Engineering programmable material-to-cell pathways via synthetic notch receptors to spatially control differentiation in multicellular constructs.
Receptors, Notch
/ metabolism
Cell Differentiation
Tissue Engineering
/ methods
Animals
Humans
Signal Transduction
Mice
Extracellular Matrix
/ metabolism
Fibroblasts
/ metabolism
Extracellular Matrix Proteins
/ metabolism
Ligands
Tissue Scaffolds
/ chemistry
Muscle, Skeletal
/ metabolism
Endothelial Cells
/ metabolism
HEK293 Cells
Journal
Nature communications
ISSN: 2041-1723
Titre abrégé: Nat Commun
Pays: England
ID NLM: 101528555
Informations de publication
Date de publication:
13 Jul 2024
13 Jul 2024
Historique:
received:
16
06
2023
accepted:
02
07
2024
medline:
14
7
2024
pubmed:
14
7
2024
entrez:
13
7
2024
Statut:
epublish
Résumé
Synthetic Notch (synNotch) receptors are genetically encoded, modular synthetic receptors that enable mammalian cells to detect environmental signals and respond by activating user-prescribed transcriptional programs. Although some materials have been modified to present synNotch ligands with coarse spatial control, applications in tissue engineering generally require extracellular matrix (ECM)-derived scaffolds and/or finer spatial positioning of multiple ligands. Thus, we develop here a suite of materials that activate synNotch receptors for generalizable engineering of material-to-cell signaling. We genetically and chemically fuse functional synNotch ligands to ECM proteins and ECM-derived materials. We also generate tissues with microscale precision over four distinct reporter phenotypes by culturing cells with two orthogonal synNotch programs on surfaces microcontact-printed with two synNotch ligands. Finally, we showcase applications in tissue engineering by co-transdifferentiating fibroblasts into skeletal muscle or endothelial cell precursors in user-defined micropatterns. These technologies provide avenues for spatially controlling cellular phenotypes in mammalian tissues.
Identifiants
pubmed: 39003263
doi: 10.1038/s41467-024-50126-1
pii: 10.1038/s41467-024-50126-1
doi:
Substances chimiques
Receptors, Notch
0
Extracellular Matrix Proteins
0
Ligands
0
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
5891Subventions
Organisme : U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS)
ID : R35GM138256
Organisme : U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS)
ID : GM143485
Organisme : NSF | ENG/OAD | Division of Chemical, Bioengineering, Environmental, and Transport Systems (CBET)
ID : 2034495
Organisme : NSF | ENG/OAD | Division of Chemical, Bioengineering, Environmental, and Transport Systems (CBET)
ID : 2145528
Informations de copyright
© 2024. The Author(s).
Références
Lim, H. Y. G. & Plachta, N. Cytoskeletal control of early mammalian development. Nat. Rev. Mol. Cell Biol. 22, 548–562 (2021).
pubmed: 33927361
doi: 10.1038/s41580-021-00363-9
Takebayashi-Suzuki, K. & Suzuki, A. Intracellular communication among morphogen signaling pathways during vertebrate body plan formation. Genes 11, 341 (2020).
pubmed: 32213808
pmcid: 7141137
doi: 10.3390/genes11030341
Bocci, F., Onuchic, J. N. & Jolly, M. K. Understanding the principles of pattern formation driven by Notch signaling by integrating experiments and theoretical models. Front. Physiol. 11, 929 (2020).
pubmed: 32848867
pmcid: 7411240
doi: 10.3389/fphys.2020.00929
Boareto, M. Patterning via local cell-cell interactions in developing systems. Dev. Biol. 460, 77–85 (2020).
pubmed: 31866513
doi: 10.1016/j.ydbio.2019.12.008
Lau, S., Slane, D., Herud, O., Kong, J. & Jürgens, G. Early embryogenesis in flowering plants: setting up the basic body pattern. Annu. Rev. Plant Biol. 63, 483–506 (2012).
pubmed: 22224452
doi: 10.1146/annurev-arplant-042811-105507
McGlinn, E. & Tabin, C. J. Mechanistic insight into how Shh patterns the vertebrate limb. Curr. Opin. Genet. Dev. 16, 426–432 (2006).
pubmed: 16806898
doi: 10.1016/j.gde.2006.06.013
Levin, M. Bioelectric signaling: reprogrammable circuits underlying embryogenesis, regeneration, and cancer. Cell 184, 1971–1989 (2021).
