References
- Akhmanova M, Osidak E, Domogatsky S, Rodin S, Domogatskaya A (2015) Physical, spatial, and molecular aspects of extracellular matrix of in vivo niches and artificial ccaffolds relevant to stem cells research. Stem Cells Int 2015:167025. https://doi.org/10.1155/2015/167025
-
Bean AC, Tuan RS (2015) Fiber diameter and seeding density influence chondrogenic differentiation of mesenchymal stem cells seeded on electrospun poly(
${\varepsilon}$ -caprolactone) scaffolds. Biomed Mater 10:015018. https://doi.org/10.1088/1748-6041/10/1/015018 - Chambers SM, Fasano CA, Papapetrou EP, Tomishima M, Sadelain M, Studer L (2009) Highly efficient neural conversion of human ES and iPS cells by dual inhibition of SMAD signaling. Nat Biotechnol 27:275-280. https://doi.org/10.1038/nbt.1529
- Christopherson GT, Song H, Mao HQ (2009) The influence of fiber diameter of electrospun substrates on neural stem cell differentiation and proliferation. Biomaterials 30:556-564. https://doi.org/10.1016/j.biomaterials.2008.10.004
- Du ZW, Chen H, Liu H, Lu J, Qian K, Huang CL, Zhong X, Fan F, Zhang SC (2015) Generation and expansion of highly pure motor neuron progenitors from human pluripotent stem cells. Nat Commun 6:6626. https://doi.org/10.1038/ncomms7626
- Heinke J, Juschkat M, Charlet A, Mnich L, Helbing T, Bode C, Patterson C, Moser M (2013) Antagonism and synergy between extracellular BMP modulators Tsg and BMPER balance blood vessel formation. J Cell Sci 126:3082-3094. https://doi.org/10.1242/jcs.122333
- Hwang DS, Sim SB, Cha HJ (2007) Cell adhesion biomaterial based on mussel adhesive protein fused with RGD peptide. Biomaterials 28:4039-4046. https://doi.org/10.1016/j.biomaterials.2007.05.028
- KarbalaeiMahdi A, Shahrousvand M, Javadi HR, Ghollasi M, Norouz F, Kamali M, Salimi A (2017) Neural differentiation of human induced pluripotent stem cells on polycaprolactone/gelatin bielectrospun nanofibers. Mater Sci Eng C Mater Biol Appl 78:1195-1202. https://doi.org/10.1016/j.msec.2017.04.083
- Kelley R, Ren R, Pi X, Wu Y, Moreno I, Willis M, Moser M, Ross M, Podkowa M, Attisano L, Patterson C (2009) A concentration-dependent endocytic trap and sink mechanism converts Bmper from an activator to an inhibitor of Bmp signaling. J Cell Biol 184:597-609. https://doi.org/10.1083/jcb.200808064
- Kim DS, Lee JS, Leem JW, Huh YJ, Kim JY, Kim HS, Park IH, Daley GQ, Hwang DY Kim DW (2010) Robust enhancement of neural differentiation from human ES and iPS cells regardless of their innate difference in differentiation propensity. Stem Cell Rev Rep 6:270-281. https://doi.org/10.1007/s12015-010-9138-1
- Klim JR, Li L, Wrighton PJ, Piekarczyk MS, Kiessling LL (2010) A defined glycosaminoglycanbinding substratum for human pluripotent stem cells. Nat Methods 7:989-994. https://doi.org/10.1038/nmeth.1532
- Kriks S, Shim JW, Piao J, Ganat YM, Wakeman DR, Xie Z, Carrillo-Reid L, Auyeung G, Antonacci C, Buch A, Yang L, Beal MF, Surmeier DJ, Kordower J H, Tabar V, Studer L (2011) Dopamine neurons derived from human ES cells efficiently engraft in animal models of Parkinson's disease. Nature 480:547-551. https://doi.org/10.1038/nature10648
- Krueger F (2020) Trim galore. Available from https://github.com/FelixKrueger/TrimGalore. Accessed at Jan 20, 2020.
