triplicate determinations; bar, S.D. *, p

    Journal: Molecular Cancer

    Article Title: Transcriptional regulation of human osteopontin promoter by histone deacetylase inhibitor, trichostatin A in cervical cancer cells

    doi: 10.1186/1476-4598-9-178

    Figure Lengend Snippet: TSA suppresses PMA-induced OPN transcription in HeLa cells . A . HeLa cells were preincubated with 0-1 μM TSA for 1 h followed by treatment with PMA (50 ng/ml) for 6 h. Whole cell lysates were analyzed by western blot using anti-OPN antibody. B . HeLa cells were pretreated with TSA followed by PMA under similar conditions as described above. Total RNA was isolated and OPN mRNA levels were detected by semiquantitative RT-PCR and analyzed by agarose gel electrophoresis. Actin was used as control. The data represents three experiments exhibiting similar results. C . HeLa cells were cotransfected with hOPN promoter deletion constructs (-500/+20, -267/+20, -127/+20, -70/+20 and -20/+20) containing luciferase reporter gene along with renilla luciferase vector, pRL followed by stimulation with PMA. The luciferase activity was measured in cell lysates and normalized to Renilla luciferase activity. Fold-changes in luciferase activity with respect to control were calculated. Columns, mean of triplicate determinations; bar, S.D. *, p

    Article Snippet: The anti-HDAC4, anti-c-Jun, anti-c-Fos, anti-acetyl-H3, anti-acetyl-H4, anti-RNA pol II, anti-TFIIB, anti-cyclin D1, anti-uPA, anti-OPN and anti-actin antibodies were purchased from Santa Cruz Biotechnology.

    Techniques: Western Blot, Isolation, Reverse Transcription Polymerase Chain Reaction, Agarose Gel Electrophoresis, Construct, Luciferase, Plasmid Preparation, Activity Assay

    Med1 ablation extended Sox2 and stem cell signatures. (A) Stem cell marker Sox2 expression in dental epithelia at three different stages; the CL (left panels), the Sec (second left), and the Mat stage (third left) in Med1 KO and CON at 4 wk (green Sox2, red Notch1, blue DAPI). The location of the 3 stages is shown in the upper diagram. Enlarged images of the boxed area of the Mat stage are also shown (far right panels), and papillary structures are indicated by dotted lines. The lower diagram shows the location of Sox2 (green) in the papillary layer. (B) The mRNA expression of Sox2 and Vwa2 at three stages (CL, Sec, and Mat) in KO (closed bars) compared to CON (open bars) at 4 wk. The SD of relative expression (% of GAPDH) and the statistical significance (n = 3, * p

    Journal: PLoS ONE

    Article Title: Ablation of Coactivator Med1 Switches the Cell Fate of Dental Epithelia to That Generating Hair

    doi: 10.1371/journal.pone.0099991

    Figure Lengend Snippet: Med1 ablation extended Sox2 and stem cell signatures. (A) Stem cell marker Sox2 expression in dental epithelia at three different stages; the CL (left panels), the Sec (second left), and the Mat stage (third left) in Med1 KO and CON at 4 wk (green Sox2, red Notch1, blue DAPI). The location of the 3 stages is shown in the upper diagram. Enlarged images of the boxed area of the Mat stage are also shown (far right panels), and papillary structures are indicated by dotted lines. The lower diagram shows the location of Sox2 (green) in the papillary layer. (B) The mRNA expression of Sox2 and Vwa2 at three stages (CL, Sec, and Mat) in KO (closed bars) compared to CON (open bars) at 4 wk. The SD of relative expression (% of GAPDH) and the statistical significance (n = 3, * p

    Article Snippet: The specimens were blocked by Power Block (BioGenex) and incubated with primary antibodies against Med1 (Santa Cruz, TRAP220), Krt71 (Progen), and loricrin (Covance), Sox2 (Epitomics), Alpl (R & D system), Notch1 (Cell Signaling), and c-Notch1 (Cell Signaling).