pubmed: 33826908
doi: 10.1016/j.cell.2021.02.034
Linask, K. K., Manisastry, S. & Han, M. Cross talk between cell–cell and cell–matrix adhesion signaling pathways during heart organogenesis: implications for cardiac birth defects. Microsc. Microanal. 11, 200–208 (2005).
pubmed: 16060972
doi: 10.1017/S1431927605050440
Perris, R. & Perissinotto, D. Role of the extracellular matrix during neural crest cell migration. Mech. Dev. 95, 3–21 (2000).
pubmed: 10906446
doi: 10.1016/S0925-4773(00)00365-8
Janmey, P. A., Wells, R. G., Assoian, R. K. & McCulloch, C. A. From tissue mechanics to transcription factors. Differentiation 86, 112–120 (2013).
pubmed: 23969122
pmcid: 4545622
doi: 10.1016/j.diff.2013.07.004
Hofer, M. & Lutolf, M. P. Engineering organoids. Nat. Rev. Mater. 6, 402–420 (2021).
pubmed: 33623712
pmcid: 7893133
doi: 10.1038/s41578-021-00279-y
Takebe, T. & Wells, J. M. Organoids by design. Science 364, 956–959 (2019).
pubmed: 31171692
pmcid: 8212787
doi: 10.1126/science.aaw7567
Brassard, J. A. & Lutolf, M. P. Engineering stem cell self-organization to build better organoids. Cell Stem Cell 24, 860–876 (2019).
pubmed: 31173716
doi: 10.1016/j.stem.2019.05.005
Shao, Y. & Fu, J. Engineering multiscale structural orders for high-fidelity embryoids and organoids. Cell Stem Cell 29, 722–743 (2022).
pubmed: 35523138
pmcid: 9097334
doi: 10.1016/j.stem.2022.04.003
Wolf, K. J., Weiss, J. D., Uzel, S. G. M., Skylar-Scott, M. A. & Lewis, J. A. Biomanufacturing human tissues via organ building blocks. Cell Stem Cell 29, 667–677 (2022).
pubmed: 35523137
pmcid: 9617289
doi: 10.1016/j.stem.2022.04.012
Ingber, D. E. Human organs-on-chips for disease modelling, drug development and personalized medicine. Nat. Rev. Genet. 23, 467–491 (2022).
pubmed: 35338360
pmcid: 8951665
doi: 10.1038/s41576-022-00466-9
Underhill, G. H., Galie, P., Chen, C. S. & Bhatia, S. N. Bioengineering methods for analysis of cells in vitro. Annu. Rev. Cell Dev. Biol. 28, 385–410 (2012).
pubmed: 23057744
doi: 10.1146/annurev-cellbio-101011-155709
Rao, K. M., Choi, S. M. & Han, S. S. A review on directional muscle cell growth in scaffolding biomaterials with aligned porous structures for cultivated meat production. Food Res. Int. 168, 112755 (2023).
pubmed: 37120206
doi: 10.1016/j.foodres.2023.112755
Rizwan, M. et al. Viscoelastic Notch signaling hydrogel induces liver bile duct organoid growth and morphogenesis. Adv. Healthc. Mater. 11, 2200880 (2022).
doi: 10.1002/adhm.202200880
Rexius-Hall, M. L., Ariyasinghe, N. R. & McCain, M. L. Engineering shape-controlled microtissues on compliant hydrogels with tunable rigidity and extracellular matrix ligands. In Programmed Morphogenesis: Methods and Protocols (eds Ebrahimkhani, M. R. & Hislop, J.) 57–72 (Springer US, New York, NY, 2021).
Batalov, I., Stevens, K. R. & DeForest, C. A. Photopatterned biomolecule immobilization to guide three-dimensional cell fate in natural protein-based hydrogels. Proc. Natl Acad. Sci. USA 118, e2014194118 (2021).
pubmed: 33468675
pmcid: 7848611
doi: 10.1073/pnas.2014194118
Manhas, J., Edelstein, H. I., Leonard, J. N. & Morsut, L. The evolution of synthetic receptor systems. Nat. Chem. Biol. 18, 244–255 (2022).
pubmed: 35058646
pmcid: 9041813
doi: 10.1038/s41589-021-00926-z
Morsut, L. et al. Engineering customized cell sensing and response behaviors using synthetic Notch receptors. Cell 164, 780–791 (2016).
