Published in Nat Protoc on March 26, 2009
A Myc network accounts for similarities between embryonic stem and cancer cell transcription programs. Cell (2010) 6.00
NANOG-dependent function of TET1 and TET2 in establishment of pluripotency. Nature (2013) 2.63
AF10 regulates progressive H3K79 methylation and HOX gene expression in diverse AML subtypes. Cancer Cell (2014) 2.33
A genome-wide map of CTCF multivalency redefines the CTCF code. Cell Rep (2013) 1.92
Regulation of pluripotency and self- renewal of ESCs through epigenetic-threshold modulation and mRNA pruning. Cell (2012) 1.76
Oct4 links multiple epigenetic pathways to the pluripotency network. Cell Res (2011) 1.69
Combinatorial assembly of developmental stage-specific enhancers controls gene expression programs during human erythropoiesis. Dev Cell (2012) 1.63
Integrated genetic approaches identify the molecular mechanisms of Sox4 in early B-cell development: intricate roles for RAG1/2 and CK1ε. Blood (2014) 1.56
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Transcription factor trapping by RNA in gene regulatory elements. Science (2015) 1.24
Mechanism and relevance of EWS/FLI-mediated transcriptional repression in Ewing sarcoma. Oncogene (2012) 1.20
Embryonic stem cell-based mapping of developmental transcriptional programs. Nat Methods (2011) 1.20
Defining the budding yeast chromatin-associated interactome. Mol Syst Biol (2010) 1.19
Yin Yang 1 extends the Myc-related transcription factors network in embryonic stem cells. Nucleic Acids Res (2011) 1.16
Pre-replication complex proteins assemble at regions of low nucleosome occupancy within the Chinese hamster dihydrofolate reductase initiation zone. Nucleic Acids Res (2010) 1.13
Distinct and combinatorial functions of Jmjd2b/Kdm4b and Jmjd2c/Kdm4c in mouse embryonic stem cell identity. Mol Cell (2013) 1.06
Novel mechanism of positive versus negative regulation by thyroid hormone receptor β1 (TRβ1) identified by genome-wide profiling of binding sites in mouse liver. J Biol Chem (2013) 0.98
Zfp281 functions as a transcriptional repressor for pluripotency of mouse embryonic stem cells. Stem Cells (2011) 0.97
Notch gain of function inhibits chondrocyte differentiation via Rbpj-dependent suppression of Sox9. J Bone Miner Res (2013) 0.97
Myc and SAGA rewire an alternative splicing network during early somatic cell reprogramming. Genes Dev (2015) 0.95
Tbx20 acts upstream of Wnt signaling to regulate endocardial cushion formation and valve remodeling during mouse cardiogenesis. Development (2013) 0.95
Developmental control of polycomb subunit composition by GATA factors mediates a switch to non-canonical functions. Mol Cell (2015) 0.92
Polycomb- and REST-associated histone deacetylases are independent pathways toward a mature neuronal phenotype. Elife (2014) 0.87
Chem-seq permits identification of genomic targets of drugs against androgen receptor regulation selected by functional phenotypic screens. Proc Natl Acad Sci U S A (2014) 0.87
Splicing factor SRSF3 represses the translation of programmed cell death 4 mRNA by associating with the 5'-UTR region. Cell Death Differ (2013) 0.87
The Sox4/Tcf7l1 axis promotes progression of BCR-ABL-positive acute lymphoblastic leukemia. Haematologica (2014) 0.85
Functional Proteomic Analysis of Repressive Histone Methyltransferase Complexes Reveals ZNF518B as a G9A Regulator. Mol Cell Proteomics (2015) 0.85
Genome-wide binding patterns of thyroid hormone receptor beta. PLoS One (2014) 0.84
DamIP: a novel method to identify DNA binding sites in vivo. Nucl Recept Signal (2010) 0.83
A generic tool for transcription factor target gene discovery in Arabidopsis cell suspension cultures based on tandem chromatin affinity purification. Plant Physiol (2014) 0.82
GATA1s induces hyperproliferation of eosinophil precursors in Down syndrome transient leukemia. Leukemia (2013) 0.81
