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4 protocols using ab33516

1

Antibody Profiling for Cellular Analysis

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The following antibodies were used in this study: CBFβ rabbit polyclonal (ab33516, Abcam, Cambridge, MA, USA) and A303-547A, A303-548A, A303-549A, Bethyl Labs, Montgomery, TX, USA). Dilutions for ab33516 were IF (1:500) and WB (1:500). Dilutions and concentration used for CBFβ Bethyl antibodies were IF (1:1000), IP (5 µg) and WB (1:1,000). GFP rabbit polyclonal (ab290, Abcam, Cambridge, MA, USA), was used at dilutions for WB (1:1000) and IP (5 µl). RUNX2 (8G5) mouse monoclonal (MBL International, Woburn, MA, USA), dilution used for IF (1:600). Filamin A (EP2405Y) rabbit polyclonal (ab76289, Abcam, Cambridge, MA, USA) dilution was used for IF (1:1000). Beta-tubulin mouse monoclonal (T-4026, Sigma Aldrich, St. Louis, MO, USA), dilution used for IF (1:1000) and WB (1:1000). PRC1 goat polyclonal (K-18) (sc-9342, Santa Cruz Biotechnology, Santa Cruz, CA, USA), dilution used for IF (1:300). KIF4A goat polyclonal (ab3815, Abcam, Cambridge, MA, USA), dilution used for IF (1:300). MRLC3 goat polyclonal (sc9449, Santa Cruz Biotechnology, Santa Cruz, CA, USA), dilution used for WB (1:200). Secondary antibodies conjugated with HRP (Santa Cruz Biotechnology, Santa Cruz, CA, USA), dilution used for WB (1:5000). Secondary antibodies conjugated with Alexa fluor 488 or 594 (Life Technologies-Invitrogen, Carlsbad, CA, USA), were used at dilution IF (1:500).
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2

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.
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3

Western Blot Analysis of Transcription Factors

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Protein was separated on an SDS–PAGE and transferred to Hybond-C Extra nitrocellulose membrane. Primary antibodies included: β-Tubulin (Abcam, ab6046), Lamin-B1 (Abcam, ab16048), CBFβ (Abcam, ab33516), RUNX1 (Abcam, ab23980), RUNX2 (MBL, D130-3), Snai2 (Cell Signalling, C19G7), FLAG (Sigma, F1804).
For all experiments three biological replicates were performed and densitometry was conducted to calculate average changes using ImageJ software, which is freely available at http://rsb.info.nih.gov/ij/.
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4

Breast Cancer Stage III Prognostic

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Human patient samples were obtained from the CHTN CPD Breast Cancer Stage III Prognostic Tissue Microarray. Details on this tissue microarray can be found at https://chtn.org/. TMAs were stained as detailed above and unmixed as described. After QC, 124 sample cores were used for further analysis including phenotyping, as well as heterogeneity and EMT score calculation, both described above. Hazard ratios were calculated with a multivariate Cox proportional hazard model, adjusting for patient age and tumor hormone status (HR+ or HR−).
CBFb staining was conducted on sequential CHTN TMAs, as above, by immunohistochemical methods (Abcam, ab33516; 1:2000). Following staining, TMAs were scored by a licensed pathologist and marked as negative, weak, moderate, or strong for nuclear and/or cytoplasmic staining, as well as percentage of cells per core. H scores, such as those used to define ER expression (60 ), were calculated using the strength of expression (negative = 0, weak = 1, moderate = 2, and strong = 3) multiplied by percentage of positively stained cells (top estimate). Hazard ratios are calculated as above.
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