pubmed: 26830878
pmcid: 4752866
doi: 10.1016/j.cell.2016.01.012
Toda, S., Blauch, L. R., Tang, S. K. Y., Morsut, L. & Lim, W. A. Programming self-organizing multicellular structures with synthetic cell-cell signaling. Science 361, 156–162 (2018).
pubmed: 29853554
pmcid: 6492944
doi: 10.1126/science.aat0271
Huang, X. et al. DNA scaffolds enable efficient and tunable functionalization of biomaterials for immune cell modulation. Nat. Nanotechnol. 16, 214–223 (2021).
pubmed: 33318641
doi: 10.1038/s41565-020-00813-z
Gordon, W. R. et al. Mechanical allostery: evidence for a force requirement in the proteolytic activation of Notch. Dev. Cell 33, 729–736 (2015).
pubmed: 26051539
pmcid: 4481192
doi: 10.1016/j.devcel.2015.05.004
Lee, J. C. et al. Instructional materials that control cellular activity through synthetic Notch receptors. Biomaterials 297, 122099 (2023).
pubmed: 37023529
pmcid: 10320837
doi: 10.1016/j.biomaterials.2023.122099
Ohashi, T. & Erickson, H. P. Fibronectin aggregation and assembly: the unfolding of the second fibronectin type III domain *. J. Biol. Chem. 286, 39188–39199 (2011).
pubmed: 21949131
pmcid: 3234744
doi: 10.1074/jbc.M111.262337
Toda, S. et al. Engineering synthetic morphogen systems that can program multicellular patterning. Science 370, 327–331 (2020).
pubmed: 33060357
pmcid: 7986291
doi: 10.1126/science.abc0033
Zhu, I. et al. Modular design of synthetic receptors for programmed gene regulation in cell therapies. Cell 185, 1431–1443.e16 (2022).
pubmed: 35427499
pmcid: 9108009
doi: 10.1016/j.cell.2022.03.023
McCain, M. L., Agarwal, A., Nesmith, H. W., Nesmith, A. P. & Parker, K. K. Micromolded gelatin hydrogels for extended culture of engineered cardiac tissues. Biomaterials 35, 5462–5471 (2014).
pubmed: 24731714
pmcid: 4057039
doi: 10.1016/j.biomaterials.2014.03.052
Santoso, J. W. et al. Engineering skeletal muscle tissues with advanced maturity improves synapse formation with human induced pluripotent stem cell-derived motor neurons. APL Bioeng. 5, 036101 (2021).
pubmed: 34286174
pmcid: 8282350
doi: 10.1063/5.0054984
Orban, J. M. et al. Crosslinking of collagen gels by transglutaminase. J. Biomed. Mater. Res. A 68A, 756–762 (2004).
doi: 10.1002/jbm.a.20110
Besser, R. R. et al. Enzymatically crosslinked gelatin–laminin hydrogels for applications in neuromuscular tissue engineering. Biomater. Sci. 8, 591–606 (2020).
pubmed: 31859298
pmcid: 7141910
doi: 10.1039/C9BM01430F
Kamiya, N. et al. S-peptide as a potent peptidyl linker for protein cross-linking by microbial transglutaminase from Streptomyces mobaraensis. Bioconjug. Chem. 14, 351–357 (2003).
pubmed: 12643745
doi: 10.1021/bc025610y
Liu, Y. et al. Functionalizing soft matter for molecular communication. ACS Biomater. Sci. Eng. 1, 320–328 (2015).
pubmed: 26501127
pmcid: 4603720
doi: 10.1021/ab500160e
Hofmann, R., Akimoto, G., Wucherpfennig, T. G., Zeymer, C. & Bode, J. W. Lysine acylation using conjugating enzymes for site-specific modification and ubiquitination of recombinant proteins. Nat. Chem. 12, 1008–1015 (2020).
pubmed: 32929246
doi: 10.1038/s41557-020-0528-y
Zhang, H., Dicker, K. T., Xu, X., Jia, X. & Fox, J. M. Interfacial bioorthogonal cross-linking. ACS Macro Lett. 3, 727–731 (2014).
pubmed: 25177528
pmcid: 4144716
doi: 10.1021/mz5002993
Blackman, M. L., Royzen, M. & Fox, J. M. Tetrazine ligation: fast bioconjugation based on inverse-electron-demand Diels−Alder reactivity. J. Am. Chem. Soc. 130, 13518–13519 (2008).
pubmed: 18798613
pmcid: 2653060
doi: 10.1021/ja8053805
Chen, C. S., Mrksich, M., Huang, S., Whitesides, G. M. & Ingber, D. E. Geometric control of cell life and death. Science 276, 1425–1428 (1997).
pubmed: 9162012
doi: 10.1126/science.276.5317.1425
Geisse, N. A., Sheehy, S. P. & Parker, K. K. Control of myocyte remodeling in vitro with engineered substrates. In Vitro. Cell. Dev. Biol. Anim. 45, 343–350 (2009).
doi: 10.1007/s11626-009-9182-9
Kuddannaya, S. et al. Surface chemical modification of poly(dimethylsiloxane) for the enhanced adhesion and proliferation of mesenchymal stem cells. ACS Appl. Mater. Interfaces 5, 9777–9784 (2013).
pubmed: 24015724
doi: 10.1021/am402903e
Qin, D., Xia, Y. & Whitesides, G. M. Soft lithography for micro- and nanoscale patterning. Nat. Protoc. 5, 491–502 (2010).
pubmed: 20203666
doi: 10.1038/nprot.2009.234
Bettadapur, A. et al. Prolonged culture of aligned skeletal myotubes on micromolded gelatin hydrogels. Sci. Rep. 6, 28855 (2016).
pubmed: 27350122
pmcid: 4924097
doi: 10.1038/srep28855
Feinberg, A. W. et al. Controlling the contractile strength of engineered cardiac muscle by hierarchal tissue architecture. Biomaterials 33, 5732–5741 (2012).
pubmed: 22594976
pmcid: 4026933
doi: 10.1016/j.biomaterials.2012.04.043
Lee, S. et al. Direct reprogramming of human dermal fibroblasts into endothelial cells using ER71/ETV2. Circ. Res. 120, 848–861 (2017).
pubmed: 28003219
doi: 10.1161/CIRCRESAHA.116.309833
Morita, R. et al. ETS transcription factor ETV2 directly converts human fibroblasts into functional endothelial cells. Proc. Natl Acad. Sci. 112, 160–165 (2015).
pubmed: 25540418
doi: 10.1073/pnas.1413234112
Cadle, R., Rogozea, D., Moldovan, L. & Moldovan, N. I. Design and implementation of anatomically inspired mesenteric and intestinal vascular patterns for personalized 3D bioprinting. Appr. Sci. 12, 4430 (2022).
doi: 10.3390/app12094430
Lee, S. H. et al. Capillary based patterning of cellular communities in laterally open channels. Anal. Chem. 82, 2900–2906 (2010).
pubmed: 20210331
doi: 10.1021/ac902903q
Sherman, B. T. et al. DAVID: a web server for functional enrichment analysis and functional annotation of gene lists (2021 update). Nucleic Acids Res. 50, W216–W221 (2022).
pubmed: 35325185
pmcid: 9252805
doi: 10.1093/nar/gkac194
Huang, D. W., Sherman, B. T. & Lempicki, R. A. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat. Protoc. 4, 44–57 (2009).
pubmed: 19131956
doi: 10.1038/nprot.2008.211
Choe, J. H. et al. SynNotch-CAR T cells overcome challenges of specificity, heterogeneity, and persistence in treating glioblastoma. Sci. Transl. Med. 13, eabe7378 (2021).
pubmed: 33910979
pmcid: 8362330
doi: 10.1126/scitranslmed.abe7378
Hyrenius-Wittsten, A. et al. SynNotch CAR circuits enhance solid tumor recognition and promote persistent antitumor activity in mouse models. Sci. Transl. Med. 13, eabd8836 (2021).
pubmed: 33910981
pmcid: 8594452
doi: 10.1126/scitranslmed.abd8836
Moghimi, B. et al. Preclinical assessment of the efficacy and specificity of GD2-B7H3 SynNotch CAR-T in metastatic neuroblastoma. Nat. Commun. 12, 511 (2021).
pubmed: 33479234
pmcid: 7820416
doi: 10.1038/s41467-020-20785-x
Allen, G. M. et al. Synthetic cytokine circuits that drive T cells into immune-excluded tumors. Science 378, eaba1624 (2022).
pubmed: 36520915
pmcid: 9970000
doi: 10.1126/science.aba1624
Ruffo, E. et al. Post-translational covalent assembly of CAR and synNotch receptors for programmable antigen targeting. Nat. Commun. 14, 2463 (2023).
pubmed: 37160880
pmcid: 10169838
doi: 10.1038/s41467-023-37863-5
Zhang, S. et al. Monitoring of cell-cell communication and contact history in mammals. Science 378, eabo5503 (2022).
pubmed: 36454848
doi: 10.1126/science.abo5503
Malaguti, M., Lebek, T., Blin, G. & Lowell, S. Enabling neighbour labelling: using synthetic biology to explore how cells influence their neighbours. Development 151, dev201955 (2024).
pubmed: 38165174
pmcid: 10820747
doi: 10.1242/dev.201955
Purnick, P. E. M. & Weiss, R. The second wave of synthetic biology: from modules to systems. Nat. Rev. Mol. Cell Biol. 10, 410–422 (2009).
pubmed: 19461664
doi: 10.1038/nrm2698
Meng, F. & Ellis, T. The second decade of synthetic biology: 2010–2020. Nat. Commun. 11, 5174 (2020).
pubmed: 33057059
pmcid: 7560693
doi: 10.1038/s41467-020-19092-2
Firas, J., Liu, X., Lim, S. M. & Polo, J. M. Transcription factor-mediated reprogramming: epigenetics and therapeutic potential. Immunol. Cell Biol. 93, 284–289 (2015).
pubmed: 25643615
doi: 10.1038/icb.2015.5
Takahashi, K. & Yamanaka, S. A decade of transcription factor-mediated reprogramming to pluripotency. Nat. Rev. Mol. Cell Biol. 17, 183–193 (2016).
pubmed: 26883003
doi: 10.1038/nrm.2016.8
Ng, A. H. M. et al. A comprehensive library of human transcription factors for cell fate engineering. Nat. Biotechnol. 39, 510 (2021).
pubmed: 33257861
doi: 10.1038/s41587-020-0742-6
Joung, J. et al. A transcription factor atlas of directed differentiation. Cell 186, 209–229.e26 (2023).
pubmed: 36608654
pmcid: 10344468
doi: 10.1016/j.cell.2022.11.026
Johnson, H. E. & Toettcher, J. E. Illuminating developmental biology with cellular optogenetics. Curr. Opin. Biotechnol. 52, 42–48 (2018).
pubmed: 29505976
pmcid: 6082700
doi: 10.1016/j.copbio.2018.02.003
Johnson, H. E., Djabrayan, N. J. V., Shvartsman, S. Y. & Toettcher, J. E. Optogenetic rescue of a patterning mutant. Curr. Biol. 30, 3414–3424.e3 (2020).
pubmed: 32707057
pmcid: 7730203
doi: 10.1016/j.cub.2020.06.059
Polstein, L. R., Juhas, M., Hanna, G., Bursac, N. & Gersbach, C. A. An engineered optogenetic switch for spatiotemporal control of gene expression, cell differentiation, and tissue morphogenesis. ACS Synth. Biol. 6, 2003–2013 (2017).
pubmed: 28793186
pmcid: 5767923
doi: 10.1021/acssynbio.7b00147
Müller, K., Engesser, R., Timmer, J., Zurbriggen, M. D. & Weber, W. Orthogonal optogenetic triple-gene control in mammalian cells. ACS Synth. Biol. 3, 796–801 (2014).
pubmed: 25343333
doi: 10.1021/sb500305v
Lee, K. Y. & Mooney, D. J. Hydrogels for tissue engineering. Chem. Rev. 101, 1869–1880 (2001).
pubmed: 11710233
doi: 10.1021/cr000108x
Qazi, T. H. et al. Programming hydrogels to probe spatiotemporal cell biology. Cell Stem Cell 29, 678–691 (2022).
pubmed: 35413278
pmcid: 9081204
doi: 10.1016/j.stem.2022.03.013
Gordon, W. R. et al. Structural basis for autoinhibition of Notch. Nat. Struct. Mol. Biol. 14, 295–300 (2007).
pubmed: 17401372
doi: 10.1038/nsmb1227
Khamaisi, B., Luca, V. C., Blacklow, S. C. & Sprinzak, D. Functional comparison between endogenous and synthetic Notch systems. ACS Synth. Biol. 11, 3343–3353 (2022).
pubmed: 36107643
pmcid: 9594772
doi: 10.1021/acssynbio.2c00247
Lin, Z. et al. Tissue-embedded stretchable nanoelectronics reveal endothelial cell–mediated electrical maturation of human 3D cardiac microtissues. Sci. Adv. 9, eade8513 (2023).
