IP Library › Granted Patent US 12,618,830
Granted Patent B2
US 12,618,830 · App. 18/065,480 · Granted May 5, 2026

Methods, culture medias and devices for generating embryos in vitro from stem cells

Inventors: Magdalena D. Zernicka-Goetz (Pasadena, CA); Gianluca Amadei (Cambridge, GB); Charlotte Handford (Cambridge, GB)
Assignee: California Institute of Technology
G01N33/5088C12N5/0604C12Q1/6841C12N2500/02C12N2501/119C12N2501/33C12N2501/392C12N2503/02C12N2506/025C12N2506/45C12N2513/00C12Q1/6869C12Q2600/158
View Patent ↗
Loading inventors, assignments & file history…
Monitor This Case
Get email alerts when status or documents change.
Order Certified Copies
Most orders are placed with the USPTO same day — all within 24 business hours.
Order via The Patent Place →
Pre-filled with this patent's details
Quick Facts
Patent No.
US 12,618,830
App. No.
18/065,480
Granted
May 5, 2026
Kind
B2
Abstract

Disclosed herein include methods and compositions for culture medias for in vitro culture of synthetic embryos from mammalian pluripotent stem cells and extra-embryonic stem cells. The methods and compositions described herein can generate synthetic embryos at different developmental stage reaching early organogenesis and beyond. Disclosed herein also include an embryo culturing system and methods of using same.

Claims (34)

1 . A method of generating a synthetic embryo in vitro, the method comprising:

(a) co-culturing at least one mammalian pluripotent stem cell and an extra-embryonic stem cell in a first culture media under a static condition allowing the mammalian pluripotent stem cell and the extra-embryonic stem cell to self-assemble into a post-implantation embryo structure;

(b) culturing the post-implantation embryo structure in a second culture media under a static condition allowing the post-implantation embryo structure embryo structure to develop into a neurulating embryo structure, wherein the second culture media comprises a basal culture medium, human cord serum, and bicarbonate or HEPES; and

(c) culturing the neurulating embryo structure for at least one day in the second culture media under a dynamic condition in a culture chamber allowing the neurulating embryo structure to develop into a synthetic embryo of at least early organogenesis stage.

2 . The method of claim 1 , wherein the at least one mammalian pluripotent stem cell comprises a wild type mammalian embryonic stem cell and a mammalian embryonic stem cells modified to express an inducible GATA transcription factor upon induction.

3 . The method of claim 1 , wherein the at least one extra-embryonic stem cell comprises a trophoblast stem cell.

4 . The method of claim 2 , wherein the GATA transcription factor is GATA4.

5 . The method of claim 1 , wherein the mammalian pluripotent stem cell and the extra-embryonic stem cell are cultured in the first culture media for up to 4 days.

6 . The method of claim 1 , wherein step (a) is from embryonic day E0-E5.5 of a mouse embryo structure, step (b) is from embryonic day E5.5 to E8.0 of a mouse embryo structure, and/or step (c) is from embryonic day E8.0 to at least E8.5 of a mouse embryo structure.

7 . The method of claim 1 , wherein the post-implantation embryo structure is a post-implantation pre-gastrulation embryo structure.

8 . The method of claim 1 , wherein the post-implantation embryo structure resembles an E5.5 natural mouse embryo structure, the neurulating embryo structure resembles an E8.0 natural mouse embryo structure, and/or the generated synthetic embryo resembles an E8.5 natural mouse embryo structure, an E9.0 natural mouse embryo structure or beyond.

9 . The method of claim 1 , wherein the mammalian pluripotent stem cell and the extra-embryonic stem cell are cultured in a substrate, and wherein the substrate comprises a dish, a U-plate, a flask, a microwell plate, or inverted pyramidal microwells.

10 . The method of claim 1 , wherein step (a) comprises culturing the mammalian pluripotent stem cell and the extra-embryonic stem cell in a feeder cell (FC) media and culturing the mammalian pluripotent stem cell and the extra-embryonic stem cell in an in vitro culture (IVC) media following culturing the mammalian pluripotent stem cell and the extra-embryonic stem cell in the FC media,

wherein the FC media and the IVC media comprise a basal culture medium and wherein the basal culture medium comprises Dulbecco's Modified Eagle Media (DMEM), DMEM Nutrient Mixture 12 (DMEM/F12), a non-human serum or serum substitute thereof, a reducing agent, an antibiotic, L-glutamine or an analogue thereof, or any combination thereof.

11 . The method of claim 10 , wherein the mammalian pluripotent stem cell and the extra-embryonic stem cell are cultured in the FC media for about 2 days and in the IVC media for about 2 days.

12 . The method of claim 10 , wherein the FC media comprises DMEM, fetal bovine serum, sodium pyruvate, L-glutamine or an analogue thereof, MEM non-essential amino acids, 2-mercaptoethanol, penicillin and/or streptomycin, or any combination thereof.

13 . The method of claim 10 , wherein the IVC media comprises:

a) insulin, an insulin analogue, or an insulin receptor agonist;

b) estrogen, an estrogen analogue, or an estrogen receptor agonist; and

c) progesterone, a progesterone analogue, or a progesterone receptor agonist.

14 . The method of claim 10 , wherein the IVC media comprises DMEM/F12, fetal bovine serum, L-glutamine or an analogue thereof, ITS-X, β-estradiol, progesterone, N-acetyl-L-cysteine, penicillin and/or streptomycin, or any combination thereof.

15 . The method of claim 1 , wherein the post-implantation embryo structure is cultured in the second culture media for up to 3 days.

16 . The method of claim 1 , wherein the second culture media comprises DMEM, rat serum, human cord serum, L-glutamine or an analogue thereof, penicillin and/or streptomycin, HEPES, or any combination thereof.

17 . The method of claim 1 , wherein step (b) comprising supplying the second culture media with at least 3 mg/ml glucose.

18 . The method of claim 1 , wherein step (b) comprises culturing the post-implantation embryo structure in a media comprising about 1 mg/ml glucose for two days and culturing the post-implantation embryo structure in a media comprising about 3 mg/ml glucose for one day.

19 . The method of claim 1 , wherein the second culture media in step (c) comprises at least 30% non-human serum.

20 . The method of claim 1 , wherein the dynamic condition comprises suspension agitation.

21 . The method of claim 1 , wherein the culturing the neurulating embryo comprises providing a plurality of gases to the culture chamber at a gas pressure of about 0.5 to 1 psi.

22 . The method of claim 1 , wherein the culture chamber has an atmosphere comprising an incremental increase of oxygen concentration from about 5% to about 25%.

23 . The method of claim 1 , wherein the synthetic embryo has established brain regions, a neural tube, a beating heart, a gut tube, developing somites, and/or primordial germ cells.

24 . The method of claim 1 , wherein the method does not comprise any in vivo step.

25 . The method of claim 1 , wherein the synthetic embryo is a mouse embryo.

26 . A synthetic embryo obtained by the method of claim 1 .

27 . The method of claim 1 , wherein oxygen is supplied to the culture chamber at a constant concentration.

Assignments (2)
ASSIGNMENT OF ASSIGNOR'S INTEREST Recorded Feb 15, 2023
From: ZERNICKA-GOETZ, MAGDALENA D.
To: CALIFORNIA INSTITUTE OF TECHNOLOGY
Reel/Frame 062712/0715 →
ASSIGNMENT OF ASSIGNOR'S INTEREST Recorded Jan 11, 2023
From: AMADEI, GIANLUCA; HANDFORD, CHARLOTTE
To: CAMBRIDGE ENTERPRISE LIMITED
Reel/Frame 062349/0637 →
Continuity (2)
Provisional Application 63289587 · Dec 14, 2021
Related Publication 20230236171A1 · Jul 27, 2023
References Cited (338)
US 5322770A · Gelfand · 1994 [cited by applicant]
US 6186796B1 · Wedge · 2001 [cited by applicant]
US 6379897B1 · Weidenhammer · 2002 [cited by applicant]
US 6451536B1 · Fodor · 2002 [cited by applicant]
US 6548257B2 · Lockhart · 2003 [cited by applicant]
US 6618679B2 · Loehrlein et al. · 2003 [cited by applicant]
US 6664377B1 · Xu · 2003 [cited by applicant]
US 7084246B2 · Coco · 2006 [cited by applicant]
US 8247531B2 · Cochran · 2012 [cited by applicant]
US 20030157485A1 · Bejanin · 2003 [cited by applicant]
US 20030215858A1 · Templeton · 2003 [cited by applicant]
US 20050112764A1 · Ivics et al. · 2005 [cited by applicant]
US 20180155789A1 · Maeder et al. · 2018 [cited by applicant]
US 20220308041A1 · Zernicka-Goetz · 2022 [cited by applicant]
CN 109749987A · 2019 [cited by applicant]
EP 0684315A1 · 1995 [cited by applicant]
KR 1020090050022A · 2009 [cited by applicant]
KR 1020100042649A · 2010 [cited by applicant]
WO WO1993022461 · 1993 [cited by applicant]
WO WO2010085699 · 2010 [cited by applicant]
WO WO2014174470 · 2014 [cited by applicant]
WO WO2016016894 · 2016 [cited by applicant]
WO WO2018046929A1 · 2018 [cited by examiner]
WO WO2020069339 · 2020 [cited by applicant]
WO WO2020152686 · 2020 [cited by applicant]
WO WO2021067854 · 2021 [cited by applicant]
WO WO2021259909 · 2021 [cited by applicant]
WO WO2022195589 · 2022 [cited by applicant]
WO WO2023114754 · 2023 [cited by applicant]
WO WO2023170682 · 2023 [cited by applicant]
Carpenedo, Richard L; et al; “Rotary Suspension Culture Enhances the Efficiency, Yield, and Homogeneity of Embryoid Body Differentiation” Stem Cells, 25,2224-2234, 2007 (Year: 2007). [cited by examiner]
Abe, Koichiro, et al. “Endoderm-specific gene expression in embryonic stem cells differentiated to embryoid bodies.” Experimental cell research 229.1 (1996): 27-34. [cited by applicant]
Aibar, Sara, et al. “SCENIC: single-cell regulatory network inference and clustering.” Nature methods 14.11 (2017): 1083-1086. [cited by applicant]
Alsanie, Walaa F., et al. “Specification of murine ground state pluripotent stem cells to regional neuronal populations.” Scientific Reports 7.1 (2017): 16001. [cited by applicant]
Altschuler, Steven J., and Lani F. Wu. “Cellular heterogeneity: do differences make a difference ?.” Cell 141.4 (2010): 559-563. [cited by applicant]
Amack, Jeffrey D., and M. Lisa Manning. “Knowing the boundaries: extending the differential adhesion hypothesis in embryonic cell sorting.” Science 338.6104 (2012): 212-215. [cited by applicant]
Anders, Simon, Paul Theodor Pyl, and Wolfgang Huber. “HTSeq—a Python framework to work with high-throughput sequencing data.” bioinformatics 31.2 (2015): 166-169. [cited by applicant]
Arnold, Sebastian J., and Elizabeth J. Robertson. “Making a commitment: cell lineage allocation and axis patterning in the early mouse embryo.” Nature reviews Molecular cell biology 10.2 (2009): 91-103. [cited by applicant]
Arslan, Feyza Nur, et al. “Holding it together: when cadherin meets cadherin.” Biophysical Journal 120.19 (2021): 4182-4192. [cited by applicant]
Ashburner, Michael, et al. “Gene ontology: tool for the unification of biology.” Nature genetics 25.1 (2000): 25-29. [cited by applicant]
Bao, Min, et al. “Stem cell-derived synthetic embryos self-assemble by exploiting cadherin codes and cortical tension.” Nature Cell Biology 24.9 (2022): 1341-1349. [cited by applicant]
Bao, Zheng-Zheng, et al. “Regulation of chamber-specific gene expression in the developing heart by Irx4.” Science 283.5405 (1999): 1161-1164. [cited by applicant]
Baran, Yael, et al. “MetaCell: analysis of single-cell RNA-seq data using K-nn graph partitions.” Genome biology 20.1 (2019): 1-19. [cited by applicant]
Bardot, Evan S., and Anna-Katerina Hadjantonakis. “Mouse gastrulation: Coordination of tissue patterning, specification and diversification of cell fate.” Mechanisms of development 163 (2020): 103617. [cited by applicant]
Bedzhov, Ivan, and Magdalena Zernicka-Goetz. “Self-organizing properties of mouse pluripotent cells initiate morphogenesis upon implantation.” Cell 156.5 (2014): 1032-1044. [cited by applicant]
Bedzhov, Ivan, et al. “Developmental plasticity, cell fate specification and morphogenesis in the early mouse embryo.” Philosophical Transactions of the Royal Society B: Biological Sciences 369.1657 (2014): 20130538. [cited by applicant]
Benchling “CRISPR Guide RNA Design Tool” available at: www.benchling.com/crispr last accessed on Oct. 26, 2023 Printed in 7 Pages. [cited by applicant]
Ben-Kiki, Oren, et al. “Metacell-2: a divide-and-conquer metacell algorithm for scalable scRNA-seq analysis.” Genome biology 23.1 (2022): 1-18. [cited by applicant]
Bergmann, Sophie, et al. “Spatial profiling of early primate gastrulation in utero.” Nature 609.7925 (2022): 136-143. [cited by applicant]
Biospherix, Oxystreamer, Cytocentric® O2 and CO2 Controller for Live Cell Microscopy, available at: https://biospherix.com/oxystreamer/ last accessed on Oct. 26, 2023 printed in 6 Pages. [cited by applicant]
Blakeley, Paul, et al. “Defining the three cell lineages of the human blastocyst by single-cell RNA-seq.” Development 142.18 (2015): 3151-3165. [cited by applicant]
Blij, S., et al. “Cdx2 Efficiently Induces Trophoblast Stem-Like Cells in Naive, but Not Primed, Pluripotent Stem Cells.” Stem Cells Dev 24.11 (2015): 1352-65. [cited by applicant]
Brassard, Jonathan A., and Matthias P. Lutolf. “Engineering stem cell self-organization to build better organoids.” Cell stem cell 24.6 (2019): 860-876. [cited by applicant]
Bray, Nicolas L., et al. “Near-optimal probabilistic RNA-seq quantification.” Nature biotechnology 34.5 (2016): 525-527. [cited by applicant]
Bredenkamp, Nicholas, et al. “Wnt inhibition facilitates RNA-mediated reprogramming of human somatic cells to naive pluripotency.” Stem Cell Reports 13.6 (2019): 1083-1098. [cited by applicant]
Brodland, G. Wayne. “The differential interfacial tension hypothesis (DITH): a comprehensive theory for the self-rearrangement of embryonic cells and tissues.” J. Biomech. Eng. 124.2 (2002): 188-197. [cited by applicant]
Cahan, Patrick, and George Q. Daley. “Origins and implications of pluripotent stem cell variability and heterogeneity.” Nature reviews Molecular cell biology 14.6 (2013): 357-368. [cited by applicant]
Canty, Laura, et al. “Sorting at embryonic boundaries requires high heterotypic interfacial tension.” Nature communications 8.1 (2017): 157. [cited by applicant]
Cao, Junyue, et al. “Comprehensive single-cell transcriptional profiling of a multicellular organism.” Science 357.6352 (2017): 661-667. [cited by applicant]
Cao, Junyue, et al. “The single-cell transcriptional landscape of mammalian organogenesis.” Nature 566.7745 (2019): 496-502. [cited by applicant]
Castillo-Venzor, Aracely, et al. “Origin and segregation of the human germline.” Life Science Alliance 6.8 (2023). [cited by applicant]
Cerchiari, Alec E., et al. “A strategy for tissue self-organization that is robust to cellular heterogeneity and plasticity.” Proceedings of the National Academy of Sciences 112.7 (2015): 2287-2292. [cited by applicant]
Chen, Di, et al. “Human primordial germ cells are specified from lineage-primed progenitors.” Cell reports 29.13 (2019): 4568-4582. [cited by applicant]
Chen, Dong-Yuan, et al. “Extracellular matrix stiffness cues junctional remodeling for 3D tissue elongation.” Nature communications 10.1 (2019): 3339. [cited by applicant]
Cheng, Saifeng, et al. “The intrinsic and extrinsic effects of TET proteins during gastrulation.” Cell 185.17 (2022): 3169-3185. [cited by applicant]
Chhabra, Sapna, and Aryeh Warmflash. “BMP-treated human embryonic stem cells transcriptionally resemble amnion cells in the monkey embryo.” Biology Open 10.9 (2021): bio058617. [cited by applicant]
Cindrova-Davies, Tereza, et al. “RNA-seq reveals conservation of function among the yolk sacs of human, mouse, and chicken.” Proceedings of the National Academy of Sciences 114.24 (2017): E4753-E4761. [cited by applicant]
Clark, Amander T., et al. “Human embryo research, stem cell-derived embryo models and in vitro gametogenesis: Considerations leading to the revised ISSCR guidelines.” Stem Cell Reports 16.6 (2021): 1416-1424. [cited by applicant]
Cockburn et al., “Making the blastocyst: lessons from the mouse,” The Journal of Clinical Investigation 2010, 120(4), 995-1003. [cited by applicant]
Cross, James C., et al. “Trophoblast functions, angiogenesis and remodeling of the maternal vasculature in the placenta.” Molecular and cellular endocrinology 187.1-2 (2002): 207-212. [cited by applicant]
Cullum Starr Ltd, “BTC Rotating Bottle Culture Unit” available at: http://www.cullumstarr.com/btc-engineering/rotating-bottle-culture-unit Printed in 2 Pages. [cited by applicant]
Deglincerti, Alessia, et al. “Self-organization of the in vitro attached human embryo.” Nature 533.7602 (2016): 251-254. [cited by applicant]
Dobin, Alexander, et al. “Star: ultrafast universal RNA-seq aligner.” Bioinformatics 29.1 (2013): 15-21. [cited by applicant]
Dobreva, Mariya P., et al. “Periostin as a biomarker of the amniotic membrane.” Stem Cells International 2012 (2012). [cited by applicant]
Dohn, Tracy E., et al. “Nr2f-dependent allocation of ventricular cardiomyocyte and pharyngeal muscle progenitors.” PLoS Genetics 15.2 (2019): e1007962. [cited by applicant]
Dong, Chen, et al. “Derivation of trophoblast stem cells from naïve human pluripotent stem cells.” elife 9 (2020): e52504. [cited by applicant]
Donnison, Martyn, et al. “Elf5 and Ets2 maintain the mouse extraembryonic ectoderm in a dosage dependent synergistic manner.” Developmental biology 397.1 (2015): 77-88. [cited by applicant]
Efremova, Mirjana, et al. “CellPhoneDB: inferring cell—cell communication from combined expression of multi-subunit ligand-receptor complexes.” Nature protocols 15.4 (2020): 1484-1506. [cited by applicant]
EMAP eMouse Atlas Project (http://www.emouseatlas.org). Human Genetics Unit, Medical Research Council, available at: “http://web.archive.org/web/20211129211233/http://www.emouseatlas.org/emap/ema/theiler_stages/StageDef… [cited by applicant]
Fierro-González, Juan Carlos, et al. “Cadherin-dependent filopodia control preimplantation embryo compaction.” Nature cell biology 15.12 (2013): 1424-1433. [cited by applicant]
Foty, Ramsey A., and Malcolm S. Steinberg. “The differential adhesion hypothesis: a direct evaluation.” Developmental biology 278.1 (2005): 255-263. [cited by applicant]
Fu, Jianping, Aryeh Warmflash, and Matthias P. Lutolf. “Stem-cell-based embryo models for fundamental research and translation.” Nature materials 20.2 (2021): 132-144. [cited by applicant]
Gao et al., “Establishment of porcine and human expanded potential stem cells,” Nature Cell Biology 2019, 21(6), 687-699. [cited by applicant]
Gao, Zhiguang, et al. “Ets1 is required for proper migration and differentiation of the cardiac neural crest.” Development 137.9 (2010): 1543-1551. [cited by applicant]
Genbank, “FGF10, partial [ [cited by applicant]
Genbank, “FGF21 [ [cited by applicant]
Genbank, “fibroblast growth factor 2 isoform 34 kDa [ [cited by applicant]
Genbank, “fibroblast growth factor 8 isoform b [ [cited by applicant]
Genbank, “Keratinocyte growth factor [ [cited by applicant]
Gene Ontology Consortium. “The Gene Ontology resource: enriching a GOld mine.” Nucleic acids research vol. 49,D1 (2021): D325-D334. [cited by applicant]
Geneassembly, “Genome assembly GRCh38” Available at https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_000001405.26/ last accessed on Sep. 27, 2023 in 5 Pages. [cited by applicant]
Geneassembly, “Genome assembly GRCm38” Available at https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_000001635.20/ last accessed on Sep. 27, 2023 in 4 Pages. [cited by applicant]
Genebank, GDF11 “growth/differentiation factor-11, partial [ [cited by applicant]
Genebank, GDF8 “growth differentiation factor 8 [ [cited by applicant]
Germain, Pierre-Luc, et al. “Doublet identification in single-cell sequencing data using scDblFinder.” F1000Research 10 (2021). [cited by applicant]
Gerri, Claudia, et al. “Initiation of a conserved trophectoderm program in human, cow and mouse embryos.” Nature 587.7834 (2020): 443-447. [cited by applicant]
Github, “Human Model” available at https://github.com/bweatherbee/human_model/tree/main last accessed on Sep. 27, 2023 in 2 Pages. [cited by applicant]
Github, “EiTiX-embryoids” available at https://github.com/hernanRubinstein/EiTiX-embryoids last accessed on Oct. 27, 2023 in 3 Pages. [cited by applicant]
Gossen, Manfred, et al. “Transcriptional activation by tetracyclines in mammalian cells.” Science 268.5218 (1995): 1766-1769. [cited by applicant]
Graf, Thomas, and Matthias Stadtfeld. “Heterogeneity of embryonic and adult stem cells.” Cell stem cell 3.5 (2008): 480-483. [cited by applicant]
Graner, François, and James A. Glazier. “Simulation of biological cell sorting using a two-dimensional extended Potts model.” Physical review letters 69.13 (1992): 2013. [cited by applicant]
Guo, Ge, et al. “Human naive epiblast cells possess unrestricted lineage potential.” Cell stem cell 28.6 (2021): 1040-1056. [cited by applicant]
Halbleib, Jennifer M., and W. James Nelson. “Cadherins in development: cell adhesion, sorting, and tissue morphogenesis.” Genes & development 20.23 (2006): 3199-3214. [cited by applicant]
Harris, Tony JC, and Ulrich Tepass. “Adherens junctions: from molecules to morphogenesis.” Nature reviews Molecular cell biology 11.7 (2010): 502-514. [cited by applicant]
Harrison et al., “In vitro generation of mouse polarized embryo-like structures from embryonic and trophoblast stem cells,” Nature Protocols 2018, 13(7), 1586-1602. [cited by applicant]
Heemskerk, Idse, and Sebastian J. Streichan. “Tissue cartography: compressing bio-image data by dimensional reduction.” Nature methods 12.12 (2015): 1139-1142. [cited by applicant]
Hendrickson et al., “Conserved roles of mouse DUX and human DUX4 in activating cleavage-stage genes and MERVL/HERVL retrotransposons,” Nature Genetics 2017, 49(6), 925-934. [cited by applicant]
Hollnagel, Angela, et al. “Id genes are direct targets of bone morphogenetic protein induction in embryonic stem cells.” Journal of Biological Chemistry 274.28 (1999): 19838-19845. [cited by applicant]
Holz, Andreas, et al. “The transcription factors Nkx2. 2 and Nkx2. 9 play a novel role in floor plate development and commissural axon guidance.” Development 137.24 (2010): 4249-4260. [cited by applicant]
Hu, Dong, and James C. Cross. “Development and function of trophoblast giant cells in the rodent placenta.” International Journal of Developmental Biology 54.2-3 (2009): 341-354. [cited by applicant]
Hu, Ze-Lan, et al. “The role of the transcription factor Rbpj in the development of dorsal root ganglia.” Neural Development 6 (2011): 1-14. [cited by applicant]
