Fibroblasts
Marchetto MC, Carromeu C, Acab A, Yu D, Yeo GW, Mu Y, Chen G, Gage FH, Muotri AR ,A model for neural development and treatment of Rett syndrome using human induced pluripotent stem cells., Cell,2010-11-12,143,527-39, Abstract

Fibroblasts
Hauke J, Riessland M, Lunke S, Eyüpoglu IY, Blümcke I, El-Osta A, Wirth B, Hahnen E, Survival motor neuron gene 2 silencing by DNA methylation correlates with spinal muscular atrophy disease severity and can be bypassed by histone deacetylase inhibition., Hum Mol Genet,2009-01-15,18,304-17, Abstract

ES cells
Pereira CF, Piccolo FM, Tsubouchi T, Sauer S, Ryan NK, Bruno L, Landeira D, Santos J, Banito A, Gil J, Koseki H, Merkenschlager M, Fisher AG, ESCs require PRC2 to direct the successful reprogramming of differentiated cells toward pluripotency., Cell Stem Cell,2010-06-04,6,547-56, Abstract

ES cells, TS cells
Alder O, Lavial F, Helness A, Brookes E, Pinho S, Chandrashekran A, Arnaud P, Pombo A, O'Neill L, Azuara V, Ring1B and Suv39h1 delineate distinct chromatin states at bivalent genes during early mouse lineage commitment., Development,2010-08-01,137,2483-92, Abstract

HeLa cells
Cong R, Das S, Ugrinova I, Kumar S, Mongelard F, Wong J, Bouvet P, Interaction of nucleolin with ribosomal RNA genes and its role in RNA polymerase I transcription., Nucleic Acids Res,2012-08-02, Abstract

HEK293T cells, NIH-3T3 cells
Guetg C, Lienemann P, Sirri V, Grummt I, Hernandez-Verdun D, Hottiger MO, Fussenegger M, Santoro R, The NoRC complex mediates the heterochromatin formation and stability of silent rRNA genes and centromeric repeats, The EMBO Journal,2010-07-07,29,2135-46, Abstract

HEK293T cells, NIH-3T3 cells
Santoro R, Lienemann P, Fussenegger M, Epigenetic engineering of ribosomal RNA genes enhances protein production., PLoS One,2009-01-01,4,e6653, Abstract

HEK293
Sabatel H, Di Valentin E, Gloire G, Dequiedt F, Piette J, Habraken Y, Phosphorylation of p65(RelA) on Ser547 by ATM Represses NF-κB-Dependent Transcription of Specific Genes after Genotoxic Stress ,PLoSONE,2012-06-08,7,e38246, Abstract

F9 cells
Herzog M, Josseaux E, Dedeurwaerder S, Calonne E, Volkmar M, Fuks F, The histone demethylase Kdm3a is essential to progression through differentiation., Nucleic Acids Res,2012-05-11, Abstract

Hippocampus
Bahari-Javan S, Maddalena A, Kerimoglu C, Wittnam J, Held T, Bähr M, Burkhardt S, Delalle I, Kügler S, Fischer A, Sananbenesi F, HDAC1 Regulates Fear Extinction in Mice., J Neurosci,2012-04-11,32,5062-5073, Abstract

Glioma stem-like cells
Orzan F, Pellegatta S, Poliani PL, Pisati F, Caldera V, Menghi F, Kapetis D, Marras C, Schiffer D, Finocchiaro G, Enhancer of Zeste 2 (EZH2) is up-regulated in malignant gliomas and in glioma stem-like cells., Neuropathol Appl Neurobiol,2011-06-01,37,381-94, Abstract

Cells: C2C12, HEK293T, HeLa-S3
Philipot O, Joliot V, Ait-Mohamed O, Pellentz C, Robin P, Fritsch L, Ait-Si-Ali S, The core binding factor CBF negatively regulates skeletal muscle terminal differentiation., PLoS One,2010-01-01,5,e942, Abstract

MDAMB231 cells
Denis H, Deplus R, Putmans P, Yamada M, Métivier R, Fuks F, Functional connection between deimination and deacetylation of histones., Mol Cell Biol,2009-09-01,29,4982-93, Abstract

Rat – brain and heart
Zibetti C, Adamo A, Binda C, Forneris F, Toffolo E, Verpelli C, Ginelli E, Mattevi A, Sala C, Battaglioli E, Alternative splicing of the histone demethylase LSD1/KDM1 contributes to the modulation of neurite morphogenesis in the mammalian nervous system., J Neurosci,2010-02-17,30,2521-32, Abstract

HCT116 cells
Gatta R, Mantovani R, NF-Y substitutes H2A-H2B on active cell-cycle promoters: recruitment of CoREST-KDM1 and fine-tuning of H3 methylations., Nucleic Acids Res,2008-11-01,36,6592-607, Abstract

ES cells
Adamo A, Sesé B, Boue S, Castaño J, Paramonov I, Barrero MJ, Izpisua Belmonte JC, LSD1 regulates the balance between self-renewal and differentiation in human embryonic stem cells., Nat Cell Biol,2011-06-01,13,652-9, Abstract

Glioma stem-like cells
Orzan F, Pellegatta S, Poliani PL, Pisati F, Caldera V, Menghi F, Kapetis D, Marras C, Schiffer D, Finocchiaro G, Enhancer of Zeste 2 (EZH2) is up-regulated in malignant gliomas and in glioma stem-like cells., Neuropathol Appl Neurobiol,2011-06-01,37,381-94, Abstract

ES cells
Pereira CF, Piccolo FM, Tsubouchi T, Sauer S, Ryan NK, Bruno L, Landeira D, Santos J, Banito A, Gil J, Koseki H, Merkenschlager M, Fisher AG, ESCs require PRC2 to direct the successful reprogramming of differentiated cells toward pluripotency., Cell Stem Cell,2010-06-04,6,547-56, Abstract

pOL cells
Sher F, Boddeke E, Olah M, Copray S, Dynamic Changes in Ezh2 Gene Occupancy Underlie Its Involvement in Neural Stem Cell Self-Renewal and Differentiation towards Oligodendrocytes, PLoS ONE,2012-07-12, Abstract

Fibroblasts
Tyan SW, Hsu CH, Peng KL, Chen CC, Kuo WH, Lee EY, Shew JY, Chang KJ, Juan LJ, Lee WH, Breast Cancer Cells Induce Stromal Fibroblasts to Secrete ADAMTS1 for Cancer Invasion through an Epigenetic Change., PLoS One,2012-04-13,7,e35128, Abstract

ES cells - mouse
Tavares L, Dimitrova E, Oxley D, Webster J, Poot R, Demmers J, Bezstarosti K, Taylor S, Ura H, Koide H, Wutz A, Vidal M, Elderkin S, Brockdorff N, RYBP-PRC1 Complexes Mediate H2A Ubiquitylation at Polycomb Target Sites Independently of PRC2 and H3K27me3., Cell,2012-02-08, Abstract

Drosphila S2 cells
Lanzuolo C, Lo Sardo F, Diamantini A, Orlando V, PcG complexes set the stage for epigenetic inheritance of gene silencing in early S phase before replication., PLoS Genet,2011-11-01,7,e1002370, Abstract

Cells: LNCaP, MCF7, MDAMB231, PC3, U2OS
Taniguchi H, Jacinto FV, Villanueva A, Fernandez AF, Yamamoto H, Carmona FJ, Puertas S, Marquez VE, Shinomura Y, Imai K, Esteller M, Silencing of Kruppel-like factor 2 by the histone methyltransferase EZH2 in human cancer., Oncogene,2011-09-05, Abstract

C2C12 cells
Palacios D, Mozzetta C, Consalvi S, Caretti G, Saccone V, Proserpio V, Marquez VE, Valente S, Mai A, Forcales SV, Sartorelli V, Puri PL, TNF/p38α/polycomb signaling to Pax7 locus in satellite cells links inflammation to the epigenetic control of muscle regeneration., Cell Stem Cell,2010-10-08,7,455-69, Abstract

P19.6 mouse embryonal carcinoma cells
Sérandour AA, Avner S, Oger F, Bizot M, Percevault F, Lucchetti-Miganeh C, Palierne G, Gheeraert C, Barloy-Hubler F, Péron CL, Madigou T, Durand E, Froguel P, Staels B, Lefebvre P, Métivier R, Eeckhoute J, Salbert G, Dynamic hydroxymethylation of deoxyribonucleic acid marks differentiation-associated enhancers., Nucleic Acids Res,2012-06-22, Abstract

Pre-B cells
Kallin EM, Rodríguez-Ubreva J, Christensen J, Cimmino L, Aifantis I, Helin K, Ballestar E, Graf T, Tet2 Facilitates the Derepression of Myeloid Target Genes during CEBPα-Induced Transdifferentiation of Pre-B Cells., Mol Cell,2012-09-12, Abstract

Mouse
Wu H, Zhang Y, Mechanisms and functions of Tet protein-mediated 5-methylcytosine oxidation., Genes Dev,2011-12-01,25,2436-52, Abstract

ES cells
Ruzov A, Tsenkina Y, Serio A, Dudnakova T, Fletcher J, Bai Y, Chebotareva T, Pells S, Hannoun Z, Sullivan G, Chandran S, Hay DC, Bradley M, Wilmut I, De Sousa P, Lineage-specific distribution of high levels of genomic 5-hydroxymethylcytosine in mammalian development., Cell Res,2011-09-01,21,1332-42,
Abstract

ES cells
Stroud H, Feng S, Morey Kinney S, Pradhan S, Jacobsen SE, 5-Hydroxymethylcytosine is associated with enhancers and gene bodies in human embryonic stem cells., Genome Biol,2011-06-20,12,R54, Abstract

ES cells
Wu H, D'Alessio AC, Ito S, Wang Z, Cui K, Zhao K, Sun YE, Zhang Y, Genome-wide analysis of 5-hydroxymethylcytosine distribution reveals its dual function in transcriptional regulation in mouse embryonic stem cells., Genes Dev,2011-04-01,25,679-84, Abstract

Rabbits - embryos
Wossidlo M, Nakamura T, Lepikhov K, Marques CJ, Zakhartchenko V, Boiani M, Arand J, Nakano T, Reik W, Walter J, 5-Hydroxymethylcytosine in the mammalian zygote is linked with epigenetic reprogramming., Nat Commun,2011-03-15,2,241, Abstract

Fungi
Boedi S, Reyes-Dominguez Y, Strauss J., Chromatin immunoprecipitation analysis in filamentous fungi., Methods Mol Biol.,2012,944,221-36, Abstract

Plants – A. thaliana
Colomé-Tatché M, Cortijo S, Wardenaar R, Morgado L, Lahouze B, Sarazin A, Etcheverry M, Martin A, Feng S, Duvernois-Berthet E, Labadie K, Wincker P, Jacobsen SE, Jansen RC, Colot V, Johannes F, Features of the Arabidopsis recombination landscape resulting from the combined loss of sequence variation and DNA methylation., Proc Natl Acad Sci U S A,2012-10-02,109,16240-5, Abstract

Huh-7 cells
Frau M, Tomasi ML, Simile MM, Demartis MI, Salis F, Latte G, Calvisi DF, Seddaiu MA, Daino L, Feo CF, Brozzetti S, Solinas G, Yamashita S, Ushijima T, Feo F, Pascale RM, Role of transcriptional and post-transcriptional regulation of methionine adenosyltransferases in liver cancer progression, Hepatology,2012-02, Abstract

