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Ubf f 9

Manufactured by Santa Cruz Biotechnology
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The UBF (F-9) is a laboratory equipment product offered by Santa Cruz Biotechnology. It serves as a core functional component, without any further interpretation or extrapolation on its intended use.

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Lab products found in correlation

Dc protein kit, by Bio-Rad (2 mentions) Polr1a rpa194 c 1, by Santa Cruz Biotechnology (2 mentions) Taf1c, by Abcam (2 mentions) Polr1b rpa135 h 15, by Santa Cruz Biotechnology (2 mentions) Rpa43 hpa022416, by Merck Group (2 mentions) Lamin a c h 110, by Santa Cruz Biotechnology (2 mentions) α tubulin, by Santa Cruz Biotechnology (2 mentions) Gapdh, by Cell Signaling Technology (2 mentions) Protease inhibitor, by Roche (2 mentions) Enhanced chemi luminescence (ecl), by PerkinElmer (2 mentions) Acetyl h3k27 d5e4, by Cell Signaling Technology (1 mentions) Hdac1, by Cell Signaling Technology (1 mentions) Phospho mst1 thr183 mst2 thr180, by Cell Signaling Technology (1 mentions) Phospho histone h2b ser14, by Merck Group (1 mentions) Phospho histone h2b ser14, by Cell Signaling Technology (1 mentions) Nucleolin 4e2, by Abcam (1 mentions) Lamin a c, by Cell Signaling Technology (1 mentions) γh2ax, by Merck Group (1 mentions) Ab33516, by Abcam (1 mentions) Hdac1 h 51, by Santa Cruz Biotechnology (1 mentions)

6 protocols using ubf f 9

1

Chromatin Enrichment Analysis: ChIP Protocol

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Chromatin enrichment of proteins was analysed using a previously described protocol (43 (link)). Antibodies used for ChIP experiments were purchased as indicated: anti-Flag (M2; Sigma), UBF (F-9; Santacruz), HDAC1 (10E2; Cell Signaling), Tip5 (Diagenode), acetyl-H3K9 (C5B11; Cell Signaling), acetyl-H3K27 (D5E4; Cell Signaling). Monoclonal antibodies to ING1 was generated in a local hybridoma facility (44 (link)). The rDNA locus primers used were those described previously (45 (link)).
Rajarajacholan U.K., Thalappilly S, & Riabowol K. (2016). ING1 regulates rRNA levels by altering nucleolar chromatin structure and mTOR localization. Nucleic Acids Research, 45(4), 1776-1792.
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2

Comprehensive Histone Protein Analysis

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MST2 (Abcam, ab52641), phospho‐histone H2B (Ser14) (Cell Signalling, 6959), phospho‐histone H2B (Ser14) (Millipore, 07‐191), MST1 (Millipore, 07‐061), RASSF1A (3F3, Santa Cruz sc‐58470), UBF (F9, Santa Cruz, sc‐13125), SAV‐1 (Atlas, HPA001808), V5 (Cell Signalling, 13202), H2B (abcam, ab52484), H2A (Abcam, ab18255), H3 (96C10, Cell Signalling, 3638), H4 (Cell Signalling, 2592), γH2AX (JBW301, Millipore, 16‐193), nucleolin (4E2, Abcam, ab13541), lamin A/C (Cell signalling, 4777), α‐tubulin (B3, Sigma, T9822), RCC1 (Cell Signalling, 5134), phospho‐MST1 (Thr183)/MST2(Thr180) (Cell Signalling, 3681), KAP1 (Bethyl, A300‐274A) and phospho‐KAP1S824 (Cell signalling, 4127).
Pefani D.E., Tognoli M.L., Pirincci Ercan D., Gorgoulis V, & O'Neill E. (2018). MST2 kinase suppresses rDNA transcription in response to DNA damage by phosphorylating nucleolar histone H2B. The EMBO Journal, 37(15), e98760.
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3

Antibody Characterization for Transcription Factor Analysis

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The following antibodies were used in this study: CBFβ rabbit polyclonal (ab33516, Abcam, Cambridge, MA), dilutions were 1:500 (IF, WB), 1:500 and 5 μg per IP (ChIP); CBFβ rabbit polyclonal (A-303-547A, Bethyl Labs, Montgomery, TX), dilutions were 1:1000 (WB) and 5 μg per IP; Runx1 (Cell Signaling Technology, Boston, MA), dilutions were 1:50 (IF) and 1:1000 (WB ); RUNX2 mouse monoclonal (8G5, MBL International, Woburn, MA), dilutions were 1:600 (IF) and 1:1000 (WB); UBF (F-9, Santa Cruz Biotechnology, Dallas, TX), dilutions were 1:500 (IF, WB); HDAC1 (H-51, Santa Cruz Biotechnology), 1:1000 dilution used for WB; beta-tubulin mouse monoclonal (T-4026, Sigma Aldrich, St. Louis, MO), 1:1000 dilution used for WB; lamin B1 (ab16048, Abcam) 1:1000 dilution used for WB; Normal IgG control (source) was used at 5 μg for IP. Secondary antibodies conjugated with HRP (Santa Cruz Biotechnology), were used at a dilution of 1:5000 for WB. Secondary antibodies conjugated with Alexa Fluor 488 or 594 (Life Technologies) were used at dilution of 1:500 for IF.
Lopez-Camacho C., van Wijnen A.J., Lian J.B., Stein J.L, & Stein G.S. (2014). Core Binding Factor β (CBFβ) and the Leukemogenic Fusion Protein CBFβ-Smooth Muscle Myosin Heavy Chain (SMMHC) Associate with Mitotic Chromosomes to Epigenetically Regulate Ribosomal Gene Expression. Journal of cellular biochemistry, 115(12), 2155-2164.
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4

