Key resources table
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Rabbit anti-NANOG | Reprocell | Cat# RCAB001P; RRID: AB_1962694 |
| Goat anti-GATA6 | R&D Systems | Cat# AF1700; RRID: AB_2108901 |
| Donkey anti-goat A568 | Invitrogen | Cat# A-11057; RRID:AB_2534104 |
| Donkey anti-rabbit A647 | Invitrogen | Cat# A-10042; RRID: AB_2534017 |
| Chemicals, Peptides, and Recombinant Proteins | ||
| Hoechst 33342 | Invitrogen | Cat# H3570 |
| FGF4 | R&D Systems | Cat# 235-f4 |
| Heparin | Sigma | Cat# H3149 |
| PD0325901 | Reprocell | Cat# 04-0006-10 |
| EmbryoMax KSOM (+AA w/o PhenolRed) | Sigma | Cat# MR-106-D |
| Mineral oil | Sigma | Cat# M5310 |
| FHM | Millipore | Cat# MR-025-D |
| Proteinase K | Roche | Cat# 03115801001 |
| PFA | Electron microscopy sciences | Cat# 15710 |
| Acid Tyrode’s | Millipore | Cat# MR-004-D |
| Glycine | Sigma | Cat# G7403 |
| Triton X-100 | Sigma | Cat# X100 |
| Horse Serum | Sigma | Cat# H0146 |
| DMEM | Life technologies | Cat# 11995073 |
| NEAA | Life technologies | Cat# 11140-050 |
| Glutamine | Life technologies | Cat# 25030164 |
| Glutamax | Life Technologies | Cat # 35050038 |
| Sodium Pyruvate | Life technologies | Cat# 11360070 |
| 2-mercaptoethanol | Life technologies | Cat# 21985023 |
| Fetal Calf Serum | VWR | Cat# 97068-085 |
| HAT supplement | Life technologies | Cat# 21060017 |
| 0.25% Trypsin EDTA | Life technologies | Cat# 25200114 |
| Fibronectin | Millipore | Cat# FC010 |
| Gelatin | Millipore | Cat# 104070 |
| Penicillin/Streptomycin | Life technologies | Cat# 15140163 |
| Mitomycin C | Sigma | Cat# M4287 |
| Deposited Data | ||
| CellProfiler pipelines, ERK-KTR C:N measurements from 3D time-lapse movies, R and Matlab scripts for data analysis | This paper | https://github.com/therealkatlab/Simon2020 |
| Confocal microscopy images | This paper | 10.6084/m9.figshare.127 94810 |
| Experimental Models: Cell Lines | ||
| Mouse: Embryonic stem cell line HprtERK-KTR-mClover | This paper | N/A |
| Experimental Models: Organisms/Strains | ||
| Mouse: R26nls-mKate2 | (Susaki, et al., 2014) | N/A |
| Mouse: HprtERK-KTR-mClover | This paper | JAX#035333 |
| Mouse: CD1 | Charles River Laboratory | Cat# 022 |
| Oligonucleotides | ||
| mKate2_F: 5’-AGATCTGGTACTCGTATGGTGAGCGA GCTGATT-3’ | (Susaki, et al., 2014) | N/A |
| mKate2_R: 5’-TGTGCCTGTAAGCTTTCTTCTGTGCCC CAGTTTGCT-3’ | (Susaki, et al., 2014) | N/A |
| Software and Algorithms | ||
| Imaris 9.1.2 | Bitplane (Oxford Instruments) | https://imaris.oxinst.com/ |
| ImageJ | (Schneider, et al., 2012) | https://imapei.nih.pov/ii/ |
| R Studio 1.0.143 | RStudio, Inc. | https://rstudio.com/ |
| Matlab R2014a/R2018a | MathWorks | https://www.mathworks.com/products/matlab.html |
| CellProfiler 2.1 | (Lamprecht, et al., 2007) | https://cellprofiler.org/ |
| MINS | (Lou, et al., 2014) | http://katlab-tools.org/ |
| ZEN | Carl Zeiss Microsystems | https://www.zeiss.com/microscopy/us/products/microscope-software/zen.html |
| Other | ||
| Glass-bottom dish | MakTek | Cat# P35G-1.5-14-C |