Identification of key factors conquering developmental arrest of somatic cell cloned embryos by combining embryo biopsy and single-cell sequencing

An ultra-low-input native ChIP-seq protocol for genome-wide profiling of rare cell populations

(2015) Julie Brind’Amour et al.   Nature Communications

Programming and Inheritance of Parental DNA Methylomes in Mammals

(2014) Lu Wang et al.   CELL

Embryonic Development following Somatic Cell Nuclear Transfer Impeded by Persisting Histone Methylation

(2014) Shogo Matoba et al.   CELL

Human Somatic Cell Nuclear Transfer Using Adult Cells

(2014) Young Gie Chung et al.   Cell Stem Cell

Human oocytes reprogram adult somatic nuclei of a type 1 diabetic to diploid pluripotent stem cells

(2014) Mitsutoshi Yamada et al.   NATURE

DNA methylation dynamics of the human preimplantation embryo

(2014) Zachary D. Smith et al.   NATURE

MOABS: model based analysis of bisulfite sequencing data

(2014) Deqiang Sun et al.   GENOME BIOLOGY

Interplay between the Cancer Genome and Epigenome

(2013) Hui Shen et al.   CELL

Human Embryonic Stem Cells Derived by Somatic Cell Nuclear Transfer

(2013) Masahito Tachibana et al.   CELL

Single-cell methylome landscapes of mouse embryonic stem cells and early embryos analyzed using reduced representation bisulfite sequencing

(2013) H. Guo et al.   GENOME RESEARCH

Genetic programs in human and mouse early embryos revealed by single-cell RNA sequencing

(2013) Zhigang Xue et al.   NATURE

The transcriptomic architecture of mouse Sertoli cell clone embryos reveals temporal–spatial-specific reprogramming

(2013) Feng Cao et al.   REPRODUCTION

Single-Cell Profiling of Epigenetic Modifiers Identifies PRDM14 as an Inducer of Cell Fate in the Mammalian Embryo

(2013) Adam Burton et al.   Cell Reports

RSeQC: quality control of RNA-seq experiments

(2012) Liguo Wang et al.   BIOINFORMATICS

Revisiting Global Gene Expression Analysis

(2012) Jakob Lovén et al.   CELL

Transient JMJD2B-Mediated Reduction of H3K9me3 Levels Improves Reprogramming of Embryonic Stem Cells into Cloned Embryos

(2012) J. Antony et al.   MOLECULAR AND CELLULAR BIOLOGY

Mouse ooplasm confers context-specific reprogramming capacity

(2012) Michelle M Chan et al.   NATURE GENETICS

Recent advancements in cloning by somatic cell nuclear transfer

(2012) A. Ogura et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Reprogramming mammalian somatic cells

(2012) N. Rodriguez-Osorio et al.   THERIOGENOLOGY

Defects in Trophoblast Cell Lineage Account for the Impaired In Vivo Development of Cloned Embryos Generated by Somatic Nuclear Transfer

(2011) Jiangwei Lin et al.   Cell Stem Cell

RNAi-mediated knockdown of Xist can rescue the impaired postimplantation development of cloned mouse embryos

(2011) S. Matoba et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Tracing the Derivation of Embryonic Stem Cells from the Inner Cell Mass by Single-Cell RNA-Seq Analysis

(2010) Fuchou Tang et al.   Cell Stem Cell

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

RNA-Seq analysis to capture the transcriptome landscape of a single cell

(2010) Fuchou Tang et al.   Nature Protocols

Identification of Inappropriately Reprogrammed Genes by Large-Scale Transcriptome Analysis of Individual Cloned Mouse Blastocysts

(2010) Atsushi Fukuda et al.   PLoS One

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

BSMAP: whole genome bisulfite sequence MAPping program

(2009) Yuanxin Xi et al.   BMC BIOINFORMATICS

mRNA-Seq whole-transcriptome analysis of a single cell

(2009) Fuchou Tang et al.   NATURE METHODS

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

(2009) Da Wei Huang et al.   Nature Protocols

A census of human transcription factors: function, expression and evolution

(2009) Juan M. Vaquerizas et al.   NATURE REVIEWS GENETICS

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY