FlsnRNA-seq: protoplasting-free full-length single-nucleus RNA profiling in plants

[1]  J. Schiefelbein,et al.  Single-nucleus RNA and ATAC sequencing reveals the impact of chromatin accessibility on gene expression in Arabidopsis roots at the single-cell level. , 2021, Molecular plant.

[2]  J. Lohmann,et al.  Transcriptional Landscape of Rice Roots at the Single Cell Resolution. , 2020, Molecular plant.

[3]  M. Libault,et al.  Isolation of Plant Root Nuclei for Single Cell RNA Sequencing. , 2020, Current protocols in plant biology.

[4]  S. Sauer,et al.  Single-nuclei RNA-sequencing of plants , 2020, bioRxiv.

[5]  David Kulp,et al.  Innovations present in the primate interneuron repertoire , 2020, Nature.

[6]  Caihuan Tian,et al.  Single-nucleus RNA-seq resolves spatiotemporal developmental trajectories in the tomato shoot apex , 2020, bioRxiv.

[7]  Y. Saeys,et al.  Vascular transcription factors guide plant epidermal responses to limiting phosphate conditions , 2020, Science.

[8]  Josh Strable,et al.  Plant stem cell organization and differentiation at single-cell resolution , 2020, bioRxiv.

[9]  Ben P. Williams,et al.  Single nucleus analysis of Arabidopsis seeds reveals new cell types and imprinting dynamics , 2020, bioRxiv.

[10]  R. Davenport,et al.  Jasmonate induced alternative splicing responses in Arabidopsis , 2020, Plant direct.

[11]  Trevor M. Nolan,et al.  A single cell Arabidopsis root atlas reveals developmental trajectories in wild type and cell identity mutants , 2020, bioRxiv.

[12]  Hong Zhang,et al.  Post-transcriptional splicing of nascent RNA contributes to widespread intron retention in plants , 2020, Nature Plants.

[13]  A. Fernie,et al.  Single-Cell Genomics and Epigenomics: Technologies and Applications in Plants. , 2020, Trends in plant science.

[14]  Aviv Regev,et al.  Systematic comparison of single-cell and single-nucleus RNA-sequencing methods , 2020, Nature Biotechnology.

[15]  Roger Volden,et al.  Highly Multiplexed Single-Cell Full-Length cDNA Sequencing of human immune cells with 10X Genomics and R2C2 , 2020, bioRxiv.

[16]  Pascal Barbry,et al.  High throughput error corrected Nanopore single cell transcriptome sequencing , 2019, Nature Communications.

[17]  Matthew T. Parker,et al.  Nanopore direct RNA sequencing maps the complexity of Arabidopsis mRNA processing and m6A modification , 2020, eLife.

[18]  S. Ott,et al.  Single-Cell Transcriptomics: A High-Resolution Avenue for Plant Functional Genomics. , 2019, Trends in plant science.

[19]  Fabian J Theis,et al.  Generalizing RNA velocity to transient cell states through dynamical modeling , 2019, Nature Biotechnology.

[20]  S. Fields,et al.  Dynamics of Gene Expression in Single Root Cells of Arabidopsis thaliana. , 2019, The Plant cell.

[21]  Bonnie Berger,et al.  Efficient integration of heterogeneous single-cell transcriptomes using Scanorama , 2019, Nature Biotechnology.

[22]  Jia-Wei Wang,et al.  A Single-Cell RNA Sequencing Profiles the Developmental Landscape of Arabidopsis Root. , 2019, Molecular plant.

[23]  Kornel Labun,et al.  tailfindr: alignment-free poly(A) length measurement for Oxford Nanopore RNA and DNA sequencing , 2019, bioRxiv.

[24]  K. Nieselt,et al.  Spatiotemporal Developmental Trajectories in the Arabidopsis Root Revealed Using High-Throughput Single-Cell RNA Sequencing. , 2019, Developmental cell.

[25]  V. K. Yadav,et al.  Epigenetic signatures associated with imprinted paternally expressed genes in the Arabidopsis endosperm , 2019, Genome Biology.

[26]  Jiming Jiang.  Faculty Opinions recommendation of Single-Cell RNA Sequencing Resolves Molecular Relationships Among Individual Plant Cells. , 2019, Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature.

[27]  H. Kang,et al.  Single-Cell RNA Sequencing Resolves Molecular Relationships Among Individual Plant Cells1[OPEN] , 2019, Plant Physiology.

[28]  V. Walbot,et al.  Defining the developmental program leading to meiosis in maize , 2018, Science.

[29]  C. Köhler,et al.  Endosperm-specific transcriptome analysis by applying the INTACT system , 2019, Plant Reproduction.

[30]  Ahmed Mahfouz,et al.  Single-cell isoform RNA sequencing characterizes isoforms in thousands of cerebellar cells , 2018, Nature Biotechnology.

[31]  D. Dickel,et al.  High-throughput single-cell transcriptome profiling of plant cell types , 2018, bioRxiv.

[32]  Erik Sundström,et al.  RNA velocity of single cells , 2018, Nature.

[33]  S. Teichmann,et al.  From Tissues to Cell Types and Back: Single-Cell Gene Expression Analysis of Tissue Architecture , 2018, Annual Review of Biomedical Data Science.

[34]  S. Teichmann,et al.  Exponential scaling of single-cell RNA-seq in the past decade , 2017, Nature Protocols.

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

[36]  Lars E. Borm,et al.  The promise of spatial transcriptomics for neuroscience in the era of molecular cell typing , 2017, Science.