Plants - Populus trichocarpa
Vining KJ, Pomraning KR, Wilhelm LJ, Priest HD, Pellegrini M, Mockler TC, Freitag M, Strauss S, Dynamic DNA cytosine methylation in the Populus trichocarpa genome: tissue-level variation and relationship to gene expression., BMC Genomics,2012-01-17,13,27, Abstract

Human left ventricular tissue
Movassagh M, Choy MK, Knowles DA, Cordeddu L, Haider S, Down T, Siggens L, Vujic A, Simeoni I, Penkett C, Goddard M, Lio P, Bennett MR, Foo RSY, Distinct Epigenomic Features in End-Stage Failing Human Hearts., Circulation,2011-11-29,124, 2411-22, Abstract

Cells: BJAB, BL41, CD3+, Murine splenocytes
Shukla S, Kavak E, Gregory M, Imashimizu M, Shutinoski B, Kashlev M, Oberdoerffer P, Sandberg R, Oberdoerffer S, CTCF-promoted RNA polymerase II pausing links DNA methylation to splicing., Nature,2011-10-02,479,74-79, Abstract

Cells: abl, LNCaP, MCF7, P19
Sérandour AA, Avner S, Percevault F, Demay F, Bizot M, Lucchetti-Miganeh C, Barloy-Hubler F, Brown M, Lupien M, Métivier R, Salbert G, Eeckhoute J, Epigenetic switch involved in activation of pioneer factor FOXA1-dependent enhancers., Genome Res,2011-04-01,21,555-65, Abstract

Leukocytes, HEK293
Pälmke N, Santacruz D, Walter J, Comprehensive analysis of DNA-methylation in mammalian tissues using MeDIP-chip., Methods,2011-02-01,53,175-84, Abstract

HeLa cells, Human cervical tissues
Yu J, Feng Q, Ruan Y, Komers R, Kiviat N, Bomsztyk K, Microplate-based platform for combined chromatin and DNA methylation immunoprecipitation assays., BMC Mol Biol,2011-01-01,12,49,
Abstract

Cells: ASC, BMMSC, HPC, MPC
Sørensen AL, Jacobsen BM, Reiner AH, Andersen IS, Collas P, Promoter DNA Methylation Patterns of Differentiated Cells Are Largely Programmed at the Progenitor Stage, Molecular Biology of the Cell,2010-06-15,21,2066-2077, Abstract

Cells: C2C12, HeLa, MSC
Delbarre E, Jacobsen BM, Reiner AH, Sørensen AL, Kuntziger T, Collas P, Chromatin Environment of Histone Variant H3.3 Revealed by Quantitative Imaging and Genome-scale Chromatin and DNA Immunoprecipitation, Molecular Biology of the Cell,2010-06-01,21,1872-1884, Abstract

Plants – A. thaliana
Castells E, Molinier J, Drevensek S, Genschik P, Barneche F, Bowler C, det1-1-induced UV-C hyposensitivity through UVR3 and PHR1 photolyase gene over-expression., Plant J,2010-05-06,63,392-404, Abstract

Human - heart
Choy MK, Movassagh M, Goh HG, Bennett MR, Down TA, Foo RS, Genome-wide conserved consensus transcription factor binding motifs are hyper-methylated., BMC Genomics,2010-01-01,11,519, Abstract

BCBL1 cells, SLK cells
Günther T, Grundhoff A, The epigenetic landscape of latent Kaposi sarcoma-associated herpesvirus genomes., PLoS Pathog,2010-01-01,6,e1000935, Abstract

Fungus – Neurospora crassa
Lewis ZA, Honda S, Khlafallah TK, Jeffress JK, Freitag M, Mohn F, Schübeler D, Selker EU, Relics of repeat-induced point mutation direct heterochromatin formation in Neurospora crassa., Genome Res,2009-03-01,19,427-37, Abstract

Pomraning KR, Smith KM, Freitag M, Genome-wide high throughput analysis of DNA methylation in eukaryotes., Methods,2009-03-01,47,142-50, Abstract

Human primary myoblast
Bodega B, Ramirez GD, Grasser F, Cheli S, Brunelli S, Mora M, Meneveri R, Marozzi A, Mueller S, Battaglioli E, Ginelli E, Remodeling of the chromatin structure of the facioscapulohumeral muscular dystrophy (FSHD) locus and upregulation of FSHD-related gene 1 (FRG1) expression during human myogenic differentiation., BMC Biol,2009-01-01,7,41, Abstract

MCF-7 cells
Weng YI, Huang TH, Yan PS, Methylated DNA immunoprecipitation and microarray-based analysis: detection of DNA methylation in breast cancer cell lines., Methods Mol Biol,2009-01-01,590,165-76, Abstract

Mouse – frontal cortex
Dong E, Nelson M, Grayson DR, Costa E,Guidotti A, Clozapine and sulpiride but not haloperidol or olanzapine activate brain DNA demethylation, PNAS,2008-09-09,105,13614-13619, Abstract

HT-1080 cells
Nakano M, Cardinale S, Noskov VN, Gassmann R, Vagnarelli P, Kandels-Lewis S, Larionov V, Earnshaw WC, Masumoto H, Inactivation of a Human Kinetochore by Specific Targeting of Chromatin Modifiers, Dev Cell,2008-04-15,14,507-522, Abstract

Liver from mouse
Bardag-Gorce F, Dedes J, French BA, Oliva JV, Li J, French SW, Mallory body formation is associated with epigenetic phenotypic change in hepatocytes in vivo., Exp Mol Pathol,2007-10-01,83,160-8, Abstract

Sperm
Tracey R, Manikkam M, Guerrero-Bosagna C, Skinner MK, Hydrocarbons (jet fuel JP-8) induce epigenetic transgenerational inheritance of obesity, reproductive disease and sperm epimutations, Reproductive Toxicology,2013-01-25, Abstract

Sperm
Manikkam M, Tracey R, Guerrero-Bosagna C, Skinner MK., Plastics Derived Endocrine Disruptors (BPA, DEHP and DBP) Induce Epigenetic Transgenerational Inheritance of Obesity, Reproductive Disease and Sperm Epimutations, PLoS ONE,2013-01-24,8,e55387, Abstract

Brain - mouse
Mellén M, Ayata P, Dewell S, Kriaucionis S, Heintz N, MeCP2 Binds to 5hmC Enriched within Active Genes and Accessible Chromatin in the Nervous System., Cell,2012-12-21,151,1417-30, Abstract

Liver - mouse
Thomson JP, Lempiäinen H, Hackett JA, Nestor CE, Müller A, Bolognani F, Oakeley EJ, Schübeler D, Terranova R, Reinhardt D, Moggs JG, Meehan RR., Non-genotoxic carcinogen exposure induces defined changes in the 5-hydroxymethylome., Genome Biol.,2012-10-03,13,R93, Abstract

Sperm
Guerrero-Bosagna C, Covert TR, Haque MM, Settles M, Nilsson EE, Anway MD, Skinner MK, Epigenetic transgenerational inheritance of vinclozolin induced mouse adult onset disease and associated sperm epigenome biomarkers., Reprod Toxicol,2012-10-02, Abstract

HeLa cells
Rothbart SB, Krajewski K, Nady N, Tempel W, Xue S, Badeaux AI, Barsyte-Lovejoy D, Martinez JY, Bedford MT, Fuchs SM, Arrowsmith CH, Strahl BD, Association of UHRF1 with methylated H3K9 directs the maintenance of DNA methylation., Nat Struct Mol Biol,2012-09-30, Abstract

Sperm
Manikkam M, Tracey R, Guerrero-Bosagna C, Skinner MK, Pesticide and Insect Repellent Mixture (Permethrin and DEET) Induces Epigenetic Transgenerational Inheritance of Disease and Sperm Epimutations., Reprod Toxicol,2012-09-10, Abstract

Mammalian cells
Borgel J, Guibert S, Weber M., Methylated DNA Immunoprecipitation (MeDIP) from Low Amounts of Cells., Methods Mol Biol.,2012-08,925,149-58, Abstract

T cells
Joosten M, Seitz V, Zimmermann K, Sommerfeld A, Berg E, Lenze D, Leser U, Stein H, Hummel M, Histone acetylation and DNA demethylation of T-cells result in an anaplastic large cell lymphoma-like phenotype., Haematologica,2012-08-16, Abstract

Sharp AJ., Whole genome methylation profiling by immunoprecipitation of methylated DNA, Methods Mol Biol.,2012-08,925,69-78, Abstract

Plants - A. thaliana
Kawanabe T, Fujimoto R, Sasaki T, Taylor JM, Dennis ES, A comparison of transcriptome and epigenetic status between closely related species in the genus Arabidopsis., Gene,2012-07-13, Abstract

Pig
Li M, Wang T, Wu H, Zhang J, Zhou C, Jiang A, Li R, Li X, Genome-Wide DNA Methylation Changes between the Superficial and Deep Backfat Tissues of the Pig, International Journal of Molecular Sciences,2012-06-08,13,7098-7108, Abstract

Mouse
Matrisciano F, Tueting P, Dalal I, Kadriu B, Grayson DR, Davis JM, Nicoletti F, Guidotti A, Epigenetic modifications of GABAergic interneurons are associated with the schizophrenia-like phenotype induced by prenatal stress in mice., Neuropharmacology,2012-04-28, Abstract

Rat - ovary
Nilsson E, Larsen G, Manikkam M, Guerrero-Bosagna C, Savenkova MI, Skinner MK, Environmentally induced epigenetic transgenerational inheritance of ovarian disease., PLoS One,2012-05-03,7,e36129, Abstract

Rat - sperm
Manikkam M, Guerrero-Bosagna C, Tracey R, Haque MM, Skinner MK, Transgenerational actions of environmental compounds on reproductive disease and identification of epigenetic biomarkers of ancestral exposures., PLoS One,2012-02-28,7,e31901, Abstract

Chicken – thalamus, hypothalamus
Natt D, Rubin CJ, Wright D, Johnsson M, Belteky J, Andersson L, Jensen P, Heritable genome-wide variation of gene expression and promoter methylation between wild and domesticated chickens., BMC Genomics,2012-02-04,13,59, Abstract

Zebrafish
Olsen AS, Sarras MP, Leontovich A, Intine RV, Heritable transmission of diabetic metabolic memory in zebrafish correlates with DNA hypomethylation and aberrant gene expression., Diabetes,2012-02-01,61,485-91, Abstract

Human - brain
Gavin DP, Sharma RP, Chase KA, Matrisciano F, Dong E, Guidotti A, Growth Arrest and DNA-Damage-Inducible, Beta (GADD45b)-Mediated DNA Demethylation in Major Psychosis., Neuropsychopharmacology,2012-01-01,37,531-42, Abstract

Human – blood samples
Sharp AJ, Stathaki E, Migliavacca E, Brahmachary M, Montgomery SB, Dupre Y, Antonarakis SE, DNA methylation profiles of human active and inactive X chromosomes., Genome Res,2011-10-01,21,1592-600, Abstract

Cells: BT474, HMEC, MDA-PCa-2b, MDAMB231, PrEC
Takeshima H, Yamashita S, Shimazu T, Ushijima T, Effects of genome architecture and epigenetic factors on susceptibility of promoter CpG islands to aberrant DNA methylation induction., Genomics,2011-09-01,98,182-8, Abstract