- Kuroda H, Fuentealba L, Ikeda A, Reversade B, De Robertis EM (2005) Default neural induction: neuralization of dissociated Xenopus cells is mediated by Ras/MAPK activation. Genes Dev 19:1022-1027. https://doi.org/10.1101/gad.1306605
- Lee BP, Messersmith PB, Israelachvili JN, Waite JH (2011) Mussel-inspired adhesives and coatings. Annu Rev Mater Res 41:99-132. https://doi.org/10.1146/annurev-matsci-062910-100429
- Li Y, Liao C, Tjong SC (2019) Electrospun polyvinylidene fluoride-based fibrous scaffolds with piezoelectric characteristics for bone and neural tissue engineering. Nanomaterials (Basel) 9:952. https://doi.org/10.3390/nano9070952
- Li Y, Liu M, Yan Y, Yang ST (2014) Neural differentiation from pluripotent stem cells: The role of natural and synthetic extracellular matrix. World J Stem Cells 6:11-23. https://doi.org/10.4252/wjsc.v6.i1.11
- Love MI, Huber W, Anders S (2014) Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol 15:550. https://doi.org/10.1186/s13059-014-0550-8
- Melkoumian Z, Weber JL, Weber DM, Fadeev AG, Zhou Y, Dolley-Sonneville P, Yang J, Qiu L, Priest CA, Shogbon C, Martin AW, Nelson J, West P, Beltzer JP, Pal S, Brandenberger R (2010) Synthetic peptide-acrylate surfaces for long-term self-renewal and cardiomyocyte differentiation of human embryonic stem cells. Nat Biotechnol 28:606-610. https://doi.org/10.1038/nbt.1629
- Niklason LE (2018) Understanding the extracellular matrix to enhance stem cell-based tissue regeneration. Cell Stem Cell 22:302-305. https://doi.org/10.1016/j.stem.2018.02.001
- Palmer I, Wingfield PT (2004) Preparation and extraction of insoluble (inclusion-body) proteins from Escherichia coli. Curr Protoc Protein Sci 38:6.3.1-6.3.18.
- Patro R, Duggal G, Love MI, Irizarry RA, Kingsford C (2017) Salmon provides fast and biasaware quantification of transcript expression. Nat Methods 14:417-419. https://doi.org/10.1038/nmeth.4197
- Perrier AL, Tabar V, Barberi T, Rubio ME, Bruses J, Topf N, Harrison NL Studer L (2004) Derivation of midbrain dopamine neurons from human embryonic stem cells. Proc Natl Acad Sci USA 101:12543-12548. https://doi.org/10.1073/pnas.0404700101
- Silantyeva EA, Nasir W, Carpenter J, Manahan O, Becker ML Willits RK (2018) Accelerated neural differentiation of mouse embryonic stem cells on aligned GYIGSR-functionalized nanofibers. Acta Biomater 75:129-139. https://doi.org/10.1016/j.actbio.2018.05.052
- Smith L,R, Cho S, Discher DE (2018) Stem cell differentiation is regulated by extracellular matrix mechanics. Physiology (Bethesda) 33:16-25. https://doi.org/10.1152/physiol.00026.2017
- Soneson C, Love MI, Robinson MD (2015) Differential analyses for RNA-seq: transcript-level estimates improve gene-level inferences. F1000Res 4:1521. https://doi.org/10.12688/f1000research.7563.2
- Wilson SI, Edlund T (2001) Neural induction: toward a unifying mechanism. Nat Neurosci 4:1161-1168. https://doi.org/10.1038/nn747
- Zhang SC, Wernig M, Duncan ID, Brustle O, Thomson JA (2001) In vitro differentiation of transplantable neural precursors from human embryonic stem cells. Nat Biotechnol 19:1129-1133. https://doi.org/10.1038/nbt1201-1129
- Zhou Y, Zhou B, Pache L, Chang M, Khodabakhshi AH, Tanaseichuk O, Benner C, Chanda SK (2019) Metascape provides a biologist-oriented resource for the analysis of systems-level datasets. Nat Commun 101523.