Key resources table.
| Reagent type (species) or resource |
Designation | Source or reference | Identifiers | Additional information |
|---|---|---|---|---|
| Strain, strain background (Mus musculus) | Crl:CD1 (ICR) |
RRID:IMSR_CRL:22 | CD1 Mus musculus wild-type outbred mouse | |
| Cell line (Mus musculus) | ES-E14 | (Hooper et al., 1987) | RRID:CVCL_C320 | Embryonic stem cell line:Mus musculus |
| Cell line (Mus musculus) | ES-R1 | (Nagy et al., 1993) | RRID:CVCL_2167 | Embryonic stem cell line:Mus musculus |
| Cell line (Mus musculus) | Sox17GFP/+ | (Kim et al., 2007) | Embryonic stem cell line:Mus musculus | |
| Cell line (Mus musculus) | TGFP/+ | (Abe and Naski, 2004) | Embryonic stem cell line: Mus musculus | |
| Cell line (Mus musculus) | 46 C cell line (Sox1GFP) | (Ying et al., 2003) | RRID:CVCL_Y482 | Embryonic stem cell line:Mus musculus |
| Cell line (Mus musculus) | GscGFP/+; HhexRedStar/+ | (Villegas et al., 2013) | Embryonic stem cell line:Mus musculus | |
| Cell line (Mus musculus) | EpiSC9 | (Najm et al., 2011) | Epiblast stem cell line: Mus musculus | |
| Antibody | anti-BRACHYURY | R and D Systems | Cat# AF2085, RRID:AB_2200235 | 1:200 |
| Antibody | anti-CDH1 | Sigma-Aldrich | Cat# U3254, RRID:AB_477600 | 1:500 |
| Antibody | anti-CDH2 | Santa Cruz Biotechnology | Cat# sc-7939, RRID:AB_647794 | 1:300 |
| Antibody | anti-CDX2 | BioGenex | Cat# AM392, RRID:AB_2650531 | 1:200 |
| Antibody | anti-DsRed | Clontech Laboratories, Inc. | Cat# 632496, RRID:AB_10013483 | 1:500 |
| Antibody | anti-FOXA2 | Abcam | Cat# ab108422, RRID:AB_11157157 | 1:500 |
| Antibody | anti-FOXF1 | R and D Systems | Cat# AF4798, RRID:AB_2105588 | 1:200 |
| Antibody | anti-GATA6 | R and D Systems | Cat# AF1700, RRID:AB_2108901 | 1:100 |
| Antibody | anti-GATA6 | Cell Signaling Technology | Cat# 5851, RRID:AB_10705521 | 1:500 |
| Antibody | anti-GFP | Aves Labs | Cat# GFP-1020, RRID:AB_10000240 | 1:500 |
| antibody | anti-KLF4 | R and D Systems | Cat# AF3158, RRID:AB_2130245 | 1:200 |
| Antibody | anti-NANOG | Thermo Fisher Scientific | Cat# 14-5761-80, RRID:AB_763613 | 1:200 |
| Antibody | anti-NANOG | Cosmo Bio Co | Cat# REC-RCAB0002PF, RRID:AB_567471 | 1:500 |
| Antibody | anti-OTX2 | R and D Systems | Cat# AF1979, RRID:AB_2157172 | 1:500 |
| Antibody | anti-POU3F1 | Millipore Sigma | MABN738 | 1:100 |
| Antibody | anti-POU5F1 | Santa Cruz Biotechnology | Cat# sc-5279, RRID:AB_628051 | 1:100 |
| Antibody | anti-pSMAD1/5/8 | a gift from Dr. Ed Laufer, Columbia University, New York, NY | N/A | 1:200 |
| Antibody | anti-SNAIL | R and D Systems | Cat# AF3639, RRID:AB_2191738 | 1:100 |
| Antibody | anti-SOX2 | Thermo Fisher Scientific | Cat# 14-9811-82, RRID:AB_11219471 | 1:200 |
| Antibody | anti-SOX17 | R and D Systems | Cat# AF1924, RRID:AB_355060 | 1:200 |
| Software, algorithm | Ilastik | http://ilastik.org/ | RRID:SCR_015246 | 3-D Nuclear mask generation |