Huang, Da Wei, Brad T. Sherman, and Richard A. Lempicki. “Systematic and integrative analysis of large gene lists using David bioinformatics resources.” Nature protocols 4.1 (2009): 44-57. [cited by applicant]
Io, Shingo, et al. “Capturing human trophoblast development with naive pluripotent stem cells in vitro.” Cell stem cell 28.6 (2021): 1023-1039. [cited by applicant]
Jo, Kyoung, et al. “Efficient differentiation of human primordial germ cells through geometric control reveals a key role for Nodal signaling.” Elife 11 (2022): e72811. [cited by applicant]
José-Edwards, Diana S., et al. “Brachyury, Foxa2 and the cis-Regulatory Origins of the Notochord.” PLoS genetics 11.12 (2015): e1005730. [cited by applicant]
Kagawa, Harunobu, et al. “Human blastoids model blastocyst development and implantation.” Nature 601.7894 (2022): 600-605. [cited by applicant]
Kahane, Nitza, and Chaya Kalcheim. “Neural tube development depends on notochord-derived sonic hedgehog released into the sclerotome.” Development 147.10 (2020): dev183996. [cited by applicant]
Kaufman, M. H., H. H. Chang, and J. P. Shaw. “Craniofacial abnormalities in homozygous Small eye (Sey/Sey) embryos and newborn mice.” Journal of anatomy 186.Pt 3 (1995): 607. [cited by applicant]
Keller, Patricia J., et al. “Mapping the cellular and molecular heterogeneity of normal and malignant breast tissues and cultured cell lines.” Breast cancer research 12 (2010): 1-17. [cited by applicant]
Kemp et al., “Expression of all Wnt genes and their secreted antagonists during mouse blastocyst and postimplantation development,” Developmental Dynamics 2005, 233(3), 1064-1075. [cited by applicant]
Keren-Shaul, Hadas, et al. “MARS-seq2. 0: an experimental and analytical pipeline for indexed sorting combined with single-cell RNA sequencing.” Nature protocols 14.6 (2019): 1841-1862. [cited by applicant]
Kime et al., “Induced 2C expression and implantation-competent blastocyst-like cysts from primed pluripotent stem cells,” Stem Cell Reports 2019, 13(3), 485-498. [cited by applicant]
Kiselev, Vladimir Yu, Andrew Yiu, and Martin Hemberg. “scmap: projection of single-cell RNA-seq data across data sets.” Nature methods 15.5 (2018): 359-362. [cited by applicant]
Koot, Y. E. M., et al. “Molecular aspects of implantation failure.” Biochimica et Biophysica Acta (BBA)-Molecular Basis of Disease 1822.12 (2012): 1943-1950. [cited by applicant]
Kovács, Mihaly, et al. “Mechanism of blebbistatin inhibition of myosin II.” Journal of Biological Chemistry 279.34 (2004): 35557-35563. [cited by applicant]
Krendl, Christian, et al. “GATA2/3-TFAP2A/C transcription factor network couples human pluripotent stem cell differentiation to trophectoderm with repression of pluripotency.” Proceedings of the National Academy of Scie… [cited by applicant]
Krieg, Michael, et al. “Tensile forces govern germ-layer organization in zebrafish.” Nature cell biology 10.4 (2008): 429-436. [cited by applicant]
Kwon, Gloria S et al. “The endoderm of the mouse embryo arises by dynamic widespread intercalation of embryonic and extraembryonic lineages.” Developmental cell vol. 15,4 (2008): 509-20. [cited by applicant]
La Manno, Gioele, et al. “Molecular architecture of the developing mouse brain.” Nature 596.7870 (2021): 92-96. [cited by applicant]
La Manno, Gioele, et al. “RNA velocity of single cells.” Nature 560.7719 (2018): 494-498. [cited by applicant]
Latos, Paulina Anna, and Myriam Hemberger. “From the stem of the placental tree: trophoblast stem cells and their progeny.” Development 143.20 (2016): 3650-3660. [cited by applicant]
Lau, Kasey YC, et al. “Mouse embryo model derived exclusively from embryonic stem cells undergoes neurulation and heart development.” Cell Stem Cell 29.10 (2022): 1445-1458. [cited by applicant]
Li et al., “Generation of blastocyst-like structures from mouse embryonic and adult cell cultures,” Cell 2019, 179(3), 687-702. [cited by applicant]
Li, Chen, et al. “Multi-omic single-cell velocity models epigenome-transcriptome interactions and improves cell fate prediction.” Nature Biotechnology 41.3 (2023): 387-398. [cited by applicant]
Linneberg-Agerholm, Madeleine, et al. “Naïve human pluripotent stem cells respond to Wnt, Nodal and LIF signalling to produce expandable naïve extra-embryonic endoderm.” Development 146.24 (2019): dev180620. [cited by applicant]
Liu, Xiaodong, et al. “Modelling human blastocysts by reprogramming fibroblasts into iBlastoids.” Nature 591.7851 (2021): 627-632. [cited by applicant]
Luckett, W. Patrick. “Origin and differentiation of the yolk sac and extraembryonic mesoderm in presomite human and rhesus monkey embryos.” American Journal of Anatomy 152.1 (1978): 59-97. [cited by applicant]
Ma, Huaixiao, et al. “In vitro culture of cynomolgus monkey embryos beyond early gastrulation.” Science 366.6467 (2019): eaax7890. [cited by applicant]
Mackinlay, Kirsty ML, et al. “An in vitro stem cell model of human epiblast and yolk sac interaction.” Elife 10 (2021): e63930. [cited by applicant]
Macklon, Nick S., Joep PM Geraedts, and Ban CJM Fauser. “Conception to ongoing pregnancy: the ‘black box’ of early pregnancy loss.” Human reproduction update 8.4 (2002): 333-343. [cited by applicant]
Maître, Jean-Léon, et al. “Adhesion functions in cell sorting by mechanically coupling the cortices of adhering cells.” science 338.6104 (2012): 253-256. [cited by applicant]
Manderfield, Lauren J., et al. “Pax3 and hippo signaling coordinate melanocyte gene expression in neural crest.” Cell reports 9.5 (2014): 1885-1895. [cited by applicant]
Martin, Beth K., et al. “An optimized protocol for single cell transcriptional profiling by combinatorial indexing.” arXiv preprint arXiv:2110.15400 (2021). [cited by applicant]
Martyn, Iain, et al. “Self-organization of a human organizer by combined Wnt and Nodal signalling.” Nature 558.7708 (2018): 132-135. [cited by applicant]
Massey et al., “Synergy with TGFβ ligands switches WNT pathway dynamics from transient to sustained during human pluripotent cell differentiation,” Proceedings of the National Academy of Sciences 2019, 116(11), 4989-499… [cited by applicant]
Melsted, Páll, et al. “Modular, efficient and constant-memory single-cell RNA-seq preprocessing.” Nature biotechnology 39.7 (2021): 813-818. [cited by applicant]
Mi, Huaiyu, et al. “Panther version 14: more genomes, a new Panther GO-slim and improvements in enrichment analysis tools.” Nucleic acids research 47.D1 (2019): D419-D426. [cited by applicant]
Mischler et al., “Two distinct trophectoderm lineage stem cells from human pluripotent stem cells,” bioRxiv 2019, in 38 Pages. [cited by applicant]
Mittnenzweig, Markus, et al. “A single-embryo, single-cell time-resolved model for mouse gastrulation.” Cell 184.11 (2021): 2825-2842. [cited by applicant]
Molè, Matteo A., Antonia Weberling, and Magdalena Zernicka-Goetz. “Comparative analysis of human and mouse development: From zygote to pre-gastrulation.” Current topics in developmental biology 136 (2020): 113-138. [cited by applicant]
Molè, Matteo A., et al. “A single cell characterisation of human embryogenesis identifies pluripotency transitions and putative anterior hypoblast centre.” Nature communications 12.1 (2021): 3679. [cited by applicant]
Molè, Matteo Amitaba, et al. “Integrin β1 coordinates survival and morphogenesis of the embryonic lineage upon implantation and pluripotency transition.” Cell Reports 34.10 (2021). [cited by applicant]
Moris, Naomi, et al. “An in vitro model of early anteroposterior organization during human development.” Nature 582.7812 (2020): 410-415. [cited by applicant]
Morris, Samantha A., et al. “Dynamics of anterior-posterior axis formation in the developing mouse embryo.” Nature communications 3.1 (2012): 673. [cited by applicant]
Munger, Clara, et al. “Microgel culture and spatial identity mapping elucidate the signalling requirements for primate epiblast and amnion formation.” Development 149.20 (2022): dev200263. [cited by applicant]
Muzumdar, Mandar Deepak, et al. “A global double-fluorescent Cre reporter mouse.” genesis 45.9 (2007): 593-605. [cited by applicant]
Naiche, L. A., and Virginia E. Papaioannou. “Loss of Tbx4 blocks hindlimb development and affects vascularization and fusion of the allantois.” (2003): 2681-2693. [cited by applicant]
Nakamura, Tomonori, et al. “A developmental coordinate of pluripotency among mice, monkeys and humans.” Nature 537.7618 (2016): 57-62. [cited by applicant]
Nastri et al., “Low versus atmospheric oxygen tension for embryo culture in assisted reproduction: a systematic review and meta-analysis,” Fertility and Sterility 2016, 106(1), 95-104. [cited by applicant]
National Library of Medicine Gene ID: 1001, “CDH3 cadherin 3 [ [cited by applicant]
National Library of Medicine Gene ID: 1004, “CDH6 cadherin 6 [ [cited by applicant]
National Library of Medicine Gene ID: 999, “CDH1 cadherin 1 [ [cited by applicant]
Nishikawa, Makiya, and Leaf Huang. “Nonviral vectors in the new millennium: delivery barriers in gene transfer.” Human gene therapy 12.8 (2001): 861-870. [cited by applicant]
Niwa, Hitoshi, and Lusubilo Mwalilino. “Ensemble of old and new techniques escorts ESCs to bona fide embryo-like structures.” Cell Stem Cell 29.10 (2022): 1423-1425. [cited by applicant]
Niwa, Hitoshi, et al. “Interaction between Oct3/4 and Cdx2 determines trophectoderm differentiation.” Cell 123.5 (2005): 917-929. [cited by applicant]
Niwayama, Ritsuya, et al. “A tug-of-war between cell shape and polarity controls division orientation to ensure robust patterning in the mouse blastocyst.” Developmental cell 51.5 (2019): 564-574. [cited by applicant]
Nose, Akinao, Akira Nagafuchi, and Masatoshi Takeichi. “Expressed recombinant cadherins mediate cell sorting in model systems.” Cell 54.7 (1988): 993-1001. [cited by applicant]
Okae, Hiroaki, et al. “Derivation of human trophoblast stem cells.” Cell stem cell 22.1 (2018): 50-63. [cited by applicant]
O'rahilly R, Müller F. Developmental stages in human embryos: revised and new measurements. Cells Tissues Organs. 2010;192(2):73-84. [cited by applicant]
Palsson, Eirikur. “A 3-D model used to explore how cell adhesion and stiffness affect cell sorting and movement in multicellular systems.” Journal of Theoretical Biology 254.1 (2008): 1-13. [cited by applicant]
Papaioannou, Virginia E., John Mkandawire, and John D. Biggers. “Development and phenotypic variability of genetically identical half mouse embryos.” Development 106.4 (1989): 817-827. [cited by applicant]
Pera, “Human embryo research and the 14-day rule,” Development 2017, 144(11), 1923-1925. [cited by applicant]
Petridou, Nicoletta I., et al. “Rigidity percolation uncovers a structural basis for embryonic tissue phase transitions.” Cell 184.7 (2021): 1914-1928. [cited by applicant]
Petropoulos, Sophie, et al. “Single-cell RNA-seq reveals lineage and X chromosome dynamics in human preimplantation embryos.” Cell 165.4 (2016): 1012-1026. [cited by applicant]
Pham, Thi Xuan Ai, et al. “Modeling human extraembryonic mesoderm cells using naive pluripotent stem cells.” Cell stem cell 29.9 (2022): 1346-1365. [cited by applicant]
Pieters, Tim, and Roy, Frans Van. “Role of cell-cell adhesion complexes in embryonic stem cell biology.” Journal of cell science 127.12 (2014): 2603-2613. [cited by applicant]
Priya, Rashmi, et al. “Tension heterogeneity directs form and fate to pattern the myocardial wall.” Nature 588.7836 (2020): 130-134. [cited by applicant]
Qiu, Chengxiang, et al. “Systematic reconstruction of cellular trajectories across mouse embryogenesis.” Nature genetics 54.3 (2022): 328-341. [cited by applicant]
Renaud, Gabriel, et al. “deML: robust demultiplexing of Illumina sequences using a likelihood-based approach.” Bioinformatics 31.5 (2015): 770-772. [cited by applicant]
Richter et al., “Quantitative grading of a human blastocyst: optimal inner cell mass size and shape,” Fertility and Sterility 2001, 76(6), 1157-1167. [cited by applicant]
Rinkenberger, Julie, and Zena Werb. “The labyrinthine placenta.” Nature genetics 25.3 (2000): 248-250. [cited by applicant]
Rivron et al., “Blastocyst-like structures generated solely from stem cells,” Nature 2018, 557(7703), 106-111. [cited by applicant]
Ross, Connor, and Thorsten E. Boroviak. “Origin and function of the yolk sac in primate embryogenesis.” Nature communications 11.1 (2020): 3760. [cited by applicant]
Rossant & Tam, “Blastocyst lineage formation, early embryonic asymmetries and axis patterning in the mouse,” Development 2009, 136(5), 701-713. [cited by applicant]
Rossant, Janet, and Patrick PL Tam. “Early human embryonic development: blastocyst formation to gastrulation.” Developmental cell 57.2 (2022): 152-165. [cited by applicant]
Rossi, Giuliana, et al. “Capturing cardiogenesis in gastruloids.” Cell stem cell 28.2 (2021): 230-240. [cited by applicant]
Rostovskaya, Maria et al. “Capacitation of human naïve pluripotent stem cells for multi-lineage differentiation.” Development (Cambridge, England) vol. 146,7 dev172916. Apr. 3, 2019. [cited by applicant]
Ruane, Peter T., et al. “Trophectoderm differentiation to invasive syncytiotrophoblast is promoted by endometrial epithelial cells during human embryo implantation.” Human Reproduction 37.4 (2022): 777-792. [cited by applicant]
Salbreux, Guillaume, Guillaume Charras, and Ewa Paluch. “Actin cortex mechanics and cellular morphogenesis.” Trends in cell biology 22.10 (2012): 536-545. [cited by applicant]
Sansom, Stephen N., et al. “The level of the transcription factor Pax6 is essential for controlling the balance between neural stem cell self-renewal and neurogenesis.” PLoS genetics 5.6 (2009): e1000511. [cited by applicant]
Sasaki, Kotaro, et al. “The germ cell fate of cynomolgus monkeys is specified in the nascent amnion.” Developmental cell 39.2 (2016): 169-185. [cited by applicant]
Scheibner, Katharina, et al. “Epithelial cell plasticity drives endoderm formation during gastrulation.” Nature cell biology 23.7 (2021): 692-703. [cited by applicant]
Schep, Alicia N et al. “chromVAR: inferring transcription-factor-associated accessibility from single-cell epigenomic data.” Nature methods vol. 14,10 (2017): 975-978. [cited by applicant]
Schliwa, Manfred. “Action of cytochalasin D on cytoskeletal networks.” The Journal of cell biology 92.1 (1982): 79-91. [cited by applicant]
Scotti, Martina, and Marie Kmita. “Recruitment of 5′ Hoxa genes in the allantois is essential for proper extra-embryonic function in placental mammals.” Development 139.4 (2012): 731-739. [cited by applicant]
Séguin, Cheryle A., et al. “Establishment of endoderm progenitors by SOX transcription factor expression in human embryonic stem cells.” Cell stem cell 3.2 (2008): 182-195. [cited by applicant]
Shahbazi, Marta N., Eric D. Siggia, and Magdalena Zernicka-Goetz. “Self-organization of stem cells into embryos: a window on early mammalian development.” Science 364.6444 (2019): 948-951. [cited by applicant]
Shahbazi, Marta N., et al. “Pluripotent state transitions coordinate morphogenesis in mouse and human embryos.” Nature 552.7684 (2017): 239-243. [cited by applicant]
Shahbazi, Marta N., et al. “Self-organization of the human embryo in the absence of maternal tissues.” Nature cell biology 18.6 (2016): 700-708. [cited by applicant]