Arid3a is essential to execution of the first cell fate decision via direct embryonic and extraembryonic transcriptional regulation. Genes Dev (2014) 0.81
DHX9 suppresses RNA processing defects originating from the Alu invasion of the human genome. Nature (2017) 0.80
Thyroid hormone receptor sumoylation is required for preadipocyte differentiation and proliferation. J Biol Chem (2015) 0.80
Steroidogenic factor-1 (SF-1)-driven differentiation of murine embryonic stem (ES) cells into a gonadal lineage. Endocrinology (2011) 0.80
Tbx3 Controls Dppa3 Levels and Exit from Pluripotency toward Mesoderm. Stem Cell Reports (2015) 0.79
Chromatin immunoprecipitation in adult zebrafish red cells. Methods Cell Biol (2011) 0.79
PROP1 triggers epithelial-mesenchymal transition-like process in pituitary stem cells. Elife (2016) 0.79
Methionine adenosyltransferase II-dependent histone H3K9 methylation at the COX-2 gene locus. J Biol Chem (2013) 0.78
In silico tandem affinity purification refines an Oct4 interaction list. Stem Cell Res Ther (2011) 0.77
LIN9, a subunit of the DREAM complex, regulates mitotic gene expression and proliferation of embryonic stem cells. PLoS One (2013) 0.77
Reprogramming of avian neural crest axial identity and cell fate. Science (2016) 0.76
The Pluripotency Factor NANOG Binds to GLI Proteins and Represses Hedgehog-mediated Transcription. J Biol Chem (2016) 0.76
Identification of Transcribed Enhancers by Genome-Wide Chromatin Immunoprecipitation Sequencing. Methods Mol Biol (2017) 0.75
Distinct global binding patterns of the Wilms tumor gene 1 (WT1) -KTS and +KTS isoforms in leukemic cells. Haematologica (2016) 0.75
The Krüppel-like factor 9 cistrome in mouse hippocampal neurons reveals predominant transcriptional repression via proximal promoter binding. BMC Genomics (2017) 0.75
The death-inducer obliterator 1 (Dido1) gene regulates embryonic stem cell self-renewal. J Biol Chem (2013) 0.75
SOX15 governs transcription in human stratified epithelia and a subset of esophageal adenocarcinomas. Cell Mol Gastroenterol Hepatol (2015) 0.75
Transcriptional Regulation of Human NANOG by Alternate Promoters in Embryonic Stem Cells. J Stem Cell Res Ther (2012) 0.75
SMYD5 regulates H4K20me3-marked heterochromatin to safeguard ES cell self-renewal and prevent spurious differentiation. Epigenetics Chromatin (2017) 0.75
GATA6 is essential for endoderm formation from human pluripotent stem cells. Biol Open (2017) 0.75
Chromatin immunoprecipitation and an open chromatin assay in zebrafish erythrocytes. Methods Cell Biol (2016) 0.75
Sp110 enhances macrophage resistance to Mycobacterium tuberculosis via inducing endoplasmic reticulum stress and inhibiting anti-apoptotic factors. Oncotarget (2017) 0.75
Fbxl19 recruitment to CpG islands is required for Rnf20-mediated H2B mono-ubiquitination. Nucleic Acids Res (2017) 0.75
Analyzing real-time PCR data by the comparative C(T) method. Nat Protoc (2008) 62.52
Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing. Nat Methods (2007) 45.04
Polycomb complexes repress developmental regulators in murine embryonic stem cells. Nature (2006) 25.90
In-gel digestion for mass spectrometric characterization of proteins and proteomes. Nat Protoc (2006) 16.56
An extended transcriptional network for pluripotency of embryonic stem cells. Cell (2008) 14.64
Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data. Nat Methods (2008) 11.61
A protein interaction network for pluripotency of embryonic stem cells. Nature (2006) 9.63
Chromatin immunoprecipitation and microarray-based analysis of protein location. Nat Protoc (2006) 7.29
Use of peptide libraries to map the substrate specificity of a peptide-modifying enzyme: a 13 residue consensus peptide specifies biotinylation in Escherichia coli. Biotechnology (N Y) (1993) 4.70
Efficient biotinylation and single-step purification of tagged transcription factors in mammalian cells and transgenic mice. Proc Natl Acad Sci U S A (2003) 4.28
Chop it, ChIP it, check it: the current status of chromatin immunoprecipitation. Front Biosci (2008) 2.15
All you wanted to know about SELEX. Mol Biol Rep (1994) 1.88
Mouse embryo fibroblast (MEF) feeder cell preparation. Curr Protoc Mol Biol (2001) 1.35
Deciphering protein complexes and protein interaction networks by tandem affinity purification and mass spectrometry: analytical perspective. Mol Cell Proteomics (2002) 1.13
Southwestern blotting in investigating transcriptional regulation. Nat Protoc (2008) 1.09
Electrophoretic mobility shift assays for the analysis of DNA-protein interactions. Methods Mol Biol (2001) 1.01
Electrophoretic mobility shift assays. Methods Mol Biol (2000) 0.99
Chromatin immunoprecipitation assay for mammalian tissues. Methods Mol Biol (2006) 0.90
An extended transcriptional network for pluripotency of embryonic stem cells. Cell (2008) 14.64
A protein interaction network for pluripotency of embryonic stem cells. Nature (2006) 9.63
Endogenous oncogenic K-ras(G12D) stimulates proliferation and widespread neoplastic and developmental defects. Cancer Cell (2004) 8.16
Prostaglandin E2 regulates vertebrate haematopoietic stem cell homeostasis. Nature (2007) 7.55
Tet1 and Tet2 regulate 5-hydroxymethylcytosine production and cell lineage specification in mouse embryonic stem cells. Cell Stem Cell (2011) 7.41
EZH1 mediates methylation on histone H3 lysine 27 and complements EZH2 in maintaining stem cell identity and executing pluripotency. Mol Cell (2008) 6.86
Human fetal hemoglobin expression is regulated by the developmental stage-specific repressor BCL11A. Science (2008) 6.66
A Myc network accounts for similarities between embryonic stem and cancer cell transcription programs. Cell (2010) 6.00
Toward improving Caenorhabditis elegans phenome mapping with an ORFeome-based RNAi library. Genome Res (2004) 5.81
A critical role for eosinophils in allergic airways remodeling. Science (2004) 5.53
Genome-wide association study shows BCL11A associated with persistent fetal hemoglobin and amelioration of the phenotype of beta-thalassemia. Proc Natl Acad Sci U S A (2008) 5.27
Targeted deletion of a high-affinity GATA-binding site in the GATA-1 promoter leads to selective loss of the eosinophil lineage in vivo. J Exp Med (2002) 5.07
Developmental origin of a bipotential myocardial and smooth muscle cell precursor in the mammalian heart. Cell (2006) 5.03
Transcriptional regulation of erythropoiesis: an affair involving multiple partners. Oncogene (2002) 4.80
Gfi-1 restricts proliferation and preserves functional integrity of haematopoietic stem cells. Nature (2004) 4.68
The SWI/SNF complex--chromatin and cancer. Nat Rev Cancer (2004) 4.59
DNA polymorphisms at the BCL11A, HBS1L-MYB, and beta-globin loci associate with fetal hemoglobin levels and pain crises in sickle cell disease. Proc Natl Acad Sci U S A (2008) 4.46
A genome-wide RNAi screen identifies a new transcriptional module required for self-renewal. Genes Dev (2009) 4.23
Wdr5 mediates self-renewal and reprogramming via the embryonic stem cell core transcriptional network. Cell (2011) 4.04
The placenta is a niche for hematopoietic stem cells. Dev Cell (2005) 3.83
Rb regulates interactions between hematopoietic stem cells and their bone marrow microenvironment. Cell (2007) 3.82
Essential role for the peroxiredoxin Prdx1 in erythrocyte antioxidant defence and tumour suppression. Nature (2003) 3.77
Jumonji modulates polycomb activity and self-renewal versus differentiation of stem cells. Cell (2009) 3.75
Expression of CD41 marks the initiation of definitive hematopoiesis in the mouse embryo. Blood (2002) 3.59
Developmental and species-divergent globin switching are driven by BCL11A. Nature (2009) 3.49
Haematopoietic stem cells retain long-term repopulating activity and multipotency in the absence of stem-cell leukaemia SCL/tal-1 gene. Nature (2003) 3.25
Intrinsic requirement for zinc finger transcription factor Gfi-1 in neutrophil differentiation. Immunity (2003) 3.17
