Literature DB >> 24056876

Accounting for technical noise in single-cell RNA-seq experiments.

Philip Brennecke1, 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.   

Abstract

Single-cell RNA-seq can yield valuable insights about the variability within a population of seemingly homogeneous cells. We developed a quantitative statistical method to distinguish true biological variability from the high levels of technical noise in single-cell experiments. Our approach quantifies the statistical significance of observed cell-to-cell variability in expression strength on a gene-by-gene basis. We validate our approach using two independent data sets from Arabidopsis thaliana and Mus musculus.

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Year:  2013        PMID: 24056876     DOI: 10.1038/nmeth.2645

Source DB:  PubMed          Journal:  Nat Methods        ISSN: 1548-7091            Impact factor:   28.547


  19 in total

1.  Nanog safeguards pluripotency and mediates germline development.

Authors:  Ian Chambers; Jose Silva; Douglas Colby; Jennifer Nichols; Bianca Nijmeijer; Morag Robertson; Jan Vrana; Ken Jones; Lars Grotewold; Austin Smith
Journal:  Nature       Date:  2007-12-20       Impact factor: 49.962

2.  RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays.

Authors:  John C Marioni; Christopher E Mason; Shrikant M Mane; Matthew Stephens; Yoav Gilad
Journal:  Genome Res       Date:  2008-06-11       Impact factor: 9.043

3.  Characterization of the single-cell transcriptional landscape by highly multiplex RNA-seq.

Authors:  Saiful Islam; Una Kjällquist; Annalena Moliner; Pawel Zajac; Jian-Bing Fan; Peter Lönnerberg; Sten Linnarsson
Journal:  Genome Res       Date:  2011-05-04       Impact factor: 9.043

4.  Synthetic spike-in standards for RNA-seq experiments.

Authors:  Lichun Jiang; Felix Schlesinger; Carrie A Davis; Yu Zhang; Renhua Li; Marc Salit; Thomas R Gingeras; Brian Oliver
Journal:  Genome Res       Date:  2011-08-04       Impact factor: 9.043

5.  CEL-Seq: single-cell RNA-Seq by multiplexed linear amplification.

Authors:  Tamar Hashimshony; Florian Wagner; Noa Sher; Itai Yanai
Journal:  Cell Rep       Date:  2012-08-30       Impact factor: 9.423

6.  Floral dip: a simplified method for Agrobacterium-mediated transformation of Arabidopsis thaliana.

Authors:  S J Clough; A F Bent
Journal:  Plant J       Date:  1998-12       Impact factor: 6.417

7.  Transcriptome-wide noise controls lineage choice in mammalian progenitor cells.

Authors:  Hannah H Chang; Martin Hemberg; Mauricio Barahona; Donald E Ingber; Sui Huang
Journal:  Nature       Date:  2008-05-22       Impact factor: 49.962

8.  Identification and characterization of subpopulations in undifferentiated ES cell culture.

Authors:  Yayoi Toyooka; Daisuke Shimosato; Kazuhiro Murakami; Kadue Takahashi; Hitoshi Niwa
Journal:  Development       Date:  2008-03       Impact factor: 6.868

9.  Differential expression analysis for sequence count data.

Authors:  Simon Anders; Wolfgang Huber
Journal:  Genome Biol       Date:  2010-10-27       Impact factor: 13.583

10.  NuRD suppresses pluripotency gene expression to promote transcriptional heterogeneity and lineage commitment.

Authors:  Nicola Reynolds; Paulina Latos; Antony Hynes-Allen; Remco Loos; Donna Leaford; Aoife O'Shaughnessy; Olukunbi Mosaku; Jason Signolet; Philip Brennecke; Tüzer Kalkan; Ita Costello; Peter Humphreys; William Mansfield; Kentaro Nakagawa; John Strouboulis; Axel Behrens; Paul Bertone; Brian Hendrich
Journal:  Cell Stem Cell       Date:  2012-05-04       Impact factor: 24.633