Mouse - colon tumors, epithelial samples
Katsurano M, Niwa T, Yasui Y, Shigematsu Y, Yamashita S, Takeshima H, Lee MS, Kim YJ, Tanaka T, Ushijima T, Early-stage formation of an epigenetic field defect in a mouse colitis model, and non-essential roles of T- and B-cells in DNA methylation induction., Oncogene,2011-06-20, Abstract

21 Breast cancer cell lines
Zuo T, Liu TM, Lan X, Weng YI, Shen R, Gu F, Huang YW, Liyanarachchi S, Deatherage DE, Hsu PY, Taslim C, Ramaswamy B, Shapiro CL, Lin HJ, Cheng AS, Jin VX, Huang TH, Epigenetic silencing mediated through activated PI3K/AKT signaling in breast cancer., Cancer Res,2011-03-01,71,1752-62,
Abstract

CD4+ T cells, Jurkat cells
Son JS, Chae CS, Hwang JS, Park ZY, Im SH, Enhanced chromatin accessibility and recruitment of JUNB mediate the sustained IL-4 expression in NFAT1 deficient T helper 2 cells., LoS One,2011-01-01,6,e22042, Abstract

Human – blood samples
Sharp AJ, Migliavacca E, Dupre Y, Stathaki E, Sailani MR, Baumer A, Schinzel A, Mackay DJ, Robinson DO, Cobellis G, Cobellis L, Brunner HG, Steiner B, Antonarakis SE, Methylation profiling in individuals with uniparental disomy identifies novel differentially methylated regions on chromosome 15., Genome Res,2010-09-01,20,1271-8, Abstract

MCF7 cells, MDECs cells
Hsu PY, Hsu HK, Singer GA, Yan PS, Rodriguez BA, Liu JC, Weng YI, Deatherage DE, Chen Z, Pereira JS, Lopez R, Russo J, Wang Q, Lamartiniere CA, Nephew KP, Huang TH, Estrogen-mediated epigenetic repression of large chromosomal regions through DNA looping., Genome Res,2010-06-01,20,733-44,
Abstract

Cells: HMC-1-8, HMEC, Hs578T, MCF7, MDA-MB453
Ruike Y, Imanaka Y, Sato F, Shimizu K, Tsujimoto G, Genome-wide analysis of aberrant methylation in human breast cancer cells using methyl-DNA immunoprecipitation combined with high-throughput sequencing., BMC Genomics,2010-01-01,11,137, Abstract

ES cells
Cohen NM, Dighe V, Landan G, Reynisdóttir S, Palsson A, Mitalipov S, Tanay A, DNA methylation programming and reprogramming in primate embryonic stem cells., Genome Res,2009-12-01,19,2193-201, http://www.pubmed.org/19887575

Prostate cancer cell lines
Takeshima H, Yamashita S, Shimazu T, Niwa T, Ushijima T, The presence of RNA polymerase II, active or stalled, predicts epigenetic fate of promoter CpG islands., Genome Res,2009-11-01,19,1974-82,
Abstract

Cells: AGS, HSC, KATOIII
Yamashita S, Hosoya K, Gyobu K, Takeshima H, Ushijima T, Development of a novel output value for quantitative assessment in methylated DNA immunoprecipitation-CpG island microarray analysis., DNA Res,2009-10-01,16,275-86, Abstract

Drosophila S2 cells
Fedoseeva DM, Kretova OV, Tchurikov NA, Molecular analysis of enhancer RNAs and chromatin modifications in the region of their synthesis in Drosophila cells possessing genetic constructs., Dokl Biochem Biophys,2012-02-01,442,7-11, Abstract

Drosophila S2 cells
Fedoseeva DM, Kretova OV, Tchurikov NA, Molecular analysis of enhancer RNAs and chromatin modifications in the region of their synthesis in Drosophila cells possessing genetic constructs., Dokl Biochem Biophys,2012-02-01,442,7-11, Abstract

HSC cells, MFB cells
Perugorria MJ, Wilson CL, Zeybel M, Walsh M, Amin S, Robinson S, White SA, Burt AD, Oakley F, Tsukamoto H, Mann DA, Mann J, The histone methyltransferase ASH1 orchestrates fibrogenic gene transcription during myofibroblast transdifferentiation., Hepatology,2012-04-04, Abstract

Mouse – ES cells
Tavares L, Dimitrova E, Oxley D, Webster J, Poot R, Demmers J, Bezstarosti K, Taylor S, Ura H, Koide H, Wutz A, Vidal M, Elderkin S, Brockdorff N, RYBP-PRC1 Complexes Mediate H2A Ubiquitylation at Polycomb Target Sites Independently of PRC2 and H3K27me3., Cell,2012-02-08, Abstract

BPH-1, LNCaP, PC3
Hauptstock V, Kuriakose S, Schmidt D, Düster R, Müller SC, von Ruecker A, Ellinger J, Glutathione-S-transferase pi 1(GSTP1) gene silencing in prostate cancer cells is reversed by the histone deacetylase inhibitor depsipeptide., Biochem Biophys Res Commun,2011-09-09,412,606-11, Abstract

HMEC cells, 21 breast cancer cell lines
Zuo T, Liu TM, Lan X, Weng YI, Shen R, Gu F, Huang YW, Liyanarachchi S, Deatherage DE, Hsu PY, Taslim C, Ramaswamy B, Shapiro CL, Lin HJ, Cheng AS, Jin VX, Huang TH, Epigenetic silencing mediated through activated PI3K/AKT signaling in breast cancer., Cancer Res,2011-03-01,71,1752-62,
Abstract

ASCs cells
Boulland JL, Mastrangelopoulou M, Boquest AC, Jakobsen R, Noer A, Glover JC, Collas P., Epigenetic Regulation of Nestin Expression During Neurogenic Differentiation of Adipose Tissue Stem Cells., Stem Cells Dev.,2012-12-21, Abstract

Drosophila
Coléno-Costes A, Jang SM, de Vanssay A, Rougeot J, Bouceba T, Randsholt NB, Gibert JM, Le Crom S, Mouchel-Vielh E, Bloyer S, Peronnet F, New partners in regulation of gene expression: the enhancer of trithorax and polycomb corto interacts with methylated ribosomal protein l12 via its chromodomain., PLoS Genet,2012-10-11,8,e1003006, Abstract

Sperm
Zeybel M, Hardy T, Wong YK, Mathers JC, Fox CR, Gackowska A, Oakley F, Burt AD, Wilson CL, Anstee QM, Barter MJ, Masson S, Elsharkawy AM, Mann DA, Mann J, Multigenerational epigenetic adaptation of the hepatic wound-healing response., Nat Med,2012-09-02, Abstract

Fibroblasts
Janzer A, Stamm K, Becker A, Zimmer A, Buettner R, Kirfel J, The H3K4me3 histone demethylase Fbxl10 is a regulator of chemokine expression, cellular morphology and the metabolome of fibroblasts, J. Biol. Chem.,2012-07-23, Abstract

U937 cells
Valente S, Lepore I, Dell'aversana C, Tardugno M, Castellano S, Sbardella G, Tomassi S, Di Maro S, Novellino E, Di Santo R, Costi R, Altucci L, Mai A, Identification of PR-SET7 and EZH2 selective inhibitors inducing cell death in human leukemia U937 cells., Biochimie,2012-06-16, Abstract

HCT116 cells
Guil S, Soler M, Portela A, Carrère J, Fonalleras E, Gómez A, Villanueva A, Esteller M, Intronic RNAs mediate EZH2 regulation of epigenetic targets., Nat Struct Mol Biol,2012-06-03, Abstract

MCF10A cells, SUM-159 cells
Peng Z, Shen R, Li YW, Teng KY, Shapiro CL, Lin HJ, Epigenetic Repression of RARRES1 Is Mediated by Methylation of a Proximal Promoter and a Loss of CTCF Binding., PLoS One,2012-05-17,7,e36891, Abstract

Schistosoma mansoni
Lepesant JM, Cosseau C, Boissier J, Freitag M, Portela J, Climent D, Perrin C, Zerlotini A, Grunau C, Chromatin structural changes around satellite repeats on the female sex chromosome in Schistosoma mansoni and their possible role in sex chromosome emergence., Genome Biol,2012-02-29,13,R14, Abstract

Zebrafish - embryos
Lindeman LC, Andersen IS, Reiner AH, Li N, Aanes H, Østrup O, Winata C, Mathavan S, Müller F, Aleström P, Collas P,Prepatterning of developmental gene expression by modified histones before zygotic genome activation.,Dev Cell,2011-12-13,21,993-1004,http://www.pubmed.org/22137762

Human embryonic stem cells
Iliou MS, Lujambio A, Portela A, Brüstle O, Koch P, Andersson-Vincent PH, Sundström E, Hovatta O, Esteller M,Bivalent histone modifications in stem cells poise miRNA loci for CpG island hypermethylation in human cancer.,Epigenetics,2011-11-01,6,1344-53,http://www.pubmed.org/22048248

Cells: LNCaP, MCF7, MDAMB231, PC3, U2OS
Taniguchi H, Jacinto FV, Villanueva A, Fernandez AF, Yamamoto H, Carmona FJ, Puertas S, Marquez VE, Shinomura Y, Imai K, Esteller M, Silencing of Kruppel-like factor 2 by the histone methyltransferase EZH2 in human cancer., Oncogene,2011-09-05, Abstract

27 cell lines
Vegliante MC, Royo C, Palomero J, Salaverria I, Balint B, Martín-Guerrero I, Agirre X, Lujambio A, Richter J, Xargay-Torrent S, Bea S, Hernandez L, Enjuanes A, Calasanz MJ, Rosenwald A, Ott G, Roman-Gomez J, Prosper F, Esteller M, Jares P, Siebert R, Campo E, Martín-Subero JI, Amador V, Epigenetic activation of SOX11 in lymphoid neoplasms by histone modifications., PLoS One,2011-01-01,6,e21382, Abstract

MCF7 cells, MDECs cells
Hsu PY, Hsu HK, Singer GA, Yan PS, Rodriguez BA, Liu JC, Weng YI, Deatherage DE, Chen Z, Pereira JS, Lopez R, Russo J, Wang Q, Lamartiniere CA, Nephew KP, Huang TH, Estrogen-mediated epigenetic repression of large chromosomal regions through DNA looping., Genome Res,2010-06-01,20,733-44, Abstract

ASCs cells, fibroblasts, keratinocytes, NCCIT cells
Barrand S, Collas P, Chromatin states of core pluripotency-associated genes in pluripotent, multipotent and differentiated cells., Biochem Biophys Res Commun,2010-01-01,391,762-7, Abstract

ES cells
Marks H, Kalkan T, Menafra R, Denissov S, Jones K, Hofemeister H, Nichols J, Kranz A, Francis Stewart A, Smith A, Stunnenberg HG, The transcriptional and epigenomic foundations of ground state pluripotency., Cell,2012-04-27,149,590-604, Abstract

Human - ES cells
Blahnik KR, Dou L, Echipare L, Iyengar S, O'Geen H, Sanchez E, Zhao Y, Marra MA, Hirst M, Costello JF, Korf I, Farnham PJ, Characterization of the contradictory chromatin signatures at the 3' exons of zinc finger genes., PLoS One,2011-02-15,6,e17121, Abstract

