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5 protocols using hoxb13

1

Chromatin Immunoprecipitation and Proteomic Analysis

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The nuclear lysate was extracted as described above in the RIME section. 50-100μl of Dynabeads Protein A (Invitrogen) and 2-5 μg specific antibody were used for each sample. ANTI-FLAG® M2 Affinity Gel (A2220, Sigma) and Anti-HA-Agarose antibody (A2095, Sigma) were used for Flag or HA fused protein IP, respectively. The antibodies used are listed as following: AR (#sc-7305), HOXB13 (#sc-28333), and beta-actin (#sc-69878) from Santa Cruz; AR-N (#ab74272) and AR-C (#ab227678) from Abcam; H3 (#9717), GAPDH (#5174), and FOXA1 (#53528) from Cell Signaling Technology.
Additional antibodies are ARv7 (#31-1109-00, RevMAb Biosciences), and Flag M2 (F1840, Sigma). Beads were eluted by rotation at 4 °C for 30 min in 100 μl of 3X FLAG peptide (F4799, Sigma) at final concentration of 150 ng/μl in TBS. ChIP was performed as previously described (35 (link)). Immunoblots shown are representative of at least three independent experiments.
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2

Immunostaining and Semiquantitative Analysis

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Immunostaining was performed using Vectastain elite ABC peroxidase kit (Vector Laboratories, Burlingame, CA) as described previously33 . Primary antibodies include HOXB13 and Chromogranin A (CHGA) (sc-28333 and sc-1488 respectively, Santa Cruz Biotechnology, Dallas, TX), FOXA2 (ab 23306-100, Abcam, Cambridge, MA), cytokeratin 5 (CK5) and 14 (CK14) (904,801 and 905,501 respectively, BioLegend, San Diego, CA). The tissue sections were counterstained, mounted, and imaged with a Zeiss microscope (White Plains, NY). The staining was evaluated using a semiquantitative H-score. Immunofluorescence staining was imaged with a Nikon fluorescence microscope (Melville, NY).
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3

Immunohistochemistry and Immunofluorescence Staining

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IHC staining was performed using Vectastain elite ABC peroxidase kit (Vector Laboratories, Burlingame, CA) as described previously (37 (link)). Primary antibodies include PKM1 and PKM2 (7067S, dilution 1:500, and 4053S, dilution 1:1000, respectively, Cell Signaling Technology, Danvers, MA), P63 and FOXA2 (ab735 and ab108422, respectively, dilution 1:500, Abcam, Cambridge, MA), HOXB13 and chromogranin A (CHGA) (sc-28333 and sc-1488, respectively, dilution 1:200, Santa Cruz Biotechnology, Dallas, TX), FOXA1 (A15278, dilution 1:500, Abclonal, Woburn, MA), Synaptophysin (SYP) (611880, dilution 1:1000, BD biosciences, San Jose, CA), and NKX3.1 (0314, dilution 1:500, Athena Enzyme Systems, Baltimore, MD). Images were taken using a Zeiss microscope (White Plains, NY). The intensity score was evaluated by a semiquantitative blinded manner and graded as 0 (negative), 1+ (low), 2+ (moderate), and 3+ (high). For IF staining, primary antibodies include CHGA (AB_1553436, dilution 1:50, Developmental Studies Hybridoma Bank, Iowa City, IA), PKM1, PKM2, P63, and SYP (source was the same as mentioned above, dilution 1:100). The IF staining was imaged with a Nikon fluorescence microscope (Melville, NY) as reported previously.
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4

Multiplex IHC and IF Staining Protocol

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IHC staining was performed using Vectastain elite ABC peroxidase kit (Vector Laboratories, Burlingame, CA) as described previously21 (link). Primary antibodies include PKM1 and PKM2 (7067S, dilution 1:500, and 4053S, dilution 1:1000, respectively, Cell Signaling Technology, Danvers, MA), p63 and FOXA2 (ab735 and ab108422, respectively, dilution 1:500, Abcam, Cambridge, MA), HOXB13 and chromogranin A (CHGA) (sc-28333 and sc-1488, respectively, dilution 1:200, Santa Cruz Biotechnology, Dallas, TX), FOXA1 (A15278, dilution 1:500, Abclonal, Woburn, MA), Synaptophysin (SYP) (611880, dilution 1:1000, BD biosciences, San Jose, CA), and NKX3.1 (0314, dilution 1:500, Athena Enzyme Systems, Baltimore, MD). Images were taken using a Zeiss microscope (White Plains, NY). The intensity of expression was graded as 0 (negative), 1+ (low), 2+ (moderate), and 3+ (high). For IF staining, primary antibodies include CHGA (AB_1553436, dilution 1:50, Developmental Studies Hybridoma Bank, Iowa City, IA), PKM1, PKM2, p63, and SYP (source was the same as mentioned above, dilution 1:100). The IF staining was imaged with a Nikon fluorescence microscope (Melville, NY) as reported previously.
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5

IHC Analysis of HOXB2 and HOXB13

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The TMA slides were processed in a Ventana Benchmark system (Roche). The primary antibodies used were HOXB2, (Santa Cruz Biotechnology, Santa Cruz CA; 1:200 dilution) and HOXB13 (Santa Cruz Biotechnology, Santa Cruz CA; 1:50 dilution). As a negative control, the primary antibody was replaced with a normal rabbit IgG. The UltraView Universal DAB detection kit was used (Ventana Medical System Inc., Tucson AZ); the slides were dehydrated using ascending-alcohol solutions; cleared in a xylol solution, and mounted in synthetic resin. TMAs were observed in a DM750 Leica microscope (Wetzlar, Germany), and digital images were obtained using the LEZ software; two independent observers evaluated the reaction. The immunostaining intensity was scored in terms of the percentage of positive cells.Data were analyzed using the PASW statistics package 18 (IBM Corp., Armonk, NY, USA).
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