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  384 in total

1.  Electrophysiological, transcriptomic and morphologic profiling of single neurons using Patch-seq.

Authors:  Cathryn R Cadwell; Athanasia Palasantza; Xiaolong Jiang; Philipp Berens; Qiaolin Deng; Marlene Yilmaz; Jacob Reimer; Shan Shen; Matthias Bethge; Kimberley F Tolias; Rickard Sandberg; Andreas S Tolias
Journal:  Nat Biotechnol       Date:  2015-12-21       Impact factor: 54.908

2.  Linking the T cell receptor to the single cell transcriptome in antigen-specific human T cells.

Authors:  Auda A Eltahla; Simone Rizzetto; Mehdi R Pirozyan; Brigid D Betz-Stablein; Vanessa Venturi; Katherine Kedzierska; Andrew R Lloyd; Rowena A Bull; Fabio Luciani
Journal:  Immunol Cell Biol       Date:  2016-02-10       Impact factor: 5.126

3.  Normalization of RNA-seq data using factor analysis of control genes or samples.

Authors:  Davide Risso; John Ngai; Terence P Speed; Sandrine Dudoit
Journal:  Nat Biotechnol       Date:  2014-08-24       Impact factor: 54.908

4.  RNA Sequencing and Analysis.

Authors:  Kimberly R Kukurba; Stephen B Montgomery
Journal:  Cold Spring Harb Protoc       Date:  2015-04-13

5.  T Helper Cell Cytokines Modulate Intestinal Stem Cell Renewal and Differentiation.

Authors:  Moshe Biton; Adam L Haber; Noga Rogel; Grace Burgin; Semir Beyaz; Alexandra Schnell; Orr Ashenberg; Chien-Wen Su; Christopher Smillie; Karthik Shekhar; Zuojia Chen; Chuan Wu; Jose Ordovas-Montanes; David Alvarez; Rebecca H Herbst; Mei Zhang; Itay Tirosh; Danielle Dionne; Lan T Nguyen; Michael E Xifaras; Alex K Shalek; Ulrich H von Andrian; Daniel B Graham; Orit Rozenblatt-Rosen; Hai Ning Shi; Vijay Kuchroo; Omer H Yilmaz; Aviv Regev; Ramnik J Xavier
Journal:  Cell       Date:  2018-11-01       Impact factor: 41.582

6.  Integrated Single-Cell Analysis Maps the Continuous Regulatory Landscape of Human Hematopoietic Differentiation.

Authors:  Jason D Buenrostro; M Ryan Corces; Caleb A Lareau; Beijing Wu; Alicia N Schep; Martin J Aryee; Ravindra Majeti; Howard Y Chang; William J Greenleaf
Journal:  Cell       Date:  2018-04-26       Impact factor: 41.582

Review 7.  Advances in Transcriptomics: Investigating Cardiovascular Disease at Unprecedented Resolution.

Authors:  Robert C Wirka; Milos Pjanic; Thomas Quertermous
Journal:  Circ Res       Date:  2018-04-27       Impact factor: 17.367

8.  Single-cell RNA-Seq analysis identifies a noncoding interleukin 4 (IL-4) RNA that post-transcriptionally up-regulates IL-4 production in T helper cells.

Authors:  Weijie Yin; Yan Song; Xing Chang
Journal:  J Biol Chem       Date:  2018-11-07       Impact factor: 5.157

9.  Gene regulatory network reconstruction using single-cell RNA sequencing of barcoded genotypes in diverse environments.

Authors:  Christopher A Jackson; Dayanne M Castro; Richard Bonneau; David Gresham; Giuseppe-Antonio Saldi
Journal:  Elife       Date:  2020-01-27       Impact factor: 8.140

10.  CANOES: detecting rare copy number variants from whole exome sequencing data.

Authors:  Daniel Backenroth; Jason Homsy; Laura R Murillo; Joe Glessner; Edwin Lin; Martina Brueckner; Richard Lifton; Elizabeth Goldmuntz; Wendy K Chung; Yufeng Shen
Journal:  Nucleic Acids Res       Date:  2014-04-25       Impact factor: 16.971

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