ES cells
Marks H, Chow JC, Denissov S, Françoijs KJ, Brockdorff N, Heard E, Stunnenberg HG, High-resolution analysis of epigenetic changes associated with X inactivation., Genome Res,2009-08-01,19,1361-73, Abstract

Yeast – S. pombe
Xhemalce B, Kouzarides T, A chromodomain switch mediated by histone H3 Lys 4 acetylation regulates heterochromatin assembly., Genes Dev,2010-04-01,24,647-52, Abstract

Zebrafish – embryos
Lindeman LC, Andersen IS, Reiner AH, Li N, Aanes H, Østrup O, Winata C, Mathavan S, Müller F, Aleström P, Collas P, Prepatterning of developmental gene expression by modified histones before zygotic genome activation., Dev Cell,2011-12-13,21,993-1004, Abstract

ASCs cells, NCCIT cells, SF cells
Barrand S, Andersen IS, Collas P, Promoter-exon relationship of H3 lysine 9, 27, 36 and 79 methylation on pluripotency-associated genes., Biochem Biophys Res Commun,2010-10-29,401,611-7, Abstract

Zebrafish - Embryos
Bogdanovic O, Fernandez-Minan A, Tena JJ, de Lacalle-Mustienes E, Hidalgo C, van Kruysbergen I, van Heeringen SJ, Veenstra GJ, Gomez-Skarmeta JL, Dynamics of enhancer chromatin signatures mark the transition from pluripotency to cell specification during embryogenesis., Genome Res,2012-05-16, Abstract

Drosophila
Carbonell A, Mazo A, Serras F, Corominas M., Ash2 acts as an Ecdysone Receptor coactivator by stabilizing the histone methyltransferase Trr., Mol Biol Cell.,2012-11-28, Abstract

NB4 cells
Saeed S, Logie C, Francoijs KJ, Frigè G, Romanenghi M, Nielsen FG, Raats L, Shahhoseini M, Huynen M, Altucci L, Minucci S, Martens JH, Stunnenberg HG, Chromatin accessibility, p300 and histone acetylation define PML-RARα and AML1-ETO binding sites in acute myeloid leukemia., Blood,2012-08-24, Abstract

U937 cells
Valente S, Lepore I, Dell'aversana C, Tardugno M, Castellano S, Sbardella G, Tomassi S, Di Maro S, Novellino E, Di Santo R, Costi R, Altucci L, Mai A ,Identification of PR-SET7 and EZH2 selective inhibitors inducing cell death in human leukemia U937 cells., Biochimie,2012-06-16, Abstract

Drosophila – S2 cells
Fedoseeva DM, Kretova OV, Tchurikov NA, Molecular analysis of enhancer RNAs and chromatin modifications in the region of their synthesis in Drosophila cells possessing genetic constructs., Dokl Biochem Biophys,2012-02-01,442,7-11, Abstract

Primary cells
O'Geen H, Echipare L, Farnham PJ, Using ChIP-Seq Technology to Generate High-Resolution Profiles of Histone Modifications, Methods in Molecular Biology,2011,791,265-286, Abstract

Human - aortic specimens
Gomez D, Coyet A, Ollivier V, Jeunemaitre X, Jondeau G, Michel JB, Vranckx R, Epigenetic control of vascular smooth muscle cells in Marfan and non-Marfan thoracic aortic aneurysms., Cardiovasc Res,2011-02-01,89,446-56, Abstract

Human – ES cells
Blahnik KR, Dou L, Echipare L, Iyengar S, O'Geen H, Sanchez E, Zhao Y, Marra MA, Hirst M, Costello JF, Korf I, Farnham PJ, Characterization of the contradictory chromatin signatures at the 3' exons of zinc finger genes., PLoS One,2011-02-15,6,e17121, Abstract

Drosophila – S2 cells
Fedoseeva DM, Kretova OV, Tchurikov NA, Molecular analysis of enhancer RNAs and chromatin modifications in the region of their synthesis in Drosophila cells possessing genetic constructs., Dokl Biochem Biophys,2012-02-01,442,7-11, Abstract

Blastocysts
Fernandez-Gonzalez R, Ramirez MA, Pericuesta E, Calle A, Gutierrez-Adan A, Histone modifications at the blastocyst Axin1(Fu) locus mark the heritability of in vitro culture-induced epigenetic alterations in mice., Biol Reprod,2010-11-01,83,720-7, Abstract

LNCaP cells
Metzger E, Imhof A, Patel D, Kahl P, Hoffmeyer K, Friedrichs N, Müller JM, Greschik H, Kirfel J, Ji S, Kunowska N, Beisenherz-Huss C, Günther T, Buettner R, Schüle R, Phosphorylation of histone H3T6 by PKCbeta(I) controls demethylation at histone H3K4., Nature,2010-04-01,464,792-6, Abstract

Fibroblasts
Janzer A, Stamm K, Becker A, Zimmer A, Buettner R, Kirfel J, The H3K4me3 histone demethylase Fbxl10 is a regulator of chemokine expression, cellular morphology and the metabolome of fibroblasts, J. Biol. Chem.,2012-07-23, Abstract

Cell lines
Gilfillan GD, Hughes T, Sheng Y, Hjorthaug HS, Straub T, Gervin K, Harris JR, Undlien DE, Lyle R, Limitations and possibilities of low cell number ChIP-seq., BMC Genomics,2012-11-21,13,645, Abstract

Drosophila – S2 cells
Fedoseeva DM, Kretova OV, Tchurikov NA, Molecular analysis of enhancer RNAs and chromatin modifications in the region of their synthesis in Drosophila cells possessing genetic constructs., Dokl Biochem Biophys,2012-02-01,442,7-11, Abstract

Zebrafish - embryos
Lindeman LC, Andersen IS, Reiner AH, Li N, Aanes H, Østrup O, Winata C, Mathavan S, Müller F, Aleström P, Collas P, Prepatterning of developmental gene expression by modified histones before zygotic genome activation., Dev Cell,2011-12-13,21,993-1004, Abstract

C. elegans
Xiao Y, Bedet C, Robert VJ, Simonet T, Dunkelbarger S, Rakotomalala C, Soete G, Korswagen HC, Strome S, Palladino F, Caenorhabditis elegans chromatin-associated proteins SET-2 and ASH-2 are differentially required for histone H3 Lys 4 methylation in embryos and adult germ cells., Proc Natl Acad Sci U S A,2011-05-17,108,8305-10, Abstract

Dictyostelium discoideum
Müller-Taubenberger A, Bönisch C, Fürbringer M, Wittek F, Hake SB, The histone methyltransferase Dot1 is required for DNA damage repair and proper development in Dictyostelium., Biochem Biophys Res Commun,2011-01-28,404,1016-22, Abstract

Mouse – ES cells
Fadloun A, Le Gras S, Jost B, Ziegler-Birling C, Takahashi H, Gorab E, Carninci P, Torres-Padilla ME, Chromatin signatures and retrotransposon profiling in mouse embryos reveal regulation of LINE-1 by RNA., Nat Struct Mol Biol,2013-01-27, Abstract

C2C12 cells, satellite cells
Woodhouse S, Pugazhendhi D, Brien P, Pell JM., Ezh2 maintains a key phase of muscle satellite cell expansion but does not regulate terminal differentiation., J Cell Sci.,2012-11-30, Abstract

Yeast
Psakhye I, Jentsch S, Protein Group Modification and Synergy in the SUMO Pathway as Exemplified in DNA Repair., Cell,2012-11-09,151,807-20, Abstract

Drosophila
Coléno-Costes A, Jang SM, de Vanssay A, Rougeot J, Bouceba T, Randsholt NB, Gibert JM, Le Crom S, Mouchel-Vielh E, Bloyer S, Peronnet F, New partners in regulation of gene expression: the enhancer of trithorax and polycomb corto interacts with methylated ribosomal protein l12 via its chromodomain., PLoS Genet,2012-10-11,8,e1003006, Abstract

Embryos from mouse
Bošković A, Bender A, Gall L, Ziegler-Birling C, Beaujean N, Torres-Padilla ME Analysis of active chromatin modifications in early mammalian embryos reveals uncoupling of H2A.Z acetylation and H3K36 trimethylation from embryonic genome activation,Epigenetics, 2012 07,7,1-11, Abstract

Cell lines
Baer C, Claus R, Frenzel LP, Zucknick M, Park YJ, Gu L, Weichenhan D, Fischer M, Pallasch CP, Herpel E, Rehli M, Byrd JC, Wendtner CM, Plass C, Extensive promoter hypermethylation and hypomethylation is associated with aberrant microRNA expression in chronic lymphocytic leukemia., Cancer Res,2012-06-18, Abstract

hMSC and hFOB1.17 cells
Karpiuk O, Najafova Z, Kramer F, Hennion M, Galonska C, König A, Snaidero N, Vogel T, Shchebet A, Begus-Nahrmann Y, Kassem M, Simons M, Shcherbata H, Beissbarth T, Johnsen SA, The histone H2B monoubiquitination regulatory pathway is required for differentiation of multipotent stem cells., Mol Cell,2012-06-08,46,705-13, Abstract

HCT116 cells
Guil S, Soler M, Portela A, Carrère J, Fonalleras E, Gómez A, Villanueva A, Esteller M, Intronic RNAs mediate EZH2 regulation of epigenetic targets., Nat Struct Mol Biol,2012-06-03, Abstract

ES cells
Marks H, Kalkan T, Menafra R, Denissov S, Jones K, Hofemeister H, Nichols J, Kranz A, Francis Stewart A, Smith A, Stunnenberg HG, The transcriptional and epigenomic foundations of ground state pluripotency., Cell,2012-04-27,149,590-604, Abstract

Cells: CCRF-SB, HSB2, Jurkat, KARPAS45, Nalm6, RS4
Waanders E, Scheijen B, van der Meer LT, van Reijmersdal SV, van Emst L, Kroeze Y, Sonneveld E, Hoogerbrugge PM, Geurts van Kessel A, van Leeuwen FN., Kuiper RP, The Origin and Nature of Tightly Clustered BTG1 Deletions in Precursor B-Cell Acute Lymphoblastic Leukemia Support a Model of Multiclonal Evolution, PLoS Genetics,2012-02-16,8,e1002533,
Abstract

ES cells
Miyanari Y, Torres-Padilla ME, Control of ground-state pluripotency by allelic regulation of Nanog., Nature,2012-02-12, Abstract

HEK293 cells
Schenk R, Jenke A, Zilbauer M, Wirth S, Postberg J, H3.5 is a novel hominid-specific histone H3 variant that is specifically expressed in the seminiferous tubules of human testes., Chromosoma,2011-06-01,120,275-85, Abstract

BeWo cells, HEK293, placenta
Nakaya Y, Shojima T, Yasuda J, Imakawa K, Miyazawa T, Epigenetic regulation on the 5'-proximal CpG island of human porcine endogenous retrovirus subgroup A receptor 2/GPR172B., Microbes Infect,2011-01-01,13,49-57, Abstract

A-549 cells
O'Byrne Kenneth J., Baird Anne-Marie, Kilmartin Lisa, Leonard Jennifer, Sacevich Calen, Gray Steven G., Epigenetic Regulation of Glucose Transporters in Non-Small Cell Lung Cancer, 2011-01-01,3,1550-1565, Abstract