Antibody Characterization for Protein Analysis

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The following antibodies were used in these experiments: β-actin (Sigma), p53 (DO-1, Santa Cruz Biotechnology, Santa Cruz, CA, USA), acethyl-p53 (lysine382, Cell Signaling Technology, Danvers, MA, USA), p21 (F-5, Santa Cruz Biotechnology), BAX (Abcam, Cambridge, MA, USA), PARP (Cell Signaling Technology), Cyclin A (H-432, Santa Cruz Biotechnology), Cyclin D1 (Cell Signaling Technology), POLR1B (N-17, Santa Cruz Biotechnology), UBF (F-9, Santa Cruz Biotechnology), POLR1A (C-1, Santa Cruz Biotechnology), TIF-IA (C-20, Santa Cruz Biotechnology), PES1 (Bethyl Laboratories, Montgomery, TX, USA), WDR3 (Acris Antibodies, San Diego, CA, USA), NOL1 (Bethyl Laboratories), UTP6 (Gene Tex, Irvine, CA, USA) and RPL11 (3A4A7, Invitrogen). The rabbit anti-MYBBP1A antibody was raised against a synthetic peptide corresponding to the human-MYBBP1A 1265–1328 amino acid sequence.
Kumazawa T., Nishimura K., Katagiri N., Hashimoto S., Hayashi Y, & Kimura K. (2015). Gradual reduction in rRNA transcription triggers p53 acetylation and apoptosis via MYBBP1A. Scientific Reports, 5, 10854.
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5

Quantitative Western Blot Analysis

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Cells were lysed in RIPA lysis buffer (50 mM Tris-HCl [pH 7.5], 150 mM NaCl, 1% NP-40, 0.1% SDS, and 1% sodium deoxycholate) supplemented with protease inhibitors (Roche), sonicated, and centrifuged at 13,200 rpm for 15 min. Protein concentrations were measured using the Dc-Protein Kit (Bio-Rad). Equal amounts of protein were separated on SDS-PAGE, blotted, probed for target proteins, and detected using ECL (Perkin Elmer). The primary antibodies used for detection were UBF (F-9; Santa Cruz Biotechnology), RRN3 (ab112052; Abcam), TAF1C (ab134394; Abcam), POLR1A/RPA194 (C-1; Santa Cruz Biotechnology), POLR1B/RPA135 (H-15; Santa Cruz Biotechnology), RPA43 (HPA022416; Sigma-Aldrich), α-tubulin (10D8; Santa Cruz Biotechnology), lamin A/C (H-110; Santa Cruz Biotechnology), and GAPDH (14C10; Cell Signaling Technology). Horseradish peroxidase (HRP)-conjugated secondary antibodies were from DAKO or Santa Cruz Biotechnology. Protein densitometry analysis was conducted using ImageJ software, and the mean value normalized with loading control was used as final protein band quantification.
Wei T., Najmi S.M., Liu H., Peltonen K., Kucerova A., Schneider D.A, & Laiho M. (2018). Small-Molecule Targeting of RNA Polymerase I Activates a Conserved Transcription Elongation Checkpoint. Cell reports, 23(2), 404-414.
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6

Quantitative Western Blot Analysis

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Cells were lysed in RIPA lysis buffer (50 mM Tris-HCl [pH 7.5], 150 mM NaCl, 1% NP-40, 0.1% SDS, and 1% sodium deoxycholate) supplemented with protease inhibitors (Roche), sonicated, and centrifuged at 13,200 rpm for 15 min. Protein concentrations were measured using the Dc-Protein Kit (Bio-Rad). Equal amounts of protein were separated on SDS-PAGE, blotted, probed for target proteins, and detected using ECL (Perkin Elmer). The primary antibodies used for detection were UBF (F-9; Santa Cruz Biotechnology), RRN3 (ab112052; Abcam), TAF1C (ab134394; Abcam), POLR1A/RPA194 (C-1; Santa Cruz Biotechnology), POLR1B/RPA135 (H-15; Santa Cruz Biotechnology), RPA43 (HPA022416; Sigma-Aldrich), α-tubulin (10D8; Santa Cruz Biotechnology), lamin A/C (H-110; Santa Cruz Biotechnology), and GAPDH (14C10; Cell Signaling Technology). Horseradish peroxidase (HRP)-conjugated secondary antibodies were from DAKO or Santa Cruz Biotechnology. Protein densitometry analysis was conducted using ImageJ software, and the mean value normalized with loading control was used as final protein band quantification.
Wei T., Najmi S.M., Liu H., Peltonen K., Kucerova A., Schneider D.A, & Laiho M. (2018). Small-Molecule Targeting of RNA Polymerase I Activates a Conserved Transcription Elongation Checkpoint. Cell reports, 23(2), 404-414.
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