Classification of low quality cells from single-cell RNA-seq data
作者： Tomislav Ilicic , Jong Kyoung Kim , Aleksandra A. Kolodziejczyk , Frederik Otzen Bagger , Davis James McCarthy
DOI: 10.1186/S13059-016-0888-1
关键词:
摘要: … To evaluate data quality we obtained raw read counts of unpublished and previously published [9] datasets comprising 5,000 CD4+ T cells, bone marrow dendritic cells (BMDCs), and …
biomedcentral.com
springer.com
genomebiology.com
core.ac.uk
figshare.com参考文章(50)
Zhong Wang, Mark Gerstein, Michael Snyder, RNA-Seq: a revolutionary tool for transcriptomics Nature Reviews Genetics. ,vol. 10, pp. 57- 63 ,(2009) , 10.1038/NRG2484
Cole Trapnell, Davide Cacchiarelli, Jonna Grimsby, Prapti Pokharel, Shuqiang Li, Michael Morse, Niall J Lennon, Kenneth J Livak, Tarjei S Mikkelsen, John L Rinn, The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells Nature Biotechnology. ,vol. 32, pp. 381- 386 ,(2014) , 10.1038/NBT.2859
Brian B. Tuch, Edith Heard, Kaiqin Lao, M. Azim Surani, Fuchou Tang, Catalin Barbacioru, Ellen Nordman, Siqin Bao, Caroline Lee, Xiaohui Wang, Deterministic and Stochastic Allele Specific Gene Expression in Single Mouse Blastomeres PLoS ONE. ,vol. 6, pp. e21208- ,(2011) , 10.1371/JOURNAL.PONE.0021208
Iain C. Macaulay, Thierry Voet, Single Cell Genomics: Advances and Future Perspectives PLOS Genetics. ,vol. 10, ,(2014) , 10.1371/JOURNAL.PGEN.1004126
Bidesh Mahata, Xiuwei Zhang, Aleksandra A Kolodziejczyk, Valentina Proserpio, Liora Haim-Vilmovsky, Angela E Taylor, Daniel Hebenstreit, Felix A Dingler, Victoria Moignard, Berthold Göttgens, Wiebke Arlt, Andrew NJ McKenzie, Sarah A Teichmann, None, Single-Cell RNA Sequencing Reveals T Helper Cells Synthesizing Steroids De Novo to Contribute to Immune Homeostasis Cell Reports. ,vol. 7, pp. 1130- 1142 ,(2014) , 10.1016/J.CELREP.2014.04.011
Florian Buettner, Kedar N Natarajan, F Paolo Casale, Valentina Proserpio, Antonio Scialdone, Fabian J Theis, Sarah A Teichmann, John C Marioni, Oliver Stegle, Computational analysis of cell-to-cell heterogeneity in single-cell RNA-sequencing data reveals hidden subpopulations of cells Nature Biotechnology. ,vol. 33, pp. 155- 160 ,(2015) , 10.1038/NBT.3102
Simone Picelli, Åsa K Björklund, Omid R Faridani, Sven Sagasser, Gösta Winberg, Rickard Sandberg, Smart-seq2 for sensitive full-length transcriptome profiling in single cells Nature Methods. ,vol. 10, pp. 1096- 1098 ,(2013) , 10.1038/NMETH.2639
Simon Anders, Davis J McCarthy, Yunshun Chen, Michal Okoniewski, Gordon K Smyth, Wolfgang Huber, Mark D Robinson, Count-based differential expression analysis of RNA sequencing data using R and Bioconductor Nature Protocols. ,vol. 8, pp. 1765- 1786 ,(2013) , 10.1038/NPROT.2013.099
Q. Deng, D. Ramskold, B. Reinius, R. Sandberg, Single-cell RNA-seq reveals dynamic, random monoallelic gene expression in mammalian cells. Science. ,vol. 343, pp. 193- 196 ,(2014) , 10.1126/SCIENCE.1245316
Philip Brennecke, Simon Anders, Jong Kyoung Kim, Aleksandra A Kołodziejczyk, Xiuwei Zhang, Valentina Proserpio, Bianka Baying, Vladimir Benes, Sarah A Teichmann, John C Marioni, Marcus G Heisler, Accounting for technical noise in single-cell RNA-seq experiments Nature Methods. ,vol. 10, pp. 1093- 1095 ,(2013) , 10.1038/NMETH.2645