Cell lines
Vegliante MC, Royo C, Palomero J, Salaverria I, Balint B, Martín-Guerrero I, Agirre X, Lujambio A, Richter J, Xargay-Torrent S, Bea S, Hernandez L, Enjuanes A, Calasanz MJ, Rosenwald A, Ott G, Roman-Gomez J, Prosper F, Esteller M, Jares P, Siebert R, Campo E, Martín-Subero JI, Amador V, Epigenetic activation of SOX11 in lymphoid neoplasms by histone modifications., PLoS One,2011-01-01,6,e21382, Abstract

U937 cells
Spicuglia S, Vincent-Fabert C, Benoukraf T, Tibéri G, Saurin AJ, Zacarias-Cabeza J, Grimwade D, Mills K, Calmels B, Bertucci F, Sieweke M, Ferrier P, Duprez E, Characterisation of genome-wide PLZF/RARA target genes., PLoS One,2011-01-01,6,e24176, http://www.pubmed.org/21949697

Zebrafish - fibroblasts
Lindeman LC, Reiner AH, Mathavan S, Aleström P, Collas P,Tiling histone H3 lysine 4 and 27 methylation in zebrafish using high-density microarrays., PLoS One,2010-12-20,5,e15651, Abstract

HEK293 cells
Vogler C, Huber C, Waldmann T, Ettig R, Braun L, Izzo A, Daujat S, Chassignet I, Lopez-Contreras AJ, Fernandez-Capetillo O, Dundr M, Rippe K, Längst G, Schneider R, Histone H2A C-terminus regulates chromatin dynamics, remodeling, and histone H1 binding., PLoS Genet,2010-12-09,6,e1001234, Abstract

Cells: AKR1, CES3, KES1, SF1-1, Sv6.1, TMAS21G
Wood MD, Hiura H, Tunster S, Arima T, Shin J-H, Higgins M, John1 RM, Autonomous silencing of the imprinted Cdkn1c gene in stem cells, Epigenetics,2010-04-01,5,214-221, Abstract

HEK293T cells, NT-2 cells
Buschbeck M, Uribesalgo I, Wibowo I, Rué P, Martin D, Gutierrez A, Morey L, Guigó R, López-Schier H, Di Croce L, The histone variant macroH2A is an epigenetic regulator of key developmental genes., Nat Struct Mol Biol,2009-10-01,16,1074-9, Abstract

ES cells
Marks H, Chow JC, Denissov S, Françoijs KJ, Brockdorff N, Heard E, Stunnenberg HG, High-resolution analysis of epigenetic changes associated with X inactivation., Genome Res,2009-08-01,19,1361-73, Abstract

HCT116 cells
Simmer F, Brinkman AB, Assenov Y, Matarese F, Kaan A, Sabatino L, Villanueva A, Huertas D, Esteller M, Lengauer T, Bock C, Colantuoni V, Altucci L, Stunnenberg HG., Comparative genome-wide DNA methylation analysis of colorectal tumor and matched normal tissues, Epigenetics,2012-12-1,7,1355-67, Abstract

Monocytes
Kleinnijenhuis J, Quintin J, Preijers F, Joosten LA, Ifrim DC, Saeed S, Jacobs C, van Loenhout J, de Jong D, Stunnenberg HG, Xavier RJ, van der Meer JW, van Crevel R, Netea MG, Bacille Calmette-Guerin induces NOD2-dependent nonspecific protection from reinfection via epigenetic reprogramming of monocytes., Proc Natl Acad Sci U S A,2012-09-17, Abstract

MCF7 cells
Phalke S, Mzoughi S, Bezzi M, Jennifer N, Mok WC, Low DH, Thike AA, Kuznetsov VA, Tan PH, Voorhoeve PM, Guccione E, p53-Independent regulation of p21Waf1/Cip1 expression and senescence by PRMT6., Nucleic Acids Res,2012-09-16, Abstract

NB4 cells
Saeed S, Logie C, Francoijs KJ, Frigè G, Romanenghi M, Nielsen FG, Raats L, Shahhoseini M, Huynen M, Altucci L, Minucci S, Martens JH, Stunnenberg HG, Chromatin accessibility, p300 and histone acetylation define PML-RARα and AML1-ETO binding sites in acute myeloid leukemia., Blood,2012-08-24, Abstract

Monocytes
Quintin J, Saeed S, Martens JH, Giamarellos-Bourboulis EJ, Ifrim DC, Logie C, Jacobs L, Jansen T, Kullberg BJ, Wijmenga C, Joosten LA, Xavier RJ, van der Meer JW, Stunnenberg HG, Netea MG, Candida albicans Infection Affords Protection against Reinfection via Functional Reprogramming of Monocytes., Cell Host Microbe,2012-08-16,12,223-32, Abstract

Zebrafish - embryos
Bogdanovic O, Fernandez-Minan A, Tena JJ, de Lacalle-Mustienes E, Hidalgo C, van Kruysbergen I, van Heeringen SJ, Veenstra GJ, Gomez-Skarmeta JL, Dynamics of enhancer chromatin signatures mark the transition from pluripotency to cell specification during embryogenesis., Genome Res,2012-05-16, Abstract

HCT116 cells, ES cells
Brinkman AB, Gu H, Bartels SJ, Zhang Y, Matarese F, Simmer F, Marks H, Bock C, Gnirke A, Meissner A, Stunnenberg HG, Sequential ChIP-bisulfite sequencing enables direct genome-scale investigation of chromatin and DNA methylation cross-talk., Genome Res,2012-03-30, Abstract

Mouse – germ cells
Henckel A, Chebli K, Kota SK, Arnaud P, Feil R, Transcription and histone methylation changes correlate with imprint acquisition in male germ cells., EMBO J,2012-02-01,31,606-615, Abstract

Human embryonic stem cells
Iliou MS, Lujambio A, Portela A, Brüstle O, Koch P, Andersson-Vincent PH, Sundström E, Hovatta O, Esteller M,Bivalent histone modifications in stem cells poise miRNA loci for CpG island hypermethylation in human cancer.,Epigenetics,2011-11-01,6,1344-53,http://www.pubmed.org/22048248

Yeast
Ribeyre Cyril, Shore David, Anticheckpoint pathways at telomeres in yeast, Nature Structural & Molecular Biology,2012-02-12, Abstract

ASCs cells, fibroblasts, keratinocytes, NCCIT cells
Barrand S, Collas P, Chromatin states of core pluripotency-associated genes in pluripotent, multipotent and differentiated cells., Biochem Biophys Res Commun,2010-01-01,391,762-7, Abstract

Yeast
Ribeyre Cyril, Shore David, Anticheckpoint pathways at telomeres in yeast, Nature Structural & Molecular Biology,2012-02-12, Abstract

Yeast
Ribeyre Cyril, Shore David, Anticheckpoint pathways at telomeres in yeast, Nature Structural & Molecular Biology,2012-02-12, Abstract

ASCs cells, NCCIT cells, SF cells
Barrand S, Andersen IS, Collas P, Promoter-exon relationship of H3 lysine 9, 27, 36 and 79 methylation on pluripotency-associated genes., Biochem Biophys Res Commun,2010-10-29,401,611-7, Abstract

ASCs cells, fibroblasts, keratinocytes, NCCIT cells
Barrand S, Collas P, Chromatin states of core pluripotency-associated genes in pluripotent, multipotent and differentiated cells., Biochem Biophys Res Commun,2010-01-01,391,762-7, Abstract

A-549 cells
Baird AM, Leonard J, Naicker KM, Kilmartin L, O'Byrne KJ, Gray SG, IL-23 is pro-proliferative, epigenetically regulated and modulated by chemotherapy in non-small cell lung cancer., Lung Cancer,2012-10-29, Abstract

U937 cells
Stolfa DA, Stefanachi A, Gajer JM, Nebbioso A, Altucci L, Cellamare S, Jung M, Carotti A ,Design, Synthesis, and Biological Evaluation of 2-Aminobenzanilide Derivatives as Potent and Selective HDAC Inhibitors., ChemMedChem,2012-05-24, Abstract

Cells: CCRF-SB, HSB2, Jurkat, KARPAS45, Nalm6, RS4
Waanders E, Scheijen B, van der Meer LT, van Reijmersdal SV, van Emst L, Kroeze Y, Sonneveld E, Hoogerbrugge PM, Geurts van Kessel A, van Leeuwen FN., Kuiper RP, The Origin and Nature of Tightly Clustered BTG1 Deletions in Precursor B-Cell Acute Lymphoblastic Leukemia Support a Model of Multiclonal Evolution, PLoS Genetics,2012-02-16,8,e1002533,
Abstract

Cells : HAFTL, RAW and C10
Rodríguez-Ubreva J, Ciudad L, Gómez-Cabrero D, Parra M, Bussmann LH, di Tullio A, Kallin EM, Tegnér J, Graf T, Ballestar E, Pre-B cell to macrophage transdifferentiation without significant promoter DNA methylation changes., Nucleic Acids Res,2011-11-15, Abstract

549 cells
Baird AM, Gray SG, O'Byrne KJ, IL-20 is epigenetically regulated in NSCLC and down regulates the expression of VEGF., Eur J Cancer,2011-08-01,47,1908-18, Abstract

Human – aortic specimens
Gomez D, Coyet A, Ollivier V, Jeunemaitre X, Jondeau G, Michel JB, Vranckx R, Epigenetic control of vascular smooth muscle cells in Marfan and non-Marfan thoracic aortic aneurysms., Cardiovasc Res,2011-02-01,89,446-56, Abstract

A-549 cells
O'Byrne Kenneth J., Baird Anne-Marie, Kilmartin Lisa, Leonard Jennifer, Sacevich Calen, Gray Steven G., Epigenetic Regulation of Glucose Transporters in Non-Small Cell Lung Cancer, 2011-01-01,3,1550-1565, Abstract

Cell lines
Vegliante MC, Royo C, Palomero J, Salaverria I, Balint B, Martín-Guerrero I, Agirre X, Lujambio A, Richter J, Xargay-Torrent S, Bea S, Hernandez L, Enjuanes A, Calasanz MJ, Rosenwald A, Ott G, Roman-Gomez J, Prosper F, Esteller M, Jares P, Siebert R, Campo E, Martín-Subero JI, Amador V, Epigenetic activation of SOX11 in lymphoid neoplasms by histone modifications., PLoS One,2011-01-01,6,e21382, Abstract

NB4 cells
Martens JH, Brinkman AB, Simmer F, Françoijs KJ, Nebbioso A, Ferrara F, Altucci L, Stunnenberg HG, PML-RARalpha/RXR Alters the Epigenetic Landscape in Acute Promyelocytic Leukemia., Cancer Cell,2010-02-17,17,173-85, Abstract

NSCLC cells
Gray SG, Al-Sarraf N, Baird AM, Cathcart MC, McGovern E, O'Byrne KJ., Regulation of EP receptors in non-small cell lung cancer by epigenetic modifications., Eur J Cancer.,2009-11,45,3087-97, Abstract

Cells: HT29, LS174T, PANC-1
Vincent A, Perrais M, Desseyn JL, Aubert JP, Pigny P, Van Seuningen I, Epigenetic regulation (DNA methylation, histone modifications) of the 11p15 mucin genes (MUC2, MUC5AC, MUC5B, MUC6) in epithelial cancer cells., Oncogene,2007-10-04,26,6566-76, Abstract

A-549 cells
Baird AM, Leonard J, Naicker KM, Kilmartin L, O'Byrne KJ, Gray SG, IL-23 is pro-proliferative, epigenetically regulated and modulated by chemotherapy in non-small cell lung cancer., Lung Cancer,2012-10-29, Abstract

SH-SY5Y cells
Barrachina M, Moreno J, Villar-Menéndez I, Juvés S, Ferrer I, Histone tail acetylation in brain occurs in an unpredictable fashion after death., Cell Tissue Bank,2011-09-16, Abstract

HEK293 cells
Schenk R, Jenke A, Zilbauer M, Wirth S, Postberg J, H3.5 is a novel hominid-specific histone H3 variant that is specifically expressed in the seminiferous tubules of human testes., Chromosoma,2011-06-01,120,275-85, Abstract

549 cells
Baird AM, Gray SG, O'Byrne KJ ,IL-20 is epigenetically regulated in NSCLC and down regulates the expression of VEGF., Eur J Cancer,2011-08-01,47,1908-18, Abstract

A-549 cells
O'Byrne Kenneth J., Baird Anne-Marie, Kilmartin Lisa, Leonard Jennifer, Sacevich Calen, Gray Steven G., Epigenetic Regulation of Glucose Transporters in Non-Small Cell Lung Cancer, 2011-01-01,3,1550-1565, Abstract

Calu-1 (NSCLC) cells, MRC5 cells
Incoronato M, Urso L, Portela A, Laukkanen MO, Soini Y, Quintavalle C, Keller S, Esteller M, Condorelli G, Epigenetic regulation of miR-212 expression in lung cancer., PLoS One,2011-01-01,6,e27722, Abstract

P. falciparum
Bártfai R, Hoeijmakers WA, Salcedo-Amaya AM, Smits AH, Janssen-Megens E, Kaan A, Treeck M, Gilberger TW, Françoijs KJ, Stunnenberg HG, H2A.Z demarcates intergenic regions of the plasmodium falciparum epigenome that are dynamically marked by H3K9ac and H3K4me3., PLoS Pathog,2010-12-16,6,e1001223, Abstract

NSCLC cells
Gray SG, Al-Sarraf N, Baird AM, Cathcart MC, McGovern E, O'Byrne KJ., Regulation of EP receptors in non-small cell lung cancer by epigenetic modifications., Eur J Cancer.,2009-11,45,3087-97, Abstract

Blastocysts
Fernandez-Gonzalez R, Ramirez MA, Pericuesta E, Calle A, Gutierrez-Adan A, Histone modifications at the blastocyst Axin1(Fu) locus mark the heritability of in vitro culture-induced epigenetic alterations in mice., Biol Reprod,2010-11-01,83,720-7, Abstract

P. falciparum
Flueck C, Bartfai R, Volz J, Niederwieser I, Salcedo-Amaya AM, Alako BT, Ehlgen F, Ralph SA, Cowman AF, Bozdech Z, Stunnenberg HG, Voss TS, Plasmodium falciparum heterochromatin protein 1 marks genomic loci linked to phenotypic variation of exported virulence factors., PLoS Pathog,2009-09-01,5,e1000569, Abstract

NCCIT cells
Dahl JA, Collas P, A rapid micro chromatin immunoprecipitation assay (microChIP)., Nat Protoc,2008-01-01,3,1032-45, Abstract

ASCs cells, fibroblasts, keratinocytes, NCCIT cells
Barrand S, Collas P, Chromatin states of core pluripotency-associated genes in pluripotent, multipotent and differentiated cells., Biochem Biophys Res Commun,2010-01-01,391,762-7, Abstract

Human – aortic specimens
Gomez D, Coyet A, Ollivier V, Jeunemaitre X, Jondeau G, Michel JB, Vranckx R, Epigenetic control of vascular smooth muscle cells in Marfan and non-Marfan thoracic aortic aneurysms., Cardiovasc Res,2011-02-01,89,446-56, Abstract

Cell lines
Vegliante MC, Royo C, Palomero J, Salaverria I, Balint B, Martín-Guerrero I, Agirre X, Lujambio A, Richter J, Xargay-Torrent S, Bea S, Hernandez L, Enjuanes A, Calasanz MJ, Rosenwald A, Ott G, Roman-Gomez J, Prosper F, Esteller M, Jares P, Siebert R, Campo E, Martín-Subero JI, Amador V, Epigenetic activation of SOX11 in lymphoid neoplasms by histone modifications., PLoS One,2011-01-01,6,e21382, Abstract

Plants – A. thaliana
Rehrauer H, Aquino C, Gruissem W, Henz SR, Hilson P, Laubinger S, Naouar N, Patrignani A, Rombauts S, Shu H, Van de Peer Y, Vuylsteke M, Weigel D, Zeller G, Hennig L, AGRONOMICS1: a new resource for Arabidopsis transcriptome profiling., Plant Physiol,2010-02-01,152,487-99, Abstract

A-549 cells
Baird AM, Leonard J, Naicker KM, Kilmartin L, O'Byrne KJ, Gray SG, IL-23 is pro-proliferative, epigenetically regulated and modulated by chemotherapy in non-small cell lung cancer., Lung Cancer,2012-10-29, Abstract

Blastocysts
Fernandez-Gonzalez R, Ramirez MA, Pericuesta E, Calle A, Gutierrez-Adan A, Histone modifications at the blastocyst Axin1(Fu) locus mark the heritability of in vitro culture-induced epigenetic alterations in mice., Biol Reprod,2010-11-01,83,720-7, Abstract

ASC cells
Noer A, Lindeman LC, Collas P, Histone H3 modifications associated with differentiation and long-term culture of mesenchymal adipose stem cells., Stem Cells Dev,2009-06-01,18,725-36, Abstract

ASCs cells
Boulland JL, Mastrangelopoulou M, Boquest AC, Jakobsen R, Noer A, Glover JC, Collas P., Epigenetic Regulation of Nestin Expression During Neurogenic Differentiation of Adipose Tissue Stem Cells., Stem Cells Dev.,2012-12-21, Abstract

F9 cells
Herzog M, Josseaux E, Dedeurwaerder S, Calonne E, Volkmar M, Fuks F, The histone demethylase Kdm3a is essential to progression through differentiation., Nucleic Acids Res,2012-05-11, Abstract

Hippocampus
Bahari-Javan S, Maddalena A, Kerimoglu C, Wittnam J, Held T, Bähr M, Burkhardt S, Delalle I, Kügler S, Fischer A, Sananbenesi F,HDAC1 Regulates Fear Extinction in Mice., J Neurosci,2012-04-11,32,5062-5073, Abstract

HCC1954 cells, HMEC cells
Hon GC, Hawkins RD, Caballero OL, Lo C, Lister R, Pelizzola M, Valsesia A, Ye Z, Kuan S, Edsall LE, Camargo AA, Stevenson BJ, Ecker JR, Bafna V, Strausberg RL, Simpson AJ, Ren B, Global DNA hypomethylation coupled to repressive chromatin domain formation and gene silencing in breast cancer., Genome Res,2012-02-01,22,246-58, Abstract

Zebrafish - embryos
Lindeman LC, Andersen IS, Reiner AH, Li N, Aanes H, Østrup O, Winata C, Mathavan S, Müller F, Aleström P, Collas P, Prepatterning of developmental gene expression by modified histones before zygotic genome activation., Dev Cell,2011-12-13,21,993-1004, Abstract

549 cells
Baird AM, Gray SG, O'Byrne KJ, IL-20 is epigenetically regulated in NSCLC and down regulates the expression of VEGF., Eur J Cancer,2011-08-01,47,1908-18, Abstract

HEK293 cells
Schenk R, Jenke A, Zilbauer M, Wirth S, Postberg J, H3.5 is a novel hominid-specific histone H3 variant that is specifically expressed in the seminiferous tubules of human testes., Chromosoma,2011-06-01,120,275-85, Abstract

Cells: ES, MEF, neuronal progenitor cells
Cortázar D, Kunz C, Selfridge J, Lettieri T, Saito Y, MacDougall E, Wirz A, Schuermann D, Jacobs AL, Siegrist F, Steinacher R, Jiricny J, Bird A, Schär P, Embryonic lethal phenotype reveals a function of TDG in maintaining epigenetic stability., Nature,2011-02-17,470,419-23, Abstract

Human – ES cells
Blahnik KR, Dou L, Echipare L, Iyengar S, O'Geen H, Sanchez E, Zhao Y, Marra MA, Hirst M, Costello JF, Korf I, Farnham PJ, Characterization of the contradictory chromatin signatures at the 3' exons of zinc finger genes., PLoS One,2011-02-15,6,e17121, Abstract

Human – aortic specimens
Gomez D, Coyet A, Ollivier V, Jeunemaitre X, Jondeau G, Michel JB, Vranckx R, Epigenetic control of vascular smooth muscle cells in Marfan and non-Marfan thoracic aortic aneurysms., Cardiovasc Res,2011-02-01,89,446-56, Abstract

K562 cells
Frietze S, O'Geen H, Blahnik KR, Jin VX, Farnham PJ, ZNF274 recruits the histone methyltransferase SETDB1 to the 3' ends of ZNF genes., PLoS One,2010-12-08,5,e15082, Abstract

Cells - ASCs, BMMSC, HPC, MPC
Sørensen AL, Jacobsen BM, Reiner AH, Andersen IS, Collas P, Promoter DNA Methylation Patterns of Differentiated Cells Are Largely Programmed at the Progenitor Stage, Molecular Biology of the Cell,2010-06-15,21,2066-2077, Abstract

Cells: C2C12, HeLa, MSC
Delbarre E, Jacobsen BM, Reiner AH, Sørensen AL, Kuntziger T, Collas P, Chromatin Environment of Histone Variant H3.3 Revealed by Quantitative Imaging and Genome-scale Chromatin and DNA Immunoprecipitation, Molecular Biology of the Cell,2010-06-01,21,1872-1884, Abstract

Mouse - retina
Kizilyaprak C, Spehner D, Devys D, Schultz P, In vivo chromatin organization of mouse rod photoreceptors correlates with histone modifications., PLoS One,2010-01-01,5,e11039, Abstract

Human - brain
Al-Mahdawi S, Pinto RM, Ismail O, Varshney D, Lymperi S, Sandi C, Trabzuni D, Pook M, The Friedreich ataxia GAA repeat expansion mutation induces comparable epigenetic changes in human and transgenic mouse brain and heart tissues., Hum Mol Genet,2008-03-01,17,735-46, Abstract

NCCIT cells
Dahl JA, Collas P, MicroChIP--a rapid micro chromatin immunoprecipitation assay for small cell samples and biopsies.,Nucleic Acids Res,2008-02-01,36,e15, Abstract

NCCIT cells
Dahl JA, Reiner AH, Collas P., Fast genomic muChIP-chip from 1,000 cells, Genome Biol,2009-02-09,10,R13, Abstract

NCCIT cells
Dahl JA, Collas P, A rapid micro chromatin immunoprecipitation assay (microChIP)., Nat Protoc,2008-01-01,3,1032-45, Abstract

U937 cells
Valente S, Lepore I, Dell'aversana C, Tardugno M, Castellano S, Sbardella G, Tomassi S, Di Maro S, Novellino E, Di Santo R, Costi R, Altucci L, Mai A, Identification of PR-SET7 and EZH2 selective inhibitors inducing cell death in human leukemia U937 cells., Biochimie,2012-06-16, Abstract

Human – aortic specimens
Gomez D, Coyet A, Ollivier V, Jeunemaitre X, Jondeau G, Michel JB, Vranckx R, Epigenetic control of vascular smooth muscle cells in Marfan and non-Marfan thoracic aortic aneurysms., Cardiovasc Res,2011-02-01,89,446-56, Abstract

HEK293
Tardat M, Brustel J, Kirsh O, Lefevbre C, Callanan M, Sardet C, Julien E, The histone H4 Lys 20 methyltransferase PR-Set7 regulates replication origins in mammalian cells., Nat Cell Biol,2010-11-01,12,1086-93, Abstract

C. elegans - embryos
Vielle A, Lang J, Dong Y, Ercan S, Kotwaliwale C, Rechtsteiner A, Appert A, Chen QB, Dose A, Egelhofer T, Kimura H, Stempor P, Dernburg A, Lieb JD, Strome S, Ahringer J, H4K20me1 Contributes to Downregulation of X-Linked Genes for C. elegans Dosage Compensation, 2012-09-13,8,e1002933, Abstract

Blastocysts
Fernandez-Gonzalez R, Ramirez MA, Pericuesta E, Calle A, Gutierrez-Adan A, Histone modifications at the blastocyst Axin1(Fu) locus mark the heritability of in vitro culture-induced epigenetic alterations in mice., Biol Reprod,2010-11-01,83,720-7, Abstract

Drosophila
Coléno-Costes A, Jang SM, de Vanssay A, Rougeot J, Bouceba T, Randsholt NB, Gibert JM, Le Crom S, Mouchel-Vielh E, Bloyer S, Peronnet F, New partners in regulation of gene expression: the enhancer of trithorax and polycomb corto interacts with methylated ribosomal protein l12 via its chromodomain., PLoS Genet,2012-10-11,8,e1003006, Abstract

Fibroblasts
Janzer A, Stamm K, Becker A, Zimmer A, Buettner R, Kirfel J ,The H3K4me3 histone demethylase Fbxl10 is a regulator of chemokine expression, cellular morphology and the metabolome of fibroblasts, J. Biol. Chem.,2012-07-23, Abstract

A431 cells
Koopmansch B, Berx G, Foidart J-M, Gilles C, Winkler R, Interplay between KLF4 and ZEB2/SIP1 in the regulation of E-cadherin expression, Biochemical and Biophysical Research Communications,2013-01-29, Abstract

JB6 cells
Ghantous A, Saikali M, Rau T, Gali-Muhtasib H, Schneider-Stock R, Darwiche N, Inhibition of Tumor Promotion by Parthenolide: Epigenetic Modulation of p21., Cancer Prev Res (Phila),2012-11-01,5,1298-309, Abstract

DU145 cells
Wang R, Asangani IA, Chakravarthi BV, Ateeq B, Lonigro RJ, Cao Q, Mani RS, Camacho DF, McGregor N, Schumann TE, Jing X, Menawat R, Tomlins SA, Zheng H, Otte AP, Mehra R, Siddiqui J, Dhanasekaran SM, Nyati MK, Pienta KJ, Palanisamy N, Kunju LP, Rubin MA, Chinnaiyan AM, Varambally S., Role of Transcriptional Corepressor CtBP1 in Prostate Cancer Progression, Neoplasia,2012-10,14,905-14, Abstract

HEK293T cells, MEF cells
Terrados G, Finkernagel F, Stielow B, Sadic D, Neubert J, Herdt O, Krause M, Scharfe M, Jarek M, Suske G, Genome-wide localization and expression profiling establish Sp2 as a sequence-specific transcription factor regulating vitally important genes., Nucleic Acids Res,2012-06-07, Abstract

HepG2 cells, MDAMB231 cells
Janzer Andreas, Lim Soyoung, Fronhoffs Florian, Niazy Naima, Buettner Reinhard, Kirfel Jutta, Lysine-specific demethylase 1 (LSD1) and histone deacetylase 1 (HDAC1) synergistically repress proinflammatory cytokines and classical complement pathway components., 2012-05-18,421,665-70, Abstract

Plants – A. thaliana
Rigal M, Kevei Z, Pélissier T, Mathieu O, DNA methylation in an intron of the IBM1 histone demethylase gene stabilizes chromatin modification patterns., EMBO J,2012-05-11, Abstract

Mouse - prostates
Viennois E, Esposito T, Dufour J, Pommier A, Fabre S, Kemeny JL, Guy L, Morel L, Lobaccaro JM, Baron S, Lxrα Regulates the Androgen Response in Prostate Epithelium., Endocrinology,2012-04-30, Abstract

Monocytes
Horejs-Hoeck J, Schwarz H, Lamprecht S, Maier E, Hainzl S, Schmittner M, Posselt G, Stoecklinger A, Hawranek T, Duschl A, Dendritic Cells Activated by IFN-γ/STAT1 Express IL-31 Receptor and Release Proinflammatory Mediators upon IL-31 Treatment., J Immunol,2012-04-25, Abstract

SW1353 cells
Hirata M, Kugimiya F, Fukai A, Saito T, Yano F, Ikeda T, Mabuchi A, Sapkota BR, Akune T, Nishida N, Yoshimura N, Nakagawa T, Tokunaga K, Nakamura K, Chung UI, Kawaguchi H, C/EBPβ and RUNX2 cooperate to degrade cartilage with MMP-13 as the target and HIF-2α as the inducer in chondrocytes., Hum Mol Genet,2012-03-01,21,1111-23, Abstract

Mouse
Winkler R, Benz V, Clemenz M, Bloch M, Foryst-Ludwig A, Wardat S, Witte N, Trappiel M, Namsolleck P, Mai K, Spranger J, Matthias G, Roloff T, Truee O, Kappert K, Schupp M, Matthias P, Kintscher U, Histone deacetylase 6 (HDAC6) is an essential modifier of glucocorticoid-induced hepatic gluconeogenesis., Diabetes,2012-02-01,61,513-23, Abstract

H522 cells
Castillo SD, Matheu A, Mariani N, Carretero J, Lopez-Rios F, Lovell-Badge R, Sanchez-Cespedes M ,Novel transcriptional targets of the SRY-HMG box transcription factor SOX4 link its expression to the development of small cell lung cancer., Cancer Res,2012-01-01,72,176-86, Abstract

VSMCs cells
Bloch M, Prock A, Paonessa F, Benz V, Bähr IN, Herbst L, Witt H, Kappert K, Spranger J, Stawowy P, Unger T, Fusco A, Sedding D, Brunetti A, Foryst-Ludwig A, Kintscher U, High-Mobility Group A1 Protein: A New Coregulator of Peroxisome Proliferator-Activated Receptor-γ-Mediated Transrepression in the Vasculature., Circ Res,2011-12-29, Abstract

Blood samples
Jungebluth P, Alici E, Baiguera S, Le Blanc K, Blomberg P, Bozóky B, Crowley C, Einarsson O, Grinnemo KH, Gudbjartsson T, Le Guyader S, Henriksson G, Hermanson O, Juto JE, Leidner B, Lilja T, Liska J, Luedde T, Lundin V, Moll G, Nilsson B, Roderburg C, Strömblad S, Sutlu T, Teixeira AI, Watz E, Seifalian A, Macchiarini P. ,Tracheobronchial transplantation with a stem-cell-seeded bioartificial nanocomposite: a proof-of-concept study., Lancet.,2011-12-10,378,1997-2004, Abstract

Human embryonic stem cells
Iliou MS, Lujambio A, Portela A, Brüstle O, Koch P, Andersson-Vincent PH, Sundström E, Hovatta O, Esteller M, Bivalent histone modifications in stem cells poise miRNA loci for CpG island hypermethylation in human cancer., Epigenetics,2011-11-01,6,1344-53, Abstract

Chicken – embryos
Acloque H, Ocaña OH, Matheu A, Rizzoti K, Wise C, Lovell-Badge R, Nieto MA, Reciprocal repression between Sox3 and snail transcription factors defines embryonic territories at gastrulation., Dev Cell,2011-09-13,21,546-58, Abstract

HEK293T and HeLa cells
Kraft M, Cirstea IC, Voss AK, Thomas T, Goehring I, Sheikh BN, Gordon L, Scott H, Smyth GK, Ahmadian MR, Trautmann U, Zenker M, Tartaglia M, Ekici A, Reis A, Dörr HG, Rauch A, Thiel CT, Disruption of the histone acetyltransferase MYST4 leads to a Noonan syndrome-like phenotype and hyperactivated MAPK signaling in humans and mice., J Clin Invest,2011-09-01,121,3479-91, Abstract

Mouse – ES cells
Tamm C, Böwer N, Annerén C, Regulation of mouse embryonic stem cell self-renewal by a Yes-YAP-TEAD2 signaling pathway downstream of LIF., J Cell Sci,2011-04-01,124,1136-44, Abstract

Blood samples
Singh NP, Madabhushi SR, Srivastava S, Senthilkumar R, Neeraja C, Khosla S, Mishra RK, Epigenetic profile of the euchromatic region of human Y chromosome., Nucleic Acids Res,2011-05-01,39,3594-606, Abstract

CD4+ cells
Maier E, Hebenstreit D, Posselt G, Hammerl P, Duschl A, Horejs-Hoeck J, Inhibition of suppressive T cell factor 1 (TCF-1) isoforms in naive CD4+ T cells is mediated by IL-4/STAT6 signaling., J Biol Chem,2011-01-14,286,919-28, Abstract

eWo cells, HEK293, placenta
Nakaya Y, Shojima T, Yasuda J, Imakawa K, Miyazawa T, Epigenetic regulation on the 5'-proximal CpG island of human porcine endogenous retrovirus subgroup A receptor 2/GPR172B., Microbes Infect,2011-01-01,13,49-57, Abstract

Cell lines
Vegliante MC, Royo C, Palomero J, Salaverria I, Balint B, Martín-Guerrero I, Agirre X, Lujambio A, Richter J, Xargay-Torrent S, Bea S, Hernandez L, Enjuanes A, Calasanz MJ, Rosenwald A, Ott G, Roman-Gomez J, Prosper F, Esteller M, Jares P, Siebert R, Campo E, Martín-Subero JI, Amador V, Epigenetic activation of SOX11 in lymphoid neoplasms by histone modifications., PLoS One,2011-01-01,6,e21382, Abstract

Fibroblasts
Hauke J, Riessland M, Lunke S, Eyüpoglu IY, Blümcke I, El-Osta A, Wirth B, Hahnen E, Survival motor neuron gene 2 silencing by DNA methylation correlates with spinal muscular atrophy disease severity and can be bypassed by histone deacetylase inhibition., Hum Mol Genet,2009-01-15,18,304-17, Abstract

Plants – A. thaliana
Exner V, Aichinger E, Shu H, Wildhaber T, Alfarano P, Caflisch A, Gruissem W, Köhler C, Hennig L, The chromodomain of LIKE HETEROCHROMATIN PROTEIN 1 is essential for H3K27me3 binding and function during Arabidopsis development., PLoS One,2009-01-01,4,e5335, Abstract

MCF7 cells
Gilfillan S, Fiorito E, Hurtado A, Functional Genomic Methods to Study Estrogen Receptor Activity., J Mammary Gland Biol Neoplasia,2012-05-16, Abstract