The emergence of hematopoietic stem cells is initiated in the placental vasculature in the absence of circulation. Cell Stem Cell (2008) 3.09
DNA methyltransferase 1 is essential for and uniquely regulates hematopoietic stem and progenitor cells. Cell Stem Cell (2009) 3.08
Insights into GATA-1-mediated gene activation versus repression via genome-wide chromatin occupancy analysis. Mol Cell (2009) 3.05
Polycomb group proteins Ezh2 and Rnf2 direct genomic contraction and imprinted repression in early mouse embryos. Dev Cell (2008) 2.96
GATA-2 plays two functionally distinct roles during the ontogeny of hematopoietic stem cells. J Exp Med (2004) 2.94
Transcriptional silencing of {gamma}-globin by BCL11A involves long-range interactions and cooperation with SOX6. Genes Dev (2010) 2.93
The efficacy and safety of pain management before and after implementation of hospital-wide pain management standards: is patient safety compromised by treatment based solely on numerical pain ratings? Anesth Analg (2005) 2.83
Epigenetic antagonism between polycomb and SWI/SNF complexes during oncogenic transformation. Cancer Cell (2010) 2.80
Conditional mouse osteosarcoma, dependent on p53 loss and potentiated by loss of Rb, mimics the human disease. Genes Dev (2008) 2.74
The journey of developing hematopoietic stem cells. Development (2006) 2.71
An erythroid enhancer of BCL11A subject to genetic variation determines fetal hemoglobin level. Science (2013) 2.71
ADAR1 is essential for the maintenance of hematopoiesis and suppression of interferon signaling. Nat Immunol (2008) 2.70
NANOG-dependent function of TET1 and TET2 in establishment of pluripotency. Nature (2013) 2.63
Fine-mapping at three loci known to affect fetal hemoglobin levels explains additional genetic variation. Nat Genet (2010) 2.63
Epigenetic regulation of hematopoietic differentiation by Gfi-1 and Gfi-1b is mediated by the cofactors CoREST and LSD1. Mol Cell (2007) 2.62
Early asymmetry of gene transcription in embryonic human left and right cerebral cortex. Science (2005) 2.56
Tel/Etv6 is an essential and selective regulator of adult hematopoietic stem cell survival. Genes Dev (2004) 2.56
Highly penetrant, rapid tumorigenesis through conditional inversion of the tumor suppressor gene Snf5. Cancer Cell (2002) 2.51
Haploinsufficiency of GATA-2 perturbs adult hematopoietic stem-cell homeostasis. Blood (2005) 2.47
Developmental stage-selective effect of somatically mutated leukemogenic transcription factor GATA1. Nat Genet (2005) 2.44
The zinc finger transcription factor Gfi1, implicated in lymphomagenesis, is required for inner ear hair cell differentiation and survival. Development (2003) 2.38
PRC1 and Suv39h specify parental asymmetry at constitutive heterochromatin in early mouse embryos. Nat Genet (2008) 2.37
Correction of sickle cell disease in adult mice by interference with fetal hemoglobin silencing. Science (2011) 2.36
TIF1gamma controls erythroid cell fate by regulating transcription elongation. Cell (2010) 2.33
Pulmonary embolism after major abdominal surgery in gynecologic oncology. Obstet Gynecol (2006) 2.31
A functional element necessary for fetal hemoglobin silencing. N Engl J Med (2011) 2.25
MicroRNA-21 promotes fibrosis of the kidney by silencing metabolic pathways. Sci Transl Med (2012) 2.20
Exome sequencing identifies GATA1 mutations resulting in Diamond-Blackfan anemia. J Clin Invest (2012) 2.15
Identification of distinct molecular phenotypes in acute megakaryoblastic leukemia by gene expression profiling. Proc Natl Acad Sci U S A (2006) 2.08
GATA-1 converts lymphoid and myelomonocytic progenitors into the megakaryocyte/erythrocyte lineages. Immunity (2003) 2.05
Rb intrinsically promotes erythropoiesis by coupling cell cycle exit with mitochondrial biogenesis. Genes Dev (2008) 2.05
Polycomb repressive complex 2 regulates normal development of the mouse heart. Circ Res (2011) 2.05