pubmed: 36888704
pmcid: 9995081
doi: 10.1126/sciadv.ade8513
Giacomelli, E. et al. Human-iPSC-derived cardiac stromal cells enhance maturation in 3D cardiac microtissues and reveal non-cardiomyocyte contributions to heart disease. Cell Stem Cell 26, 862–879.e11 (2020).
pubmed: 32459996
pmcid: 7284308
doi: 10.1016/j.stem.2020.05.004
& Ng, W. H. et al. Recapitulating human cardio-pulmonary co-development using simultaneous multilineage differentiation of pluripotent stem cells. eLife 11, e67872 (2022).
pubmed: 35018887
pmcid: 8846595
doi: 10.7554/eLife.67872
Skylar-Scott, M. A. et al. Orthogonally induced differentiation of stem cells for the programmatic patterning of vascularized organoids and bioprinted tissues. Nat. Biomed. Eng. 6, 449–462 (2022).
pubmed: 35332307
pmcid: 9506705
doi: 10.1038/s41551-022-00856-8
Daly, A. C., Prendergast, M. E., Hughes, A. J. & Burdick, J. A. Bioprinting for the Biologist. Cell 184, 18–32 (2021).
pubmed: 33417859
pmcid: 10335003
doi: 10.1016/j.cell.2020.12.002
Hoffman, T. et al. Tissue engineering: synthetic biology and tissue engineering: toward fabrication of complex and smart cellular constructs (Adv. Funct. Mater. 26/2020). Adv. Funct. Mater. 30, 2070169 (2020).
doi: 10.1002/adfm.202070169
Sasai, Y. Next-generation regenerative medicine: organogenesis from stem cells in 3D culture. Cell Stem Cell 12, 520–530 (2013).
pubmed: 23642363
doi: 10.1016/j.stem.2013.04.009
Huch, M., Knoblich, J. A., Lutolf, M. P. & Martinez-Arias, A. The hope and the hype of organoid research. Development 144, 938–941 (2017).
pubmed: 28292837
doi: 10.1242/dev.150201
Takebe, T., Zhang, B. & Radisic, M. Synergistic engineering: organoids meet organs-on-a-chip. Cell Stem Cell 21, 297–300 (2017).
pubmed: 28886364
doi: 10.1016/j.stem.2017.08.016
Aydin, O. et al. Principles for the design of multicellular engineered living systems. APL Bioeng. 6, 010903 (2022).
pubmed: 35274072
pmcid: 8893975
doi: 10.1063/5.0076635
Kamm, R. D. et al. Perspective: the promise of multi-cellular engineered living systems. APL Bioeng. 2, 040901 (2018).
pubmed: 31069321
pmcid: 6481725
doi: 10.1063/1.5038337
Kuduğ, H., Ataman, B., İmamoğlu, R., Düzgün, D. & Gökçe, İ. Production of red fluorescent protein (mCherry) in an inducible E. coli expression system in a bioreactor, purification and characterization. Int. Adv. Res. Eng. J. 3, 20–25 (2019).
Rezakhaniha, R. et al. Experimental investigation of collagen waviness and orientation in the arterial adventitia using confocal laser scanning microscopy. Biomech. Model Mechanobiol. 11, 461–473 (2012).
pubmed: 21744269
doi: 10.1007/s10237-011-0325-z
Shirahama, H., Lee, B. H., Tan, L. P. & Cho, N.-J. Precise tuning of facile one-pot gelatin methacryloyl (GelMA) synthesis. Sci. Rep. 6, 31036 (2016).
pubmed: 27503340
pmcid: 4977492
doi: 10.1038/srep31036
Dobin, A. et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29, 15–21 (2013).
pubmed: 23104886
doi: 10.1093/bioinformatics/bts635
Liao, Y., Smyth, G. K. & Shi, W. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics 30, 923–930 (2014).
pubmed: 24227677
doi: 10.1093/bioinformatics/btt656
Love, M. I., Huber, W. & Anders, S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 15, 550 (2014).
pubmed: 25516281
pmcid: 4302049
doi: 10.1186/s13059-014-0550-8
Wu, T. et al. clusterProfiler 4.0: a universal enrichment tool for interpreting omics data. Innovation 2, 100141 (2021).
pubmed: 34557778
pmcid: 8454663