MCF7 cells
Welboren WJ, van Driel MA, et al., ChIP-Seq of ERalpha and RNA polymerase II defines genes differentially responding to ligands., EMBO J.,2009,28,1418-1428, Abstract

MCF7 cells
Fullwood MJ, Liu MH, Pan YF, Liu J, Xu H, Mohamed YB, Orlov YL, Velkov S, Ho A, Mei PH, Chew EG, Huang PY, Welboren WJ, Han Y, Ooi HS, Ariyaratne PN, Vega VB, Luo Y, Tan PY, Choy PY, Wansa KD, Zhao B, Lim KS, Leow SC, Yow JS, Joseph R, Li H, Desai KV, Thomsen JS, Lee YK, Karuturi RK, Herve T, Bourque G, Stunnenberg HG, Ruan X, Cacheux-Rataboul V, Sung WK, Liu ET, Wei CL, Cheung E, Ruan Y, An oestrogen-receptor-alpha-bound human chromatin interactome., Nature,2009-11-05,462,58-64, Abstract

HeLa cells
Rao NA, McCalman MT, Moulos P, Françoijs KJ, Chatziioannou A, Kolisis FN, Alexis MN, Mitsiou DJ, Stunnenberg HG, Coactivation of GR and NFKB alters the repertoire of their binding sites and target genes., Genome Res,2011-09-01,21,1404-16, Abstract

HEK293T cells
Szanto A, Balint BL, Nagy ZS, Barta E, Dezso B, Pap A, Szeles L, Poliska S, Oros M, Evans RM, Barak Y, Schwabe J, Nagy L, STAT6 transcription factor is a facilitator of the nuclear receptor PPARγ-regulated gene expression in macrophages and dendritic cells., Immunity,2010-11-24,33,699-712, Abstract

Brain – mouse and rat
Sato H, Fukutani Y, Yamamoto Y, Tatara E, Takemoto M, Shimamura K, Yamamoto N, Thalamus-derived molecules promote survival and dendritic growth of developing cortical neurons., J Neurosci,2012-10-31,32,15388-402, Abstract

Brain – mouse
Terakawa YW, Inoue YU, Asami J, Hoshino M, Inoue T, A Sharp Cadherin-6 Gene Expression Boundary in the Developing Mouse Cortical Plate Demarcates the Future Functional Areal Border., Cereb Cortex,2012-08-08, Abstract

P. falciparum
Zhu X, Yahata K, Alexandre JS, Tsuboi T, Kaneko O, The N-terminal segment of Plasmodium falciparum SURFIN(4.1) is required for its trafficking to the red blood cell cytosol through the endoplasmic reticulum., Parasitol Int,2012-12-31, Abstract

293T cells
Costessi A, Mahrour N, Sharma V, Stunnenberg R, Stoel MA, Tijchon E, Conaway JW, Conaway RC, Stunnenberg HG, The Human EKC/KEOPS Complex Is Recruited to Cullin2 Ubiquitin Ligases by the Human Tumour Antigen PRAME., PLoS One,2012-08-13,7,e42822, Abstract

Trypanosoma brucei
Pusnik M, Mani J, Schmidt O, Niemann M, Oeljeklaus S, Schnarwiler F, Warscheid B, Lithgow T, Meisinger C, Schneider A., An essential novel component of the non-canonical mitochondrial outer membrane protein import system of trypanosomatids., Mol Biol Cell. ,2012-07-11, Abstract

Yeast
Suzuki K, Morimoto M, Kondo C, Ohsumi Y, Selective autophagy regulates insertional mutagenesis by the Ty1 retrotransposon in Saccharomyces cerevisiae., Dev Cell,2011-08-16,21,358-65, Abstract

K562 cells
Costessi A, Mahrour N, Tijchon E, Stunnenberg R, Stoel MA, Jansen PW, Sela D, Martin-Brown S, Washburn MP, Florens L, Conaway JW, Conaway RC, Stunnenberg HG, The tumour antigen PRAME is a subunit of a Cul2 ubiquitin ligase and associates with active NFY promoters., EMBO J,2011-08-05,30,3786-98, Abstract

Mouse – ES cells
Hofemeister H, Ciotta G, Fu J, Seibert PM, Schulz A, Maresca M, Sarov M, Anastassiadis K, Stewart AF, Recombineering, transfection, Western, IP and ChIP methods for protein tagging via gene targeting or BAC transgenesis., Methods,2011-04-01,53,437-52, Abstract

HaCaT cells
Borrelli S, Testoni B, Callari M, Alotto D, Castagnoli C, Romano RA, Sinha S, Viganò AM, Mantovani R, Reciprocal regulation of p63 by C/EBP delta in human keratinocytes., BMC Mol Biol,2007-01-01,8,85, Abstract

CD34+ cells
Martens JH, Mandoli A, Simmer F, Wierenga BJ, Saeed S, Singh AA, Altucci L, Vellenga E, Stunnenberg HG ,ERG and FLI1 binding sites demarcate targets for aberrant epigenetic regulation by AML1-ETO in acute myeloid leukemia., Blood,2012-09-14, Abstract

Xenopus – embryos
Akkers RC, Jacobi UG, Veenstra GJ., Chromatin Immunoprecipitation Analysis of Xenopus Embryos, Methods Mol Biol.,2012-08-01,917,279-92, Abstract

ES cells
Marks H, Kalkan T, Menafra R, Denissov S, Jones K, Hofemeister H, Nichols J, Kranz A, Francis Stewart A, Smith A, Stunnenberg HG, The transcriptional and epigenomic foundations of ground state pluripotency., Cell,2012-04-27,149,590-604, Abstract

Mouse – frozen liver
Boergesen M, Pedersen TA, Gross B, van Heeringen SJ, Hagenbeek D, Bindesbøll C, Caron S, Lalloyer F, Steffensen KR, Nebb H, Gustafsson JA, Stunnenberg HG, Staels B, Mandrup S, Genome-wide profiling of LXR, RXR and PPARα in mouse liver reveals extensive sharing of binding sites., Mol Cell Biol,2011-12-12, Abstract

NB4 cells
Ederveen TH, Mandemaker IK, Logie C, The human histone H3 complement anno 2011., Biochim Biophys Acta,2011-10-01,1809,577-86, Abstract

HeLa cells
Rao NA, McCalman MT, Moulos P, Françoijs KJ, Chatziioannou A, Kolisis FN, Alexis MN, Mitsiou DJ, Stunnenberg HG, Coactivation of GR and NFKB alters the repertoire of their binding sites and target genes., Genome Res,2011-09-01,21,1404-16, Abstract

NB4 cells
Martens JH, Brinkman AB, Simmer F, Françoijs KJ, Nebbioso A, Ferrara F, Altucci L, Stunnenberg HG, PML-RARalpha/RXR Alters the Epigenetic Landscape in Acute Promyelocytic Leukemia., Cancer Cell,2010-02-17,17,173-85, Abstract

Mouse - liver
Thoren LA, Nørgaard GA, Weischenfeldt J, Waage J, Jakobsen JS, Damgaard I, Bergström FC, Blom AM, Borup R, Bisgaard HC, Porse BT, UPF2 is a critical regulator of liver development, function and regeneration., PLoS One,2010-01-01,5,e11650, Abstract

Xenopus - embryos
Akkers RC, van Heeringen SJ, Jacobi UG, Janssen-Megens EM, Françoijs KJ, Stunnenberg HG, Veenstra GJ, A hierarchy of H3K4me3 and H3K27me3 acquisition in spatial gene regulation in Xenopus embryos., Dev Cell,2009-09-01,17,425-34, Abstract

ES cells
Marks H, Chow JC, Denissov S, Françoijs KJ, Brockdorff N, Heard E, Stunnenberg HG, High-resolution analysis of epigenetic changes associated with X inactivation., Genome Res,2009-08-01,19,1361-73, Abstract

MCF7 cells
Welboren WJ, van Driel MA, et al., ChIP-Seq of ERalpha and RNA polymerase II defines genes differentially responding to ligands., EMBO J.,2009,28,1418-1428, Abstract

Xenopus - oocytes
Akhtar W, Veenstra GJ, TBP2 is a substitute for TBP in Xenopus oocyte transcription., BMC Biol,2009-01-01,7,45, Abstract

NB4 cells
Martens JH, Brinkman AB, Simmer F, Françoijs KJ, Nebbioso A, Ferrara F, Altucci L, Stunnenberg HG, PML-RARalpha/RXR Alters the Epigenetic Landscape in Acute Promyelocytic Leukemia., Cancer Cell,2010-02-17,17,173-85, Abstract

H522 cells
Castillo SD, Matheu A, Mariani N, Carretero J, Lopez-Rios F, Lovell-Badge R, Sanchez-Cespedes M, Novel transcriptional targets of the SRY-HMG box transcription factor SOX4 link its expression to the development of small cell lung cancer., Cancer Res,2012-01-01,72,176-86, Abstract

HEK293T cells
Génin P, Lin R, Hiscott J, Civas A, Recruitment of histone deacetylase 3 to the interferon-a gene promoters attenuates interferon expression., PLoS One,2012-06-07,7,e38336, Abstract

HeLa cells
Rao NA, McCalman MT, Moulos P, Françoijs KJ, Chatziioannou A, Kolisis FN, Alexis MN, Mitsiou DJ, Stunnenberg HG, Coactivation of GR and NFKB alters the repertoire of their binding sites and target genes., Genome Res,2011-09-01,21,1404-16, Abstract

Mouse – T cell lines
Koch F, Fenouil R, Gut M, Cauchy P, Albert TK, Zacarias-Cabeza J, Spicuglia S, de la Chapelle AL, Heidemann M, Hintermair C, Eick D, Gut I, Ferrier P, Andrau JC, Suppl. information - Transcription initiation platforms and GTF recruitment at tissue-specific enhancers and promoters., Nat Struct Mol Biol,2011-08-01,18,956-63, Abstract

U2OS cells
Smeenk L, van Heeringen SJ, Koeppel M, Gilbert B, Janssen-Megens E, Stunnenberg HG, Lohrum M, Role of p53 serine 46 in p53 target gene regulation., PLoS One,2011-01-01,6,e17574, Abstract

T cell lines
Maruyama T, Li J, Vaque JP, Konkel JE, Wang W, Zhang B, Zhang P, Zamarron BF, Yu D, Wu Y, Zhuang Y, Gutkind JS, Chen W, Control of the differentiation of regulatory T cells and T(H)17 cells by the DNA-binding inhibitor Id3., Nat Immunol,2010-12-05,12,86-95, Abstract

ES cells
Marks H, Chow JC, Denissov S, Françoijs KJ, Brockdorff N, Heard E, Stunnenberg HG, High-resolution analysis of epigenetic changes associated with X inactivation., Genome Res,2009-08-01,19,1361-73, Abstract

U2OS cells
Pitulescu ME, Teichmann M, Luo L, Kessel M, TIPT2 and geminin interact with basal transcription factors to synergize in transcriptional regulation., BMC Biochem,2009-01-01,10,16, Abstract

U2OS cells
Denissov S, van Driel M, Voit R, Hekkelman M, Hulsen T, Hernandez N, Grummt I, Wehrens R, Stunnenberg H., Identification of novel functional TBP-binding sites and general factor repertoires, EMBO J.,2007-02-21,26,944-54, Abstract