    Techniques: Marker, Expressing, Size-exclusion Chromatography, Gene Knockout

    Deletion of Med1 generated hairs on the labial side of incisors while disrupting enamel formation. (A, B) Hairs were generated from the labial side of chalky-colored incisors lacking enamel in Med1 KO mice (12 wk) (A) and in dissected jaws (12 wk) (B). (C) Hairs (black triangle) were observed in the tissue between the bone and the dental epithelial layer (left panel) in Med1 KO. Hairs originated from abnormal tissues (red triangles) underlying the non-polarized ameloblasts and the papillary layer (enlarged image in right panel) (12 wk). (D, E) Micro CT analysis shows the enamel hypoplasia in the Med1 KO. The 3D-reconstructed µCT images showed the structure of the mandible in CON and KO mice (10 wk) and the location of hairs (red triangle) (D). Enlarged sections of the µCT images (squares) are shown (E). The high density mineralized layer (enamel) was present on the labial side of incisors in CON incisors but absent in Med1 KO (triangles) (10 wk) with changes starting at P17. Hair was observed consistently in over 20 litters of Med1 KO mice. The entire mandibles of two mice (CON and KO) from 2 litters (10 and 12 wk) were scanned using µCT, and reproducibility was confirmed. A mineralized layer was never detected in Med1 KO incisors.

    Journal: PLoS ONE

    Article Title: Ablation of Coactivator Med1 Switches the Cell Fate of Dental Epithelia to That Generating Hair

    doi: 10.1371/journal.pone.0099991

    Figure Lengend Snippet: Deletion of Med1 generated hairs on the labial side of incisors while disrupting enamel formation. (A, B) Hairs were generated from the labial side of chalky-colored incisors lacking enamel in Med1 KO mice (12 wk) (A) and in dissected jaws (12 wk) (B). (C) Hairs (black triangle) were observed in the tissue between the bone and the dental epithelial layer (left panel) in Med1 KO. Hairs originated from abnormal tissues (red triangles) underlying the non-polarized ameloblasts and the papillary layer (enlarged image in right panel) (12 wk). (D, E) Micro CT analysis shows the enamel hypoplasia in the Med1 KO. The 3D-reconstructed µCT images showed the structure of the mandible in CON and KO mice (10 wk) and the location of hairs (red triangle) (D). Enlarged sections of the µCT images (squares) are shown (E). The high density mineralized layer (enamel) was present on the labial side of incisors in CON incisors but absent in Med1 KO (triangles) (10 wk) with changes starting at P17. Hair was observed consistently in over 20 litters of Med1 KO mice. The entire mandibles of two mice (CON and KO) from 2 litters (10 and 12 wk) were scanned using µCT, and reproducibility was confirmed. A mineralized layer was never detected in Med1 KO incisors.

    Article Snippet: The specimens were blocked by Power Block (BioGenex) and incubated with primary antibodies against Med1 (Santa Cruz, TRAP220), Krt71 (Progen), and loricrin (Covance), Sox2 (Epitomics), Alpl (R & D system), Notch1 (Cell Signaling), and c-Notch1 (Cell Signaling).

    Techniques: Generated, Gene Knockout, Mouse Assay, Micro-CT

    Gene expression profiling predicted changes in Notch and calcium signaling upon Med1 deletion. (A) Strategy of microarray analyses. CL and Mat tissues were dissected from Med1 KO and CON mice at 4 wk and 10 wk. Array 1 calculated fold changes in CL/Mat in control mice revealed genes that are enriched in CL compared to the Mat stage, which are DE-SC signature candidates. Array 2 calculated fold changes in KO/CON at CL shows genes up-or down-regulated in Med1 KO compared with CON. Arrays were performed on RNA samples from Med1 KO and CON. (B) These analyses revealed a list of DE-SC signatures affected in the CL of Med1 KO in comparison with gene pools identified through other stem cells of ESC or HF-SC. Green letters show down-regulation, and the red letters indicate up-regulation. Fold increases and other details are listed in Table S4 (10 wk). (C, D) The IPA pathway analysis predicted that Notch1 (C) and calcium (D) are potential upstream regulators to cause these changes in Med1 KO. The sub-cellular location and the up- and down-regulation of genes are shown by red and green, respectively. (E) The protein expressions of Notch1 at 4 wk are shown in CL of Med1 KO and CON.

