Bisulfite-free epigenomics and genomics of single cells through methylation-sensitive restriction

[1]  L. F. Cheow,et al.  DNA Analysis by Restriction Enzyme (DARE) enables concurrent genomic and epigenomic characterization of single cells , 2019, Nucleic acids research.

[2]  Leland McInnes,et al.  UMAP: Uniform Manifold Approximation and Projection , 2018, J. Open Source Softw..

[3]  Martin Hirst,et al.  High-Resolution Single-Cell DNA Methylation Measurements Reveal Epigenetically Distinct Hematopoietic Stem Cell Subpopulations , 2018, Stem cell reports.

[4]  K. Metzeler,et al.  Gene mutations and clonal architecture in myelodysplastic syndromes and changes upon progression to acute myeloid leukaemia and under treatment , 2018, British journal of haematology.

[5]  T. Ley,et al.  DNMT3AR882-associated hypomethylation patterns are maintained in primary AML xenografts, but not in the DNMT3AR882C OCI-AML3 leukemia cell line , 2018, Blood Cancer Journal.

[6]  Je-Gun Joung,et al.  SIDR: simultaneous isolation and parallel sequencing of genomic DNA and total RNA from single cells , 2018, Genome research.

[7]  M. Araúzo-Bravo,et al.  DNA methylation regulates discrimination of enhancers from promoters through a H3K4me1-H3K4me3 seesaw mechanism , 2017, BMC Genomics.

[8]  Jeff E. Mold,et al.  Comparison of whole genome amplification techniques for human single cell exome sequencing , 2017, PloS one.

[9]  Michael P. Snyder,et al.  Bisulfite-independent analysis of CpG island methylation enables genome-scale stratification of single cells , 2017, Nucleic acids research.

[10]  Bettina Budeus,et al.  TruePrime is a novel method for whole-genome amplification from single cells based on TthPrimPol , 2016, Nature Communications.

[11]  K. Metzeler,et al.  Molecular Genetic Characterization of Individual Cancer Cells Isolated via Single-Cell Printing , 2016, PloS one.

[12]  Stephen R Quake,et al.  Single-cell multimodal profiling reveals cellular epigenetic heterogeneity , 2016, Nature Methods.

[13]  Pao-Yang Chen,et al.  Profiling genome-wide DNA methylation , 2016, Epigenetics & Chromatin.

[14]  Zhigang Xue,et al.  Simultaneous profiling of transcriptome and DNA methylome from a single cell , 2016, Genome Biology.

[15]  Fidel Ramírez,et al.  deepTools2: a next generation web server for deep-sequencing data analysis , 2016, Nucleic Acids Res..

[16]  Ken Chen,et al.  Monovar: single nucleotide variant detection in single cells , 2016, Nature Methods.

[17]  Sijia Lu,et al.  Single-Cell Whole-Genome Amplification and Sequencing: Methodology and Applications. , 2015, Annual review of genomics and human genetics.

[18]  C. Ponting,et al.  G&T-seq: parallel sequencing of single-cell genomes and transcriptomes , 2015, Nature Methods.

[19]  Sijia Lu,et al.  Single Cell Transcriptome Amplification with MALBAC , 2015, PloS one.

[20]  S. Quake,et al.  Multiplexed locus-specific analysis of DNA methylation in single cells , 2015, Nature Protocols.

[21]  Michael Q. Zhang,et al.  Integrative analysis of 111 reference human epigenomes , 2015, Nature.

[22]  Siddharth S. Dey,et al.  Integrated genome and transcriptome sequencing from the same cell , 2014, Nature Biotechnology.

[23]  Mingming Jia,et al.  COSMIC: exploring the world's knowledge of somatic mutations in human cancer , 2014, Nucleic Acids Res..

[24]  Thomas Lengauer,et al.  Comprehensive Analysis of DNA Methylation Data with RnBeads , 2014, Nature Methods.

[25]  O. Stegle,et al.  Single-Cell Genome-Wide Bisulfite Sequencing for Assessing Epigenetic Heterogeneity , 2014, Nature Methods.

[26]  Francesco Marabita,et al.  A beta-mixture quantile normalization method for correcting probe design bias in Illumina Infinium 450 k DNA methylation data , 2012, Bioinform..

[27]  X. Xie,et al.  Genome-Wide Detection of Single-Nucleotide and Copy-Number Variations of a Single Human Cell , 2012, Science.

[28]  P. Laird,et al.  Bis-SNP: Combined DNA methylation and SNP calling for Bisulfite-seq data , 2012, Genome Biology.

[29]  J. Schouten,et al.  Methylation-Specific MLPA (MS-MLPA): simultaneous detection of CpG methylation and copy number changes of up to 40 sequences , 2005, Nucleic acids research.

[30]  L. Larizza,et al.  Amplification of a novel c-Kit activating mutation Asn(822)-Lys in the Kasumi-1 cell line: a t(8;21)-Kit mutant model for acute myeloid leukemia. , 2002, The hematology journal : the official journal of the European Haematology Association.

[31]  O. Britanova,et al.  Amplification of cDNA ends based on template-switching effect and step-out PCR. , 1999, Nucleic acids research.

[32]  C. Korch,et al.  In-vivo-modified gonococcal plasmid pJD1. A model system for analysis of restriction enzyme sensitivity to DNA modifications. , 1986, European journal of biochemistry.