Single-cell RNA-sequencing of differentiating iPS cells reveals dynamic genetic effects on gene expression

John C. Marioni | Ewan Birney | Daniel D. Seaton | Kedar Nath Natarajan | Andreas Leha | Richard Durbin | Ludovic Vallier | Angus I. Lamond | Fiona M. Watt | Laura Clarke | Petr Danecek | Pedro Madrigal | Oliver Stegle | Florian Buettner | Reena Halai | Dalila Bensaddek | Helena Kilpinen | Davis J. McCarthy | Yasin Memari | Daniel J. Gaffney | Shane A. McCarthy | Willem H. Ouwehand | Ruta Meleckyte | Francesco Paolo Casale | Peter W. Harrison | R. Durbin | E. Birney | M. Bonder | W. Ouwehand | J. Marioni | F. Buettner | A. Leha | P. Danecek | O. Stegle | L. Clarke | F. Watt | K. Natarajan | F. P. Casale | A. Lamond | P. W. Harrison | H. Kilpinen | P. Beales | D. Gaffney | Pedro Madrigal | Ângela Gonçalves | A. Knights | L. Vallier | D. Seaton | Ian Streeter | Minal J. Patel | Y. Memari | D. Bensaddek | Ruta Meleckyte | N. Moens | Chukwuma A. Agu | A. Alderton | S. Harper | Reena Halai | C. Kirton | A. Kolb-Kokocinski | A. Cuomo | Davis J McCarthy | I. Martinez | J. Garcia-Bernardo | Shradha Amatya | Abigail Isaacson | Mariya K Chhatriwala | Anja Kolb-Kokocinski | Ian Streeter | Marc Jan Bonder | Minal Patel | Jose Garcia-Bernardo | Andrew Knights | Angela Goncalves | Chukwuma A. Alex Petr Rachel Richard Daniel J. Angela Reena Agu Alderton Danecek Denton Durbin Gaffn | Rachel Denton | Davide Denovi | Sarah Harper | Abigail Isaacson | Anna S. E. Cuomo | Iker Martinez | Shradha Amatya | Alex Alderton | Rachel Denton | Christopher M. Kirton | Davide Denovi | Natalie Moens | Philip Beales | Mariya Chhatriwala | Mariya Chhatriwala

[1]  Davis J. McCarthy,et al.  Publisher Correction: Single-cell RNA-sequencing of differentiating iPS cells reveals dynamic genetic effects on gene expression , 2020, Nature Communications.

[2]  Alissa M. Resch,et al.  Correction to: DNA copy number evolution in Drosophila cell lines , 2019, Genome Biology.

[3]  Helen E. Parkinson,et al.  The NHGRI-EBI GWAS Catalog of published genome-wide association studies, targeted arrays and summary statistics 2019 , 2018, Nucleic Acids Res..

[4]  M. Bonder,et al.  Population-scale proteome variation in human induced pluripotent stem cells , 2018, bioRxiv.

[5]  Sarah A. Teichmann,et al.  Cardelino: Integrating whole exomes and single-cell transcriptomes to reveal phenotypic impact of somatic variants , 2018, bioRxiv.

[6]  Hideki Uosaki,et al.  Tbx6 Induces Nascent Mesoderm from Pluripotent Stem Cells and Temporally Controls Cardiac versus Somite Lineage Diversification. , 2018, Cell stem cell.

[7]  Patrick Flick,et al.  GOATOOLS: A Python library for Gene Ontology analyses , 2018, Scientific Reports.

[8]  K. D. Sørensen,et al.  Association analyses of more than 140,000 men identify 63 new prostate cancer susceptibility loci , 2018, Nature Genetics.

[9]  Davis J. McCarthy,et al.  Combined single-cell profiling of expression and DNA methylation reveals splicing regulation and heterogeneity , 2018, Genome Biology.

[10]  L. Vallier,et al.  Human Pluripotent Stem Cell-Derived Endoderm for Modeling Development and Clinical Applications. , 2018, Cell stem cell.

[11]  Kaur Alasoo,et al.  Shared genetic effects on chromatin and gene expression indicate a role for enhancer priming in immune response , 2018, Nature Genetics.

[12]  Chun Jimmie Ye,et al.  Multiplexed droplet single-cell RNA-sequencing using natural genetic variation , 2017, Nature Biotechnology.

[13]  Astrid Gall,et al.  Ensembl 2018 , 2017, Nucleic Acids Res..

[14]  Fabian J Theis,et al.  SCANPY: large-scale single-cell gene expression data analysis , 2018, Genome Biology.

[15]  Davis J. McCarthy,et al.  f-scLVM: scalable and versatile factor analysis for single-cell RNA-seq , 2017, Genome Biology.

[16]  Manuel A. R. Ferreira,et al.  Shared genetic origin of asthma, hay fever and eczema elucidates allergic disease biology , 2017, Nature Genetics.

[17]  Davis J. McCarthy,et al.  Common genetic variation drives molecular heterogeneity in human iPSCs , 2017, Nature.

[18]  John D. Blischak,et al.  A comparative study of endoderm differentiation in humans and chimpanzees , 2017, Genome Biology.

[19]  Gaurav Pandey,et al.  Analysis of Transcriptional Variability in a Large Human iPSC Library Reveals Genetic and Non-genetic Determinants of Heterogeneity. , 2017, Cell stem cell.

[20]  Christopher D. Brown,et al.  Large, Diverse Population Cohorts of hiPSCs and Derived Hepatocyte-like Cells Reveal Functional Genetic Variation at Blood Lipid-Associated Loci. , 2017, Cell stem cell.

[21]  Rob Patro,et al.  Salmon provides fast and bias-aware quantification of transcript expression , 2017, Nature Methods.

[22]  Geet Duggal,et al.  Salmon: fast and bias-aware quantification of transcript expression using dual-phase inference , 2017, Nature Methods.

[23]  Daniel J. Gaffney,et al.  Molecular and functional variation in iPSC-derived sensory neurons , 2017, bioRxiv.

[24]  M. Pellegrini,et al.  Human Embryonic Stem Cells Do Not Change Their X Inactivation Status during Differentiation. , 2017, Cell reports.

[25]  David A. Knowles,et al.  Allele-specific expression reveals interactions between genetic variation and environment , 2015, Nature Methods.

[26]  GTEx consortium Genetic effects on gene expression across human tissues , 2017 .

[27]  Su-Chun Zhang,et al.  Neural Subtype Specification from Human Pluripotent Stem Cells. , 2016, Cell stem cell.

[28]  Xiang Zhou,et al.  High-throughput allele-specific expression across 250 environmental conditions , 2016, Genome research.

[29]  Davis J. McCarthy,et al.  A step-by-step workflow for low-level analysis of single-cell RNA-seq data with Bioconductor , 2016, F1000Research.

[30]  Peter Kraft,et al.  Genome-wide association study identifies 14 novel risk alleles associated with basal cell carcinoma , 2022 .

[31]  R. Stewart,et al.  Single-cell RNA-seq reveals novel regulators of human embryonic stem cell differentiation to definitive endoderm , 2016, Genome Biology.

[32]  Aaron T. L. Lun,et al.  Scater: pre-processing, quality control, normalization and visualization of single-cell RNA-seq data in R , 2017, Bioinform..

[33]  Fabian J Theis,et al.  Diffusion pseudotime robustly reconstructs lineage branching , 2016, Nature Methods.

[34]  Pedro Madrigal,et al.  Initiation of stem cell differentiation involves cell cycle-dependent regulation of developmental genes by Cyclin D , 2016, Genes & development.

[35]  Joseph L. Herman,et al.  Characterizing transcriptional heterogeneity through pathway and gene set overdispersion analysis , 2015, Nature Methods.

[36]  Tom R. Gaunt,et al.  The UK10K project identifies rare variants in health and disease , 2016 .

[37]  Emmanouil T. Dermitzakis,et al.  Fast and efficient QTL mapper for thousands of molecular phenotypes , 2015, bioRxiv.

[38]  Christoph Lippert,et al.  Efficient set tests for the genetic analysis of correlated traits , 2015, Nature Methods.

[39]  Fabian J Theis,et al.  Computational analysis of cell-to-cell heterogeneity in single-cell RNA-sequencing data reveals hidden subpopulations of cells , 2015, Nature Biotechnology.

[40]  M. Bonder,et al.  Genotype harmonizer: automatic strand alignment and format conversion for genotype data integration , 2014, BMC Research Notes.

[41]  D. Bates,et al.  Fitting Linear Mixed-Effects Models Using lme4 , 2014, 1406.5823.

[42]  Ben Lehner,et al.  The effects of genetic variation on gene expression dynamics during development , 2013, Nature.

[43]  David Haussler,et al.  The UCSC Genome Browser database: 2014 update , 2013, Nucleic Acids Res..

[44]  Åsa K. Björklund,et al.  Full-length RNA-seq from single cells using Smart-seq2 , 2014, Nature Protocols.

