Clone cdx2 88

The following primary antibodies were used: Mouse anti-OCT3/4 (Santa Cruz Biotechnology, Clone C-10, #sc-5279, 1:50), Rabbit anti-CDX2 (BioGenex, Clone EP25, #NU777-5UC, 1:100), Mouse anti-CDX2 (BioGenex, Clone CDX2-88, #MU392A-5UC, 1:100), Rabbit anti-EOMES (Abcam, #ab23345, 1:100), Mouse anti-SMA (SIGMA ALDRICH, Clone 1A4, #A2547, 1:200), Mouse anti-TUJ1 (Biolegend, Clone TUJ1, #801201, 1:200), Goat anti-GATA6 (R&D Systems, #AF1700, 1:100), Mouse anti-5mC (Millipore, Clone 33D3, #MABE146, 1:200), Rabbit anti-H3K27me3 (Millipore, #07-449, 1:100) and Rabbit anti-H3K9me3 (Abcam, #ab8898, 1:100). The secondary antibodies used were: Goat anti-Mouse IgG FITC-conjugated (Thermo Fisher Scientific, #62-6511, 1:50), Goat anti-Mouse IgG Alexa Fluor^R 555 (Abcam, #ab150114, 1:1000), Donkey anti-Goat IgG Alexa Fluor^TM 488 (Thermo Fisher Scientific, #A11055, 1:1000), Donkey anti-Mouse IgG Alexa Fluor^TM 555 (Thermo Fisher Scientific, #A31570, 1:1000), Donkey anti-Rabbit IgG Alexa Fluor^TM 555 (Thermo Fisher Scientific, #A31572, 1:1000), and Donkey anti-Rabbit IgG Alexa Fluor^TM 488 (Thermo Fisher Scientific, #A21206, 1:1000).

Embryos were treated as previously described (Nichols and Smith, 2009 (link)). Primary antibodies used are as follows: anti-CDX2 (Biogenex, clone CDX2-88), anti-H3K9me2 (Abcam, UK, ab1220), anti-GFP (Nacalai tesque, Japan, GF090R), anti-G9a (Cell Signaling, MA, 68851T), anti-GLP (Research and Diagnostic Systems, MN, PP-B0422-00), anti-SOX2 (Abcam, UK, ab92494), anti-SOX17(Research and Diagnostic Systems, MN, AF1924). Mean nuclear intensities of IF and DAPI signal were quantified using mageJ and corrected for the staining background. As nuclear size is changing between stages all IF measurements were normalised to DAPI signal as a proxy for DNA content.

Immunohistochemical (IHC) staining was performed on 5-μm-thick unstained sections from tissue microarray blocks using antibodies to cytokeratin 7 (CK7) (clone OV-TL12/30; Dako, Carpinteria, CA, USA; 1:300 dilution), to cytokeratin 20 (CK20) (clone Ks20.8; Dako; 1:200 dilution), to homeobox protein CDX2 (clone CDX2-88; Abcam, Cambridge, MA, USA; 1:100 dilution), and to epidermal growth factor receptor(EGFR) (clone 3C6; Roche Diagnostics, Mannheim, Germany; 1:100 dilution). IHC staining of human epidermal growth factor receptor 2 (HER2) was performed using the Ventana Ultra View DAB detection kit (Ventana Medical Systems, Tucson, AZ, USA) and the Ventana PATHWAY HER2/neu rabbit monoclonal antibody (4B5) on a Ventana BenchMark XT immunostainer (Ventana Medical Systems). All slides from each tumor were evaluated by a single pathologist independently based on the following criteria. Expression of CK7, CK20, and CDX2 was considered positive if 10% of the tumor cells showed immunoreactivity. For EGFR, both the percentage of positive tumor cells and the intensity of positive staining were graded according to a previous report [23 (link)]. Total grades were generated on a scale of 0–6 and considered positive if the score was 2–6. The staining for HER2 was graded according to the guidelines for such testing in gastric cancers [24 (link)].