Sherman, Brad T., et al. “David: a web server for functional enrichment analysis and functional annotation of gene lists (2021 update).” Nucleic acids research 50.W1 (2022): W216-W221. [cited by applicant]
Simmons, David G., and James C. Cross. “Determinants of trophoblast lineage and cell subtype specification in the mouse placenta.” Developmental biology 284.1 (2005): 12-24. [cited by applicant]
Simunovic, Mijo, et al. “A 3D model of a human epiblast reveals BMP4-driven symmetry breaking.” Nature cell biology 21.7 (2019): 900-910. [cited by applicant]
Simunovic, Mijo, et al. “In vitro attachment and symmetry breaking of a human embryo model assembled from primed embryonic stem cells.” Cell stem cell 29.6 (2022): 962-972. [cited by applicant]
Sozen et al., “Self-organization of mouse stem cells into an extended potential blastoid,” Developmental Cell 2019, 51(6), 698-712. [cited by applicant]
Sozen, Berna, et al. “Reconstructing aspects of human embryogenesis with pluripotent stem cells.” Nature communications 12.1 (2021): 5550. [cited by applicant]
Sozen, Berna, et al. “Reconstructing human early embryogenesis in vitro with pluripotent stem cells.” Biorxiv (2021): 2021-03. [cited by applicant]
Steinberg, Malcolm S. “Does differential adhesion govern self-assembly processes in histogenesis? Equilibrium configurations and the emergence of a hierarchy among populations of embryonic cells.” Journal of Experimenta… [cited by applicant]
Steinberg, Malcolm S. “Reconstruction of tissues by dissociated cells: some morphogenetic tissue movements and the sorting out of embryonic cells may have a common explanation.” Science 141.3579 (1963): 401-408. [cited by applicant]
Stower, Matthew J., and Shankar Srinivas. “The head's tale: anterior-posterior axis formation in the mouse embryo.” Current topics in developmental biology 128 (2018): 365-390. [cited by applicant]
Stuart, Tim, et al. “Single-cell chromatin state analysis with Signac.” Nature methods 18.11 (2021): 1333-1341. [cited by applicant]
Takei, Yodai, et al. “Integrated spatial genomics reveals global architecture of single nuclei.” Nature 590.7845 (2021): 344-350. [cited by applicant]
Tarazi, Shadi, et al. “Post-gastrulation synthetic embryos generated ex utero from mouse naive ESCs.” Cell 185.18 (2022): 3290-3306. [cited by applicant]
Tarkowski, “Experiments on the development of isolated blastomeres of mouse eggs,” Nature 1959, 184, 1286-1287. [cited by applicant]
Ten Berge, Derk, et al. “Wnt signaling mediates self-organization and axis formation in embryoid bodies.” Cell stem cell 3.5 (2008): 508-518. [cited by applicant]
Tepass, Ulrich, et al. “Cadherins in embryonic and neural morphogenesis.” Nature reviews Molecular cell biology 1.2 (2000): 91-100. [cited by applicant]
Thomas, Paul, and Beddington, Rosa. “Anterior primitive endoderm may be responsible for patterning the anterior neural plate in the mouse embryo.” Current Biology 6.11 (1996): 1487-1496. [cited by applicant]
Toda, Satoshi, et al. “Programming self-organizing multicellular structures with synthetic cell-cell signaling.” Science 361.6398 (2018): 156-162. [cited by applicant]
Townes, F. William, and Rafael A. Irizarry. “Quantile normalization of single-cell RNA-seq read counts without unique molecular identifiers.” Genome biology 21.1 (2020): 1-17. [cited by applicant]
Tsai, Tony Y-C., et al. “An adhesion code ensures robust pattern formation during tissue morphogenesis.” Science 370.6512 (2020): 113-116. [cited by applicant]
Tyser, Richard CV, et al. “Characterization of a common progenitor pool of the epicardium and myocardium.” Science 371.6533 (2021): eabb2986. [cited by applicant]
Tyser, Richard CV, et al. “Single-cell transcriptomic characterization of a gastrulating human embryo.” Nature 600.7888 (2021): 285-289. [cited by applicant]
UniProt “P12830 ⋅ CADH1_HUMAN” Available at: https://www.uniprot.org/uniprotkb/P12830 last accessed on Sep. 19, 2023 in 13 Pages. [cited by applicant]
UniProt “P22223 ⋅CADH3_HUMAN” Available at: https://www.uniprot.org/uniprotkb/P22223 last accessed on Sep. 19, 2023 in 14 Pages. [cited by applicant]
UniProt “P55285 ⋅ CADH6_HUMAN” Available at: https://www.uniprot.org/uniprotkb/P55285 last accessed on Sep. 19, 2023 in 12 Pages. [cited by applicant]
Viotti, Manuel, Sonja Nowotschin, and Anna-Katerina Hadjantonakis. “SOX17 links gut endoderm morphogenesis and germ layer segregation.” Nature cell biology 16.12 (2014): 1146-1156. [cited by applicant]
Viukov, Sergey, et al. “Human primed and naïve PSCs are both able to differentiate into trophoblast stem cells.” Stem cell reports 17.11 (2022): 2484-2500. [cited by applicant]
Wamaitha, Sissy E., et al. “Gata6 potently initiates reprograming of pluripotent and differentiated cells to extraembryonic endoderm stem cells.” Genes & development 29.12 (2015): 1239. [cited by applicant]
Wang, Xue, Xianjun Chen, and Yi Yang. “Spatiotemporal control of gene expression by a light-switchable transgene system.” Nature methods 9.3 (2012): 266-269. [cited by applicant]
Wang, Xuepeng, and Qiang Wu. “The divergent pluripotent states in mouse and human cells.” Genes 13.8 (2022): 1459. [cited by applicant]
Warmflash, Aryeh, et al. “A method to recapitulate early embryonic spatial patterning in human embryonic stem cells.” Nature methods 11.8 (2014): 847-854. [cited by applicant]
Weatherbee, Bailey AT, et al. “Modeling human embryo development with embryonic and extra-embryonic stem cells.” Developmental biology 474 (2021): 91-99. [cited by applicant]
Weatherbee, Bailey AT, et al. “Pluripotent stem cell-derived model of the post-implantation human embryo.” Nature (Jun. 27, 2023): 1-10. [cited by applicant]
Weatherbee, Bailey AT, et al. “Transgene directed induction of a stem cell-derived human embryo model.” bioRxiv (Jun. 15, 2023): 2023-06. [cited by applicant]
West, Rachel C., et al. “Dynamics of trophoblast differentiation in peri-implantation—stage human embryos.” Proceedings of the National Academy of Sciences 116.45 (2019): 22635-22644. [cited by applicant]
Wickstroem, Sara A., and Carien M. Niessen. “Cell adhesion and mechanics as drivers of tissue organization and differentiation: local cues for large scale organization.” Current opinion in cell biology 54 (2018): 89-97. [cited by applicant]
Xiang, Lifeng, et al. “A developmental landscape of 3D-cultured human pre-gastrulation embryos.” Nature 577.7791 (2020): 537-542. [cited by applicant]
Yagi, Shinomi, and Nobuyoshi Shiojiri. “Identification of novel genetic markers for mouse yolk sac cells by using microarray analyses.” Placenta 49 (2017): 68-71. [cited by applicant]
Yan, Liying, et al. “Single-cell RNA-Seq profiling of human preimplantation embryos and embryonic stem cells.” Nature structural & molecular biology 20.9 (2013): 1131-1139. [cited by applicant]
Yanagida, Ayaka, et al. “Cell surface fluctuations regulate early embryonic lineage sorting.” Cell 185.5 (2022): 777-793. [cited by applicant]
Yanagida, Ayaka, et al. “Naive stem cell blastocyst model captures human embryo lineage segregation.” Cell stem cell 28.6 (2021): 1016-1022. [cited by applicant]
Yang et al., “Derivation of pluripotent stem cells with in vivo embryonic and extraembryonic potency,” Cell 2017, 169(2), 243-257. [cited by applicant]
Yang et al., “Establishment of mouse expanded potential stem cells,” Nature 2017, 550(7676), 393-397. [cited by applicant]
Yang, Ran, et al. “Amnion signals are essential for mesoderm formation in primates.” Nature communications 12.1 (2021): 5126. [cited by applicant]
Young, Matthew D., et al. “Single-cell transcriptomes from human kidneys reveal the cellular identity of renal tumors.” science 361.6402 (2018): 594-599. [cited by applicant]