miR-125b-2 is a potential oncomiR on human chromosome 21 in megakaryoblastic leukemia. Genes Dev (2010) 2.05
Affinity adsorption of lysozyme with Reactive Red 120 modified magnetic chitosan microspheres. Food Chem (2013) 2.04
MicroRNA-21 limits in vivo immune response-mediated activation of the IL-12/IFN-gamma pathway, Th1 polarization, and the severity of delayed-type hypersensitivity. J Immunol (2011) 2.00
Coregulator-dependent facilitation of chromatin occupancy by GATA-1. Proc Natl Acad Sci U S A (2004) 1.99
The zinc-finger proto-oncogene Gfi-1b is essential for development of the erythroid and megakaryocytic lineages. Genes Dev (2002) 1.99
Discovery of distinct protein profiles specific for lung tumors and pre-malignant lung lesions by SELDI mass spectrometry. Lung Cancer (2003) 1.96
GATA-1 as a regulator of mast cell differentiation revealed by the phenotype of the GATA-1low mouse mutant. J Exp Med (2003) 1.96
A human stem cell model of early Alzheimer's disease pathology in Down syndrome. Sci Transl Med (2012) 1.95
Differential roles of Sall4 isoforms in embryonic stem cell pluripotency. Mol Cell Biol (2010) 1.88
MAnorm: a robust model for quantitative comparison of ChIP-Seq data sets. Genome Biol (2012) 1.88
Lysophospholipids are potential biomarkers of ovarian cancer. Cancer Epidemiol Biomarkers Prev (2004) 1.87
ETV1 directs androgen metabolism and confers aggressive prostate cancer in targeted mice and patients. Genes Dev (2013) 1.87
Mapping cellular hierarchy by single-cell analysis of the cell surface repertoire. Cell Stem Cell (2013) 1.80
Antagonism of FOG-1 and GATA factors in fate choice for the mast cell lineage. J Exp Med (2008) 1.79
Comparative outcomes analysis of procedures performed in physician offices and ambulatory surgery centers. Arch Surg (2003) 1.78
TEL-AML1 corrupts hematopoietic stem cells to persist in the bone marrow and initiate leukemia. Cell Stem Cell (2009) 1.77
GATA-factor dependence of the multitype zinc-finger protein FOG-1 for its essential role in megakaryopoiesis. Proc Natl Acad Sci U S A (2002) 1.77
The SCL complex regulates c-kit expression in hematopoietic cells through functional interaction with Sp1. Blood (2002) 1.76
MicroRNA-21 integrates pathogenic signaling to control pulmonary hypertension: results of a network bioinformatics approach. Circulation (2012) 1.75
Targeted disruption of the EZH2-EED complex inhibits EZH2-dependent cancer. Nat Chem Biol (2013) 1.75
Advances in the understanding of haemoglobin switching. Br J Haematol (2010) 1.74
PIDD death-domain phosphorylation by ATM controls prodeath versus prosurvival PIDDosome signaling. Mol Cell (2012) 1.71
Direct recruitment of polycomb repressive complex 1 to chromatin by core binding transcription factors. Mol Cell (2012) 1.71
Oct4 links multiple epigenetic pathways to the pluripotency network. Cell Res (2011) 1.69
Defective neural tube closure and anteroposterior patterning in mice lacking the LIM protein LMO4 or its interacting partner Deaf-1. Mol Cell Biol (2004) 1.68
Requirement of Nanog dimerization for stem cell self-renewal and pluripotency. Proc Natl Acad Sci U S A (2008) 1.68
Oct4 dependence of chromatin structure within the extended Nanog locus in ES cells. Genes Dev (2008) 1.68
PRC2 directly methylates GATA4 and represses its transcriptional activity. Genes Dev (2012) 1.66
The zebrafish moonshine gene encodes transcriptional intermediary factor 1gamma, an essential regulator of hematopoiesis. PLoS Biol (2004) 1.64
Gonadal differentiation, sex determination and normal Sry expression in mice require direct interaction between transcription partners GATA4 and FOG2. Development (2002) 1.64
Combinatorial assembly of developmental stage-specific enhancers controls gene expression programs during human erythropoiesis. Dev Cell (2012) 1.63
Specification of astrocytes by bHLH protein SCL in a restricted region of the neural tube. Nature (2005) 1.62