    Journal: PLoS ONE

    Article Title: Ablation of Coactivator Med1 Switches the Cell Fate of Dental Epithelia to That Generating Hair

    doi: 10.1371/journal.pone.0099991

    Figure Lengend Snippet: Gene expression profiling predicted changes in Notch and calcium signaling upon Med1 deletion. (A) Strategy of microarray analyses. CL and Mat tissues were dissected from Med1 KO and CON mice at 4 wk and 10 wk. Array 1 calculated fold changes in CL/Mat in control mice revealed genes that are enriched in CL compared to the Mat stage, which are DE-SC signature candidates. Array 2 calculated fold changes in KO/CON at CL shows genes up-or down-regulated in Med1 KO compared with CON. Arrays were performed on RNA samples from Med1 KO and CON. (B) These analyses revealed a list of DE-SC signatures affected in the CL of Med1 KO in comparison with gene pools identified through other stem cells of ESC or HF-SC. Green letters show down-regulation, and the red letters indicate up-regulation. Fold increases and other details are listed in Table S4 (10 wk). (C, D) The IPA pathway analysis predicted that Notch1 (C) and calcium (D) are potential upstream regulators to cause these changes in Med1 KO. The sub-cellular location and the up- and down-regulation of genes are shown by red and green, respectively. (E) The protein expressions of Notch1 at 4 wk are shown in CL of Med1 KO and CON.

    Article Snippet: The specimens were blocked by Power Block (BioGenex) and incubated with primary antibodies against Med1 (Santa Cruz, TRAP220), Krt71 (Progen), and loricrin (Covance), Sox2 (Epitomics), Alpl (R & D system), Notch1 (Cell Signaling), and c-Notch1 (Cell Signaling).

    Techniques: Expressing, Microarray, Gene Knockout, Mouse Assay, Indirect Immunoperoxidase Assay

    A proposed model in which Med1 ablation alters epithelial cell fate. Med1 regulates Notch signaling by activating Notch1 target genes (upper diagram). Med1 maintains the niche architecture containing Sox2-expressing dental epithelial stem cells (DE-SC) (blue). Enamel is formed as dental epithelia differentiate in control incisors partly due to Notch signaling. In contrast, DE-SCs fail to commit to the dental lineage when Med1 is ablated (lower diagram). Instead, Sox2-expressing cells (blue) extend into the differentiating zones. Med1 deficient cells are exposed to extracellular calcium through the blood vessels (red-dotted circles) adjacent to the papillary layers (yellow). Med1 deficient cells are differentiated into epidermal cells (light green) and hair keratinocyte-like cells (green) and produce mature hair shafts (black) in the Med1 KO incisors (inserted picture).

    Journal: PLoS ONE

    Article Title: Ablation of Coactivator Med1 Switches the Cell Fate of Dental Epithelia to That Generating Hair

    doi: 10.1371/journal.pone.0099991

    Figure Lengend Snippet: A proposed model in which Med1 ablation alters epithelial cell fate. Med1 regulates Notch signaling by activating Notch1 target genes (upper diagram). Med1 maintains the niche architecture containing Sox2-expressing dental epithelial stem cells (DE-SC) (blue). Enamel is formed as dental epithelia differentiate in control incisors partly due to Notch signaling. In contrast, DE-SCs fail to commit to the dental lineage when Med1 is ablated (lower diagram). Instead, Sox2-expressing cells (blue) extend into the differentiating zones. Med1 deficient cells are exposed to extracellular calcium through the blood vessels (red-dotted circles) adjacent to the papillary layers (yellow). Med1 deficient cells are differentiated into epidermal cells (light green) and hair keratinocyte-like cells (green) and produce mature hair shafts (black) in the Med1 KO incisors (inserted picture).

    Article Snippet: The specimens were blocked by Power Block (BioGenex) and incubated with primary antibodies against Med1 (Santa Cruz, TRAP220), Krt71 (Progen), and loricrin (Covance), Sox2 (Epitomics), Alpl (R & D system), Notch1 (Cell Signaling), and c-Notch1 (Cell Signaling).

    Techniques: Expressing, Gene Knockout

    Med1 regulates cell fate through calcium and Notch signaling. (A) Cervical loop derived dental epithelial (CLDE) cells were established, and Med1 was silenced by siRNA (siMed1). (B) Sox2 was present in CLDE cells that were maintained in low calcium (upper panels), was decreased in high calcium (1.5 mM) (middle panels) (4 days culture), but sustained in siMed1 cells in high calcium (lower panels) (Sox2 green, DAPI blue). The numbers of Sox2 positive cells were counted (bar graph). (C) Control (open bars) and siMed1-treated cells (closed bars) were maintained for 1–13 days in 1.5 mM calcium, and the mRNA expression of Alpl (blue in A), Lor (red in A), Sox2, and Hes1 were measured. Data are shown as the mean±SD of triplicate measurements. The statistically significant increases or decreases in siMed1 compared with sicontrol at each stage are shown by asterisks ( p

    Journal: PLoS ONE

    Article Title: Ablation of Coactivator Med1 Switches the Cell Fate of Dental Epithelia to That Generating Hair

    doi: 10.1371/journal.pone.0099991

    Figure Lengend Snippet: Med1 regulates cell fate through calcium and Notch signaling. (A) Cervical loop derived dental epithelial (CLDE) cells were established, and Med1 was silenced by siRNA (siMed1). (B) Sox2 was present in CLDE cells that were maintained in low calcium (upper panels), was decreased in high calcium (1.5 mM) (middle panels) (4 days culture), but sustained in siMed1 cells in high calcium (lower panels) (Sox2 green, DAPI blue). The numbers of Sox2 positive cells were counted (bar graph). (C) Control (open bars) and siMed1-treated cells (closed bars) were maintained for 1–13 days in 1.5 mM calcium, and the mRNA expression of Alpl (blue in A), Lor (red in A), Sox2, and Hes1 were measured. Data are shown as the mean±SD of triplicate measurements. The statistically significant increases or decreases in siMed1 compared with sicontrol at each stage are shown by asterisks ( p

    Article Snippet: The specimens were blocked by Power Block (BioGenex) and incubated with primary antibodies against Med1 (Santa Cruz, TRAP220), Krt71 (Progen), and loricrin (Covance), Sox2 (Epitomics), Alpl (R & D system), Notch1 (Cell Signaling), and c-Notch1 (Cell Signaling).

    Techniques: Derivative Assay, Expressing

    Med1 ablation resulted in defects in the DE-SC niche. (A) A diagram to show the location of the labial CL in mouse mandible, where DE-SCs reside. The CL is composed of OEE, IEE, SI, and SR (left). (B) Histological analyses of CL in Med1 KO and CON at 4 wk. Med1 is abundantly expressed in OEE/IEE/SR in the CL but diminished in the KO (Med1, brown signals with blue counterstaining). Histological staining shows the morphological alterations of the CL in KO (HE, red triangles). Cell proliferation is increased in OEE/IEE and IDE equivalent to transient amplifying cells (TA) in KO (PCNA staining, brown signals with blue counterstaining). Vwa2 expression in the basement membrane of OEE and IEE decreased in Med1 KO (Vwa2 brown staining with blue counterstaining). The results were reproduced in two independent experiments using two Med1 KO mice from different litters.