Yu, Leqian, et al. “Blastocyst-like structures generated from human pluripotent stem cells.” Nature 591.7851 (2021): 620-626. [cited by applicant]
Zeevaert, Kira, et al. “Cell mechanics in embryoid bodies.” Cells 9.10 (2020): 2270. [cited by applicant]
Zernicka-Goetz, M et al. “Following cell fate in the living mouse embryo.” Development (Cambridge, England) vol. 124,6 (1997): 1133-7. [cited by applicant]
Zhang, Shaopeng, et al. “Implantation initiation of self-assembled embryo-like structures generated using three types of mouse blastocyst-derived stem cells.” Nature communications 10.1 (2019): 496. [cited by applicant]
Zhang, Ying, et al. “Computer simulations of cell sorting due to differential adhesion.” PloS one 6.10 (2011): e24999. [cited by applicant]
Zhao, Hui-Fen, et al. “A coumermycin/novobiocin-regulated gene expression system.” Human gene therapy 14.17 (2003): 1619-1629. [cited by applicant]
Zheng, Yi, et al. “Controlled modelling of human epiblast and amnion development using stem cells.” Nature 573.7774 (2019): 421-425. [cited by applicant]
Zheng, Yi, et al. “Single-cell analysis of embryoids reveals lineage diversification roadmaps of early human development.” Cell Stem Cell 29.9 (2022): 1402-1419. [cited by applicant]
Zhou, Fan, et al. “Reconstituting the transcriptome and DNA methylome landscapes of human implantation.” Nature 572.7771 (2019): 660-664. [cited by applicant]
Zhu et al., “Actomyosin polarisation through PLC-PKC triggers symmetry breaking of the mouse embryo,” Nature Communications 2017, 8(1), in 16 Pages. [cited by applicant]
Zhu et al., “Mechanism of cell polarisation and first lineage segregation in the human embryo,” bioRxiv 2020, in 26 Pages. [cited by applicant]
International Search Report and Written Opinion dated Apr. 17, 2023 in PCT Patent Application No. PCT/US2022/081424. [cited by applicant]
Harrison et al., “Assembly of embryonic and extraembryonic stem cells to mimic embryogenesis in vitro”, Science 2017, 356(6334), in 23 pages. [cited by applicant]
Acampora et al., “OTD/OTX2 functional equivalence depends on 5′ and 3′ UTR-mediated control of Otx2 mRNA for nucleo-cytoplasmic export and epiblast-restricted translation,” Development 2001, 128 (23), 4801-4813. [cited by applicant]
Addgene, “pSAM2_mCherry_Gata4,” addgene.org 2023, in 4 pages. https://www.addgene.org/72690/. [cited by applicant]
Aguilera-Castrejon et al., “Ex utero mouse embryogenesis from pre-gastrulation to late organogenesis,” Nature 2021, 593(7857), 119-124. [cited by applicant]
Amadei et al., “Embryo model completes gastrulation to neurulation and organogenesis,” Nature 2022, 610(7930), 143-153. [cited by applicant]
Amadei et al., “Inducible stem-cell-derived embryos capture mouse morphogenetic events in vitro,” Developmental Cell 2021, 56(3), 366-382. [cited by applicant]
Andrews, “FastQC: a quality control tool for high throughput sequence data,” Github 2023, in 3 pages. [cited by applicant]
Ang et al., “Positive and negative signals from mesoderm regulate the expression of mouse Otx2 in ectoderm explants,” Development 1994, 120(10), 2979-2989. [cited by applicant]
Beccari et al., “Multi-axial self-organization properties of mouse embryonic stem cells into gastruloids,” Nature 2018, 562(7726), 272-276. [cited by applicant]
Bedzhov et al., “In vitro culture of mouse blastocysts beyond the implantation stages,” Nature Protocols 2014, 9(12), 2732-2739. [cited by applicant]
Bergen et al., “Generalizing RNA velocity to transient cell states through dynamical modeling,” Nature Biotechnology 2020, 38(12), 1408-1414. [cited by applicant]
Boulanger et al., “Patch-based nonlocal functional for denoising fluorescence microscopy image sequences,” IEEE Transactions on Medical Imaging 2010, 29(2), 442-454. [cited by applicant]
Briggs et al., “The dynamics of gene expression in vertebrate embryogenesis at single-cell resolution,” Science 2018, 360(6392), in 10 pages. [cited by applicant]
Briscoe et al., “Homeobox gene Nkx2. 2 and specification of neuronal identity by graded Sonic hedgehog signalling,” Nature 1999, 398(6728), 622-627. [cited by applicant]
Burren et al., “Gene-environment interactions in the causation of neural tube defects: folate deficiency increases susceptibility conferred by loss of Pax3 function,” Human Molecular Genetics 2008, 17(23), 3675-3685. [cited by applicant]
Compton, “Nucleic acid sequence-based amplification,” Nature 1991, 350(6313), 91-92. [cited by applicant]
Copp et al., “Neural tube defects: recent advances, unsolved questions, and controversies,” The Lancet Neurology 2013, 12(8), 799-810. [cited by applicant]
Copp et al., “The genetic basis of mammalian neurulation,” Nature Reviews Genetics 2003, 4(10), 784-793. [cited by applicant]
Dicicco-Bloom et al., “The developmental neurobiology of autism spectrum disorder,” Journal of Neuroscience 2006, 26(26), 6897-6906. [cited by applicant]
Egli et al., “Developmental reprogramming after chromosome transfer into mitotic mouse zygotes,” Nature 2007, 447(7145), 679-685. [cited by applicant]
Ericson et al., “Pax6 controls progenitor cell identity and neuronal fate in response to graded Shh signaling,” Cell 1997, 90(1), 169-180. [cited by applicant]
Girgin et al., “Bioengineered embryoids mimic post-implantation development in vitro,” Nature Communications 2021, 12(1), in 15 pages. [cited by applicant]
Guatelli et al., “Isothermal, in vitro amplification of nucleic acids by a multienzyme reaction modeled after retroviral replication,” Proceedings of the National Academy of Sciences 1990, 87(5), 1874-1878. [cited by applicant]
Hettige & Ernst, “FOXG1 dose in brain development,” Frontiers in Pediatrics 2019, 7, in 12 pages. [cited by applicant]
Klein et al., “Droplet barcoding for single-cell transcriptomics applied to embryonic stem cells,” Cell 2015, 161(5), 1187-1201. [cited by applicant]
Koch et al., “Antagonistic activities of Sox2 and brachyury control the fate choice of neuro-mesodermal progenitors,” Developmental Cell 2017, 42(5), 514-526. [cited by applicant]
Korsunsky et al., “Fast, sensitive and accurate integration of single-cell data with Harmony,” Nature Methods 2019, 16(12), 1289-1296. [cited by applicant]
Kwoh et al., “Transcription-based amplification system and detection of amplified human immunodeficiency virus type 1 with a bead-based sandwich hybridization format,” Proceedings of the National Academy of Sciences 198… [cited by applicant]
Lalit et al., “Lineage reprogramming of fibroblasts into proliferative induced cardiac progenitor cells by defined factors,” Cell Stem Cell 2016, 18(3), 354-367. [cited by applicant]
Landegren et al., “A ligase-mediated gene detection technique,” Science 1988, 241(4869), 1077-1080. [cited by applicant]
Lawson & Hage, “Clonal analysis of the origin of primordial germ cells in the mouse,” Ciba Foundation Symposium 182-Germline Development: Germline Development: Ciba Foundation Symposium 182 2007, 84-91, Abstract Only. [cited by applicant]
Marshall et al., “Detection of HCV RNA by the asymmetric gap ligase chain reaction,” Genome Research 1994, 4(2), 80-84. [cited by applicant]
Mesnard et al., “The anterior-posterior axis emerges respecting the morphology of the mouse embryo that changes and aligns with the uterus before gastrulation,” Current Biology 2004, 14(3), 184-196. [cited by applicant]
Novitch et al., “Coordinate regulation of motor neuron subtype identity and pan-neuronal properties by the bHLH repressor Olig2,” Neuron 2001, 31(5), 773-789. [cited by applicant]
Nowotschin et al., “The emergent landscape of the mouse gut endoderm at single-cell resolution,” Nature 2019, 569(7756), 361-367. [cited by applicant]
