Why is the aqueous layer cloudy after breaking GEMs? (2021) Isolation of nuclei for single cell RNA sequencing (2021) Guidelines for accurate target cell counts using 10x Genomics® Single Cell Solutions (2021) Ĭhromium single cell applications - guidelines for optimal sample preparation (2021) Importance of cell stock concentration for accurate target cell recovery (2019) Interpreting cell ranger web summary files for Single Cell Gene Expression Assays (2021) Ĭhan LL, Smith T, Kumph KA, Kuksin D, Kessel S, Dery O, Cribbes S, Lai N, Qiu J (2016) A high-throughput AO/PI-based cell concentration and viability detection method using the Celigo image cytometry. Īlessandri L, Cordero F, Beccuti M, Arigoni M, Olivero M, Romano G, Rabellino S, Licheri N, De Libero G, Pace L, Calogero RA (2019) rCASC: reproducible classification analysis of single-cell sequencing data. Īlessandri L, Ratto ML, Contaldo SG, Beccuti M, Cordero F, Arigoni M, Calogero RA (2021) Sparsely connected autoencoders: a multi-purpose tool for single cell omics analysis. KAPA library quantification kits (2021) ,Īlessandri L, Cordero F, Beccuti M, Licheri N, Arigoni M, Olivero M, Di Renzo MF, Sapino A, Calogero R (2021) Sparsely-connected autoencoder (SCA) for single cell RNAseq data mining. How can I assess the quality of my nuclei for Single Cell ATAC or Single Cell Multiome ATAC+GEX Sequencing? (2021) Single Cell protocols - cell preparation guide (2021) What buffers can be used for washing and cell resuspension? (2021) Removal of dead cells from single cell suspensions improves performance for 10x Genomics® Single Cell Applications (2019) Ĭhromium Single Cell 3' Reagent kits user guide (v3.1 Chemistry Dual Index). ĭe Simone M, Rossetti G, Pagani M (2019) Chromium 10x single-cell 3' mRNA sequencing of tumor-infiltrating lymphocytes. Zheng GX, Terry JM, Belgrader P, Ryvkin P, Bent ZW, Wilson R, Ziraldo SB, Wheeler TD, McDermott GP, Zhu J, Gregory MT, Shuga J, Montesclaros L, Underwood JG, Masquelier DA, Nishimura SY, Schnall-Levin M, Wyatt PW, Hindson CM, Bharadwaj R, Wong A, Ness KD, Beppu LW, Deeg HJ, McFarland C, Loeb KR, Valente WJ, Ericson NG, Stevens EA, Radich JP, Mikkelsen TS, Hindson BJ, Bielas JH (2017) Massively parallel digital transcriptional profiling of single cells. These documents and user guides are continuously improved and updated hence, it is important to regularly check the company’s website for the most recent version. which can be downloaded from the Support section on the 10x Genomics website (10x Genomics website. The descriptions of these tips and tricks refer to the current version of the 10x Genomics User Guide (Chromium Single Cell 3' Reagent Kits User Guide (v3.1 Chemistry Dual Index). Methods Mol Biol 1979:87–110, 2019), in this chapter we will focus on the importance of the quality of the initial cell suspension, as well as common mistakes that can occur while running a Single Cell Gene Expression assay. While the workflow itself has been detailed elsewhere (De Simone et al. A successful workflow relies on a cell suspension which is fully dissociated, extremely clean, and of high viability. Obtaining high-data quality is the key to being able to make these meaningful discoveries, which in turn is directly linked to the quality of the initial cell (or nuclei) suspension that is used to load the 10x Genomics Chromium Single Cell Gene Expression assay. Nat Commun 8:14049, 2017)-capturing thousands of cells at once-has shaped life sciences ever since and allowed researchers to discover new insights within their respective fields of study such as oncology, neurobiology, and immunology (among others). Utilizing the power of the single cell on a large scale (Zheng et al. One such assay was launched in 2016 by the US-based company 10x Genomics Inc. The demand for technologies that allow the study of gene expression at single cell resolution continues to increase.
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