    Journal: PLoS ONE

    Article Title: Ablation of Coactivator Med1 Switches the Cell Fate of Dental Epithelia to That Generating Hair

    doi: 10.1371/journal.pone.0099991

    Figure Lengend Snippet: Med1 ablation resulted in defects in the DE-SC niche. (A) A diagram to show the location of the labial CL in mouse mandible, where DE-SCs reside. The CL is composed of OEE, IEE, SI, and SR (left). (B) Histological analyses of CL in Med1 KO and CON at 4 wk. Med1 is abundantly expressed in OEE/IEE/SR in the CL but diminished in the KO (Med1, brown signals with blue counterstaining). Histological staining shows the morphological alterations of the CL in KO (HE, red triangles). Cell proliferation is increased in OEE/IEE and IDE equivalent to transient amplifying cells (TA) in KO (PCNA staining, brown signals with blue counterstaining). Vwa2 expression in the basement membrane of OEE and IEE decreased in Med1 KO (Vwa2 brown staining with blue counterstaining). The results were reproduced in two independent experiments using two Med1 KO mice from different litters.

    Article Snippet: The specimens were blocked by Power Block (BioGenex) and incubated with primary antibodies against Med1 (Santa Cruz, TRAP220), Krt71 (Progen), and loricrin (Covance), Sox2 (Epitomics), Alpl (R & D system), Notch1 (Cell Signaling), and c-Notch1 (Cell Signaling).

    Techniques: Gene Knockout, Staining, Expressing, Mouse Assay

    Med1 ablation prevents dental fate but drives epidermal fate. The IPA pathway analysis on 4(A) The expressions of dental genes were decreased in KO at the Mat stage. Instead, hair genes (B) and epidermal genes (C) increased in KO at the Sec and Mat stages. The full list of altered genes with fold changes and detailed information is shown in Tables S1 , 2 and 3. Green letters indicate down-regulation and red letters indicate up-regulation. The mRNA levels of representative genes for dental (A, b Klk4), hair (B, b Krt71), and epidermal (C, b Lor) are confirmed by QPCR. The average and SD of relative expressions (% of GAPDH) in CL, Sec and Mat at 4 wk are shown. The numbers show the value of the relative expression, which are too low to represent using bars. The statistically significant increases/decreases in Med1 KO (closed bars) compared to KO (open bars) at each stage are shown by asterisks (n = 3, p

    Journal: PLoS ONE

    Article Title: Ablation of Coactivator Med1 Switches the Cell Fate of Dental Epithelia to That Generating Hair

    doi: 10.1371/journal.pone.0099991

    Figure Lengend Snippet: Med1 ablation prevents dental fate but drives epidermal fate. The IPA pathway analysis on 4(A) The expressions of dental genes were decreased in KO at the Mat stage. Instead, hair genes (B) and epidermal genes (C) increased in KO at the Sec and Mat stages. The full list of altered genes with fold changes and detailed information is shown in Tables S1 , 2 and 3. Green letters indicate down-regulation and red letters indicate up-regulation. The mRNA levels of representative genes for dental (A, b Klk4), hair (B, b Krt71), and epidermal (C, b Lor) are confirmed by QPCR. The average and SD of relative expressions (% of GAPDH) in CL, Sec and Mat at 4 wk are shown. The numbers show the value of the relative expression, which are too low to represent using bars. The statistically significant increases/decreases in Med1 KO (closed bars) compared to KO (open bars) at each stage are shown by asterisks (n = 3, p

    Article Snippet: The specimens were blocked by Power Block (BioGenex) and incubated with primary antibodies against Med1 (Santa Cruz, TRAP220), Krt71 (Progen), and loricrin (Covance), Sox2 (Epitomics), Alpl (R & D system), Notch1 (Cell Signaling), and c-Notch1 (Cell Signaling).

    Techniques: Indirect Immunoperoxidase Assay, Gene Knockout, Size-exclusion Chromatography, Real-time Polymerase Chain Reaction, Expressing