[37]  O. Stegle,et al.  Single-cell epigenomics: Recording the past and predicting the future , 2017, Science.

[38]  Michael J. T. Stubbington,et al.  Single-cell transcriptomics to explore the immune system in health and disease , 2017, Science.

[39]  Xiu-Jie Wang,et al.  Single-cell transcriptome analysis reveals widespread monoallelic gene expression in individual rice mesophyll cells. , 2017, Science bulletin.

[40]  Aviv Regev,et al.  Massively-parallel single nucleus RNA-seq with DroNc-seq , 2017, Nature Methods.

[41]  Erin E. Sparks,et al.  Uncovering Gene Regulatory Networks Controlling Plant Cell Differentiation. , 2017, Trends in genetics : TIG.

[42]  Zhou Du,et al.  agriGO v2.0: a GO analysis toolkit for the agricultural community, 2017 update , 2017, Nucleic Acids Res..

[43]  Michael D. Nodine,et al.  Widespread Contamination of Arabidopsis Embryo and Endosperm Transcriptome Data Sets[OPEN] , 2017, Plant Cell.

[44]  Niranjan Nagarajan,et al.  Fast and accurate de novo genome assembly from long uncorrected reads. , 2017, Genome research.

[45]  L. Hennig,et al.  Applying the INTACT method to purify endosperm nuclei and to generate parental-specific epigenome profiles , 2017, Nature Protocols.

[46]  P. Benfey,et al.  High-Resolution Expression Map of the Arabidopsis Root Reveals Alternative Splicing and lincRNA Regulation. , 2016, Developmental cell.

[47]  Cynthia C. Hession,et al.  Div-Seq: Single-nucleus RNA-Seq reveals dynamics of rare adult newborn neurons , 2016, Science.

[48]  Charles H. Yoon,et al.  Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq , 2016, Science.

[49]  Sara B. Linker,et al.  Using single nuclei for RNA-seq to capture the transcriptome of postmortem neurons , 2016, Nature Protocols.

[50]  Michael B. Stadler,et al.  Analysis of intronic and exonic reads in RNA-seq data characterizes transcriptional and post-transcriptional regulation , 2015, Nature Biotechnology.

[51]  Evan Z. Macosko,et al.  Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets , 2015, Cell.

[52]  L. Colombo,et al.  Networks controlling seed size in Arabidopsis , 2015, Plant Reproduction.

[53]  A. Bleckmann,et al.  The beginning of a seed: regulatory mechanisms of double fertilization , 2014, Front. Plant Sci..

[54]  G. Bell,et al.  Natural epigenetic polymorphisms lead to intraspecific variation in Arabidopsis gene imprinting , 2014, eLife.

[55]  C. Köhler,et al.  Embryo and endosperm, partners in seed development. , 2014, Current opinion in plant biology.

[56]  S. Brady,et al.  Comprehensive developmental profiles of gene activity in regions and subregions of the Arabidopsis seed , 2013, Proceedings of the National Academy of Sciences.

[57]  D. Zilberman,et al.  Active DNA Demethylation in Plant Companion Cells Reinforces Transposon Methylation in Gametes , 2012, Science.

[58]  S. Henikoff,et al.  Genomic Analysis of Parent-of-Origin Allelic Expression in Arabidopsis thaliana Seeds , 2011, PloS one.

[59]  Guoli Ji,et al.  Genome-wide landscape of polyadenylation in Arabidopsis provides evidence for extensive alternative polyadenylation , 2011, Proceedings of the National Academy of Sciences.

[60]  Robert L. Fischer,et al.  Regulation of imprinted gene expression in Arabidopsis endosperm , 2011, Proceedings of the National Academy of Sciences.

[61]  Eytan Domany,et al.  Coupled pre-mRNA and mRNA dynamics unveil operational strategies underlying transcriptional responses to stimuli , 2013 .

[62]  R. Macknight,et al.  Transcriptome Analysis of Proliferating Arabidopsis Endosperm Reveals Biological Implications for the Control of Syncytial Division, Cytokinin Signaling, and Gene Expression Regulation[C][W][OA] , 2008, Plant Physiology.

[63]  Jean-Loup Guillaume,et al.  Fast unfolding of communities in large networks , 2008, 0803.0476.

[64]  Daniel L. Mace,et al.  A High-Resolution Root Spatiotemporal Map Reveals Dominant Expression Patterns , 2007, Science.

[65]  Jon Penterman,et al.  DEMETER DNA Glycosylase Establishes MEDEA Polycomb Gene Self-Imprinting by Allele-Specific Demethylation , 2006, Cell.

[66]  R. Fischer,et al.  Imprinting and Seed Development , 2004, The Plant Cell Online.

[67]  D. Shasha,et al.  A Gene Expression Map of the Arabidopsis Root , 2003, Science.

[68]  R. C. Brown,et al.  Events during the first four rounds of mitosis establish three developmental domains in the syncytial endosperm of Arabidopsis thaliana , 2003, Protoplasma.

[69]  Hilde van der Togt,et al.  Publisher's Note , 2003, J. Netw. Comput. Appl..

[70]  F. Berger,et al.  Cellularisation in the endosperm of Arabidopsis thaliana is coupled to mitosis and shares multiple components with cytokinesis , 2002, Development.

[71]  Christopher J. Lee,et al.  Multiple sequence alignment using partial order graphs , 2002, Bioinform..

[72]  O. Olsen,et al.  Development of endosperm in Arabidopsis thaliana , 1999, Sexual Plant Reproduction.