references.bib

@article{martinOptimizedSinglenucleus2023,
  title = {Optimized Single-Nucleus Transcriptional Profiling by Combinatorial Indexing},
  author = {Martin, Beth K. and Qiu, Chengxiang and Nichols, Eva and Phung, Melissa and {Green-Gladden}, Rula and Srivatsan, Sanjay and {Blecher-Gonen}, Ronnie and Beliveau, Brian J. and Trapnell, Cole and Cao, Junyue and Shendure, Jay},
  year = {2023},
  month = jan,
  journal = {Nat Protoc},
  volume = {18},
  number = {1},
  pages = {188--207},
  publisher = {{Nature Publishing Group}},
  issn = {1750-2799},
  doi = {10.1038/s41596-022-00752-0},
  urldate = {2023-05-15},
  abstract = {Single-cell combinatorial indexing RNA sequencing (sci-RNA-seq) is a powerful method for recovering gene expression data from an exponentially scalable number of individual cells or nuclei. However, sci-RNA-seq is a complex protocol that has historically exhibited variable performance on different tissues, as well as lower sensitivity than alternative methods. Here, we report a simplified, optimized version of the sci-RNA-seq protocol with three rounds of split-pool indexing that is faster, more robust and more sensitive and has a higher yield than the original protocol, with reagent costs on the order of 1 cent per cell or less. The total hands-on time from nuclei isolation to final library preparation takes 2\textendash 3 d, depending on the number of samples sharing the experiment. The improvements also allow RNA profiling from tissues rich in RNases like older mouse embryos or adult tissues that were problematic for the original method. We showcase the optimized protocol via whole-organism analysis of an E16.5 mouse embryo, profiling \textasciitilde 380,000 nuclei in a single experiment. Finally, we introduce a `Tiny-Sci' protocol for experiments in which input material is very limited.},
  copyright = {2022 Springer Nature Limited},
  langid = {english},
  keywords = {Gene expression profiling,RNA sequencing}
}

@article{crasComparisonChemical1999,
  title = {Comparison of Chemical Cleaning Methods of Glass in Preparation for Silanization},
  author = {Cras, J. J and {Rowe-Taitt}, C. A and Nivens, D. A and Ligler, F. S},
  year = {1999},
  month = dec,
  journal = {Biosensors and Bioelectronics},
  volume = {14},
  number = {8},
  pages = {683--688},
  issn = {0956-5663},
  doi = {10.1016/S0956-5663(99)00043-3},
  urldate = {2023-05-24},
  abstract = {The uniform deposition of a silane monolayer upon glass has been shown to require small amounts of water along with hydroxyl groups in an isolated or geminal configuration on the substrate surface. In order to expose these groups, organic compounds at the surface must be removed. We present a qualitative evaluation of eight chemical methods commonly used to clean glass microscope slides in preparation for silanization. Mean contact angle of deionized water was measured before covalent attachment of (3-mercaptopropyl)triethoxysilane to assess the efficacy of each procedure. Contact angles were also measured after silanization as a means of determining the uniformity and reproducibility of the silane monolayer. The results indicate that a 1:1 methanol/HC1 wash followed by a bath in concentrated H2SO4 removes surface contaminants most effectively and allows for a very even silanization of the glass surface.},
  langid = {english},
  keywords = {(3-Mercaptopropyl)silane,Cleaning methods,Glass surface,Silanization,Soda lime}
}

@article{a.schlechtFunctionalizationGlass2011,
  title = {Functionalization of Glass Substrates: Mechanistic Insights into the Surface Reaction of Trialkoxysilanes},
  shorttitle = {Functionalization of Glass Substrates},
  author = {A.~Schlecht, Clifford and A.~Maurer, Joshua},
  year = {2011},
  journal = {RSC Advances},
  volume = {1},
  number = {8},
  pages = {1446--1448},
  publisher = {{Royal Society of Chemistry}},
  doi = {10.1039/C1RA00421B},
  urldate = {2023-05-24},
  langid = {english}
}