[45]  Ral Garreta,et al.  Learning scikit-learn: Machine Learning in Python , 2013 .

[46]  Jie Zhang,et al.  Practical Guidelines for the Comprehensive Analysis of ChIP-seq Data , 2013, PLoS Comput. Biol..

[47]  S. Pauklin,et al.  The Cell-Cycle State of Stem Cells Determines Cell Fate Propensity , 2013, Cell.

[48]  J. I. Izpisúa Belmonte,et al.  Mitochondrial regulation in pluripotent stem cells. , 2013, Cell metabolism.

[49]  J. I. Izpisúa Belmonte,et al.  Macro Histone Variants Are Critical for the Differentiation of Human Pluripotent Cells* , 2013, The Journal of Biological Chemistry.

[50]  Ludovic Vallier,et al.  Production of hepatocyte-like cells from human pluripotent stem cells , 2013, Nature Protocols.

[51]  Liangdan Sun,et al.  Association analyses identify three susceptibility Loci for vitiligo in the Chinese Han population. , 2013, The Journal of investigative dermatology.

[52]  Thomas R. Gingeras,et al.  STAR: ultrafast universal RNA-seq aligner , 2013, Bioinform..

[53]  ENCODEConsortium,et al.  An Integrated Encyclopedia of DNA Elements in the Human Genome , 2012, Nature.

[54]  M. Sur,et al.  Molecular signatures of human induced pluripotent stem cells highlight sex differences and cancer genes. , 2012, Cell stem cell.

[55]  O. Delaneau,et al.  A linear complexity phasing method for thousands of genomes , 2011, Nature Methods.

[56]  Martin Renqiang Min,et al.  An integrated encyclopedia of DNA elements in the human genome , 2012 .

[57]  Robert Grossman,et al.  PeakRanger: A cloud-enabled peak caller for ChIP-seq data , 2011, BMC Bioinformatics.

[58]  Marcel Martin Cutadapt removes adapter sequences from high-throughput sequencing reads , 2011 .

[59]  Michael J. Ziller,et al.  Reference Maps of Human ES and iPS Cell Variation Enable High-Throughput Characterization of Pluripotent Cell Lines , 2011, Cell.

[60]  R. Pedersen,et al.  Generation of functional hepatocytes from human embryonic stem cells under chemically defined conditions that recapitulate liver development , 2010, Hepatology.

[61]  Aaron R. Quinlan,et al.  Bioinformatics Applications Note Genome Analysis Bedtools: a Flexible Suite of Utilities for Comparing Genomic Features , 2022 .

[62]  Kari Stefansson,et al.  Genome-wide association and replication studies identify four variants associated with prostate cancer susceptibility , 2009, Nature Genetics.

[63]  Roger A. Pedersen,et al.  Early Cell Fate Decisions of Human Embryonic Stem Cells and Mouse Epiblast Stem Cells Are Controlled by the Same Signalling Pathways , 2009, PloS one.

[64]  P. Donnelly,et al.  A Flexible and Accurate Genotype Imputation Method for the Next Generation of Genome-Wide Association Studies , 2009, PLoS genetics.

[65]  L. Cantley,et al.  Understanding the Warburg Effect: The Metabolic Requirements of Cell Proliferation , 2009, Science.

[66]  Richard Durbin,et al.  Sequence analysis Fast and accurate short read alignment with Burrows – Wheeler transform , 2009 .

[67]  Atsushi Miyawaki,et al.  Visualizing Spatiotemporal Dynamics of Multicellular Cell-Cycle Progression , 2008, Cell.

[68]  Manuel A. R. Ferreira,et al.  PLINK: a tool set for whole-genome association and population-based linkage analyses. , 2007, American journal of human genetics.

[69]  M. Trotter,et al.  Derivation of pluripotent epiblast stem cells from mammalian embryos , 2007, Nature.

[70]  Delbert Dueck,et al.  Clustering by Passing Messages Between Data Points , 2007, Science.

[71]  T. Hastie,et al.  Principal Curves , 2007 .

[72]  A. Kulkarni,et al.  Dph3, a Small Protein Required for Diphthamide Biosynthesis, Is Essential in Mouse Development , 2006, Molecular and Cellular Biology.

[73]  E. Kroon,et al.  Efficient differentiation of human embryonic stem cells to definitive endoderm , 2005, Nature Biotechnology.

[74]  John D. Storey,et al.  Statistical significance for genomewide studies , 2003, Proceedings of the National Academy of Sciences of the United States of America.