Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets
Evan Z. Macosko,Evan Z. Macosko,Anindita Basu,Anindita Basu,Rahul Satija,Rahul Satija,James Nemesh,James Nemesh,Karthik Shekhar,Melissa Goldman,Melissa Goldman,Itay Tirosh,Allison R. Bialas,Nolan Kamitaki,Nolan Kamitaki,Emily M. Martersteck,John J. Trombetta,David A. Weitz,Joshua R. Sanes,Alex K. Shalek,Alex K. Shalek,Alex K. Shalek,Aviv Regev,Aviv Regev,Aviv Regev,Steven A. McCarroll,Steven A. McCarroll +26 more
TL;DR: Drop-seq will accelerate biological discovery by enabling routine transcriptional profiling at single-cell resolution by separating them into nanoliter-sized aqueous droplets, associating a different barcode with each cell's RNAs, and sequencing them all together.
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About: This article is published in Cell. The article was published on 21 May 2015. and is currently open access. The article focuses on the topics: Single-cell analysis & Single cell sequencing.
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Citations
Deep learning and alignment of spatially resolved single-cell transcriptomes with Tangram.
Tommaso Biancalani,Gabriele Scalia,Gabriele Scalia,Lorenzo Buffoni,Raghav Avasthi,Raghav Avasthi,Ziqing Lu,Ziqing Lu,Aman Sanger,Neriman Tokcan,Charles R. Vanderburg,Asa Segerstolpe,Meng Zhang,Meng Zhang,Inbal Avraham-Davidi,Sanja Vickovic,Mor Nitzan,Mor Nitzan,Mor Nitzan,Sai Ma,Sai Ma,Sai Ma,Ayshwarya Subramanian,Michal Lipinski,Michal Lipinski,Jason D. Buenrostro,Jason D. Buenrostro,Nik Bear Brown,Duccio Fanelli,Xiaowei Zhuang,Xiaowei Zhuang,Evan Z. Macosko,Aviv Regev +32 more
TL;DR: Tangram as mentioned in this paper aligns single-cell and single-nucleus RNA-seq data to various forms of spatial data collected from the same region, including MERFISH, STARmap, smFISH and histological images.
Fast interpolation-based t-SNE for improved visualization of single-cell RNA-seq data
TL;DR: Kluger et al. as mentioned in this paper proposed a heatmap-style visualization for scRNA-seq based on one-dimensional t-distributed stochastic neighbor embedding (t-SNE) for simultaneously visualizing the expression patterns of thousands of genes.
481
Massively parallel single-cell chromatin landscapes of human immune cell development and intratumoral T cell exhaustion
Ansuman T. Satpathy,Jeffrey M. Granja,Kathryn E. Yost,Yanyan Qi,Francesca Meschi,Geoffrey P. McDermott,Brett N. Olsen,Maxwell R. Mumbach,Sarah E. Pierce,M. Ryan Corces,Preyas Shah,Jason C. Bell,Darisha Jhutty,Corey M. Nemec,Jean Wang,Li Wang,Yifeng Yin,Paul G. Giresi,Anne Lynn S. Chang,Grace X.Y. Zheng,William J. Greenleaf,Howard Y. Chang +21 more
TL;DR: It is anticipated that droplet-based single-cell chromatin accessibility will provide a broadly applicable means of identifying regulatory factors and elements that underlie cell type and function.
Transcriptional and Cellular Diversity of the Human Heart
Nathan R. Tucker,Mark Chaffin,Stephen J. Fleming,Amelia W. Hall,Victoria A. Parsons,Kenneth Bedi,Amer-Denis Akkad,Caroline N. Herndon,Alessandro Arduini,Irinna Papangeli,Carolina Roselli,François Aguet,Seung Hoan Choi,Kristin G. Ardlie,Mehrtash Babadi,Kenneth B. Margulies,Christian Stegmann,Patrick T. Ellinor +17 more
TL;DR: Using large-scale single nuclei RNA sequencing, the transcriptional and cellular diversity in the normal human heart was defined and the identification of discrete cell subtypes and differentially expressed genes within the heart will ultimately facilitate the development of new therapeutics for cardiovascular diseases.
478
Cell Types of the Human Retina and Its Organoids at Single-Cell Resolution.
Cameron S. Cowan,Magdalena Renner,Magdalena Renner,Martina De Gennaro,Brigitte Gross-Scherf,David Goldblum,Yanyan Hou,Martin Munz,Tiago M. Rodrigues,Jacek Krol,Tamas Szikra,Rachel Cuttat,Annick Waldt,Panagiotis Papasaikas,Panagiotis Papasaikas,Roland Diggelmann,Claudia P. Patino-Alvarez,Patricia Galliker,Stefan E. Spirig,Dinko Pavlinic,Nadine Gerber-Hollbach,Sven Schuierer,Aldin Srdanovic,Márton Balogh,Riccardo Panero,Akos Kusnyerik,Arnold Szabo,Michael B. Stadler,Michael B. Stadler,Selim Orgül,Simone Picelli,Pascal W. Hasler,Andreas Hierlemann,Hendrik P. N. Scholl,Hendrik P. N. Scholl,Guglielmo Roma,Florian Nigsch,Botond Roska,Botond Roska +38 more
TL;DR: This resource identifies cellular targets for studying disease mechanisms in organoids and for targeted repair in human retinas and implicate unexpected cell types in diseases such as macular degeneration.
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