Parekh et al., “zUMIs-A fast and flexible pipeline to process RNA sequencing data with UMIs,” Gigascience 2018, in 9 pages. [cited by applicant]
Pevny et al., “A role for SOX1 in neural determination,” Development 1998, 125(10), 1967-1978. [cited by applicant]
Pijuan-Sala et al., “A single-cell molecular map of mouse gastrulation and early organogenesis,” Nature 2019, 566(7745), 490-495. [cited by applicant]
Pourquié, “3 Segmentation of the Paraxial Mesoderm and Vertebrate Somitogenesis,” Current Topics in Developmental Biology 1999, 47, 81-105. [cited by applicant]
Rhee et al., “In vivo imaging and differential localization of lipid-modified GFP-variant fusions in embryonic stem cells and mice,” Genesis 2006, 44(4), 202-218. [cited by applicant]
Ribes et al., “Distinct Sonic Hedgehog signaling dynamics specify floor plate and ventral neuronal progenitors in the vertebrate neural tube,” Genes & Development 2010, 24(11), 1186-1200. [cited by applicant]
Saitou & Yamaji, “Primordial germ cells in mice,” Cold Spring Harbor Perspectives in Biology 2012, 4(11), in 20 pages. [cited by applicant]
Saitou et al., “A molecular programme for the specification of germ cell fate in mice,” Nature 2002, 418(6895), 293-300. [cited by applicant]
Sasaki & Hogan, “HNF-3β as a regulator of floor plate development,” Cell 1994, 76(1), 103-115. [cited by applicant]
Schindelin et al., “Fiji: an open-source platform for biological-image analysis,” Nature Methods 2012, 9(7), 676-682. [cited by applicant]
Serbedzija & Mcmahon, “Analysis of neural crest cell migration in Splotch mice using a neural crest-specific LacZ reporter,” Developmental Biology 1997, 185(2), 139-147. [cited by applicant]
Southard-Smith et al., “Sox10 mutation disrupts neural crest development in Dom Hirschsprung mouse model,” Nature Genetics 1998, 18(1), 60-64. [cited by applicant]
Sozen et al., “Self-assembly of embryonic and two extra-embryonic stem cell types into gastrulating embryo-like structures,” Nature Cell Biology 2018, 20(8), 979-989. [cited by applicant]
Stuart et al., “Comprehensive integration of single-cell data,” Cell 2019, 177(7), 1888-1902. [cited by applicant]
Tadeu & Valerie Horsley, “Notch signaling represses p63 expression in the developing surface ectoderm,” Development 2013, 140(18), 3777-3786. [cited by applicant]
Tam & Snow, “Proliferation and migration of primordial germ cells during compensatory growth in mouse embryos,” Journal of embryology and experimental morphology 1981, 64, 133-147. [cited by applicant]
Tanaka et al., “Circulation-independent differentiation pathway from extraembryonic mesoderm toward hematopoietic stem cells via hemogenic angioblasts,” Cell Reports 2014, 8(1), 31-39. [cited by applicant]
Towbin et al., “Electrophoretic transfer of proteins from polyacrylamide gels to nitrocellulose sheets: procedure and some applications,” Proceedings of the National Academy of Sciences 1979, 76(9), 4350-4354. [cited by applicant]
Turner et al., “Anteroposterior polarity and elongation in the absence of extra-embryonic tissues and of spatially localised signalling in gastruloids: mammalian embryonic organoids,” Development 2017, 144(21), 3894-390… [cited by applicant]
Tzouanacou et al., “Redefining the progression of lineage segregations during mammalian embryogenesis by clonal analysis,” Developmental Cell 2009, 17(3), 365-376. [cited by applicant]
Van Den Brink et al., “Single-cell and spatial transcriptomics reveal somitogenesis in gastruloids,” Nature 2020, 582(7812), 405-409. [cited by applicant]
Van Den Brink et al., “Symmetry breaking, germ layer specification and axial organisation in aggregates of mouse embryonic stem cells,” Development 2014, 141(22), 4231-4242. [cited by applicant]
Veenvliet et al., “Mouse embryonic stem cells self-organize into trunk-like structures with neural tube and somites,” Science 2020, 370(6522), in 8 pages. [cited by applicant]
Walker et al., “Strand displacement amplification (SDA) and transient-state fluorescence polarization detection of [cited by applicant]
Wang & Fenech, “A comparison of folic acid and 5-methyltetrahydrofolate for prevention of DNA damage and cell death in human lymphocytes in vitro,” Mutagenesis 2003, 18(1), 81-86. [cited by applicant]
Wolf et al., “SCANPY: large-scale single-cell gene expression data analysis,” Genome Biology 2018, 19 in 5 pages. [cited by applicant]
Wolock et al., “Scrublet: computational identification of cell doublets in single-cell transcriptomic data,” Cell Systems 2019, 8(4), 281-291. [cited by applicant]
Wu & Wallace, “The ligation amplification reaction (LAR)—amplification of specific DNA sequences using sequential rounds of template-dependent ligation,” Genomics 1989, 4(4), 560-569. [cited by applicant]
Xu et al., “Construction of a mammalian embryo model from stem cells organized by a morphogen signalling centre,” Nature Communications 2021, 12(1), in 22 pages. [cited by applicant]
Zilionis et al., “Single-cell barcoding and sequencing using droplet microfluidics,” Nature Protocols 2017, 12(1), 44-73. [cited by applicant]
Advisory Action dated Jul. 26, 2024 in U.S. Appl. No. 17/692,790. [cited by applicant]
Eiselleova, Livia, et al. “A complex role for FGF-2 in self-renewal, survival, and adhesion of human embryonic stem cells.” Stem cells 27.8 (2009): 1847-1857. [cited by applicant]
Final office action dated Jun. 6, 2024 in U.S. Appl. No. 17/692,790. [cited by applicant]
Hui, Qi, et al. “FGF family: from drug development to clinical application.” International journal of molecular sciences 19.7 (2018): 1875. [cited by applicant]
International Search Report and Written Opinion dated Dec. 26, 2023 in PCT Patent Application No. PCT/US2023/073377. [cited by applicant]
International Search Report and Written Opinion dated Mar. 7, 2024 in PCT Patent Application No. PCT/US2023/073364. [cited by applicant]
Irvine Scientific, “Irvine Scientific Introduces Continuous Single Culture-NX Low-lactate Culture Media for IVF” 2017 available at: https://fujifilmbiosciences.fujifilm.com/media/files/pr/10728ART_Press_release_CSCM-NX.… [cited by applicant]
Jinek, Martin, et al. “RNA-programmed genome editing in human cells.” (2013). [cited by applicant]
Kosaka, Nobuyoshi, et al. “FGF-4 regulates neural progenitor cell proliferation and neuronal differentiation.” The FASEB journal 20.9 (2006): 1484-1485. [cited by applicant]
Li, Qiuhui, et al. “Cancer stem cells and cell size: A causal link?.” Seminars in cancer biology. vol. 35. Academic Press, 2015. [cited by applicant]
Millman, Jeffrey R., Jit Hin Tan, and Clark K. Colton. “The effects of low oxygen on self-renewal and differentiation of embryonic stem cells.” Current opinion in organ transplantation 14.6 (2009): 694-700. [cited by applicant]
Non-final office action dated Jan. 31, 2025 in U.S. Appl. No. 17/692,790. [cited by applicant]
Non-final office action dated Jan. 4, 2024 in U.S. Appl. No. 17/692,790. [cited by applicant]
Notice of Allowance dated Jul. 16, 2025 in U.S. Appl. No. 17/692,790. [cited by applicant]
Schutte, Bert, et al. “Keratin 8/18 breakdown and reorganization during apoptosis.” Experimental cell research 297.1 (2004): 11-26. [cited by applicant]
Select Science, “Continuous Single Culture-NX Complete by Irvine Scientific”, 2020, available at: https://www.selectscience.net/product/continuous-single-culture-nx-complete#description, last accessed on Aug. 14, 2025, … [cited by applicant]
Zachar, Vladimir, et al. “The effect of human embryonic stem cells (hESCs) long-term normoxic and hypoxic cultures on the maintenance of pluripotency.” In Vitro Cellular & Developmental Biology-Animal 46.3 (2010): 276-2… [cited by applicant]