Acevedo,, L. G., Leonardo Iniguez,, A., Holster,, H. L., Zhang,, X., Green,, R., & Farnham,, P. J. (2007). Genome‐scale ChIP‐chip analysis using 10,000 human cells. BioTechniques, 43(6), 791–797. http://doi.org/10.2144/000112625
Adli,, M., Zhu,, J., & Bernstein,, B. E. (2010). Genomewide chromatin maps derived from limited numbers of hematopoietic progenitors. Nature Methods, 7(8), 615–618.
Afgan,, E., Baker,, D., van den Beek,, M., Blankenberg,, D., Bouvier,, D., Čech,, M., … Goecks,, J. (2016). The galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update. Nucleic Acids Research, 44(Web Server issue), W3–W10.
Albert,, I., Mavrich,, T. N., Tomsho,, L. P., Qi,, J., Zanton,, S. J., Schuster,, S. C., & Pugh,, B. F. (2007). Translational and rotational settings of H2A.Z nucleosomes across the Saccharomyces cerevisiae genome. Nature, 446, 572–576.
Andreu‐Vieyra,, C. V., Chen,, R., Agno,, J. E., Glaser,, S., Anastassiadis,, K., Stewart,, A. F., & Matzuk,, M. M. (2010). MLL2 is required in oocytes for bulk histone 3 lysine 4 trimethylation and transcriptional silencing. PLoS Biology, 8(8), e1000453. http://doi.org/10.1371/journal.pbio.1000453
Aughey,, G. N., & Southall,, T. D. (2016). Dam it`s good! DamID profiling of protein‐DNA interactions. WIREs Developmental Biology, 5(1), 25–37.
Bailey,, T. L., Johnson,, J., Grant,, C. E., & Noble,, W. S. (2015). The MEME suite. Nucleic Acids Research, 43(Web Server issue), W39–W49.
Barski,, A., Cuddapah,, S., Cui,, K., Roh,, T.‐Y., Schones,, D. E., Wang,, Z., … Zhao,, K. (2007). High‐resolution profiling of histone methylations in the human genome. Cell, 129(4), 823–837.
Blat,, Y., & Kleckner,, N. (1999). Cohesins bind to preferential sites along yeast chromosome III, with differential regulation along arms versus the centric region. Cell, 98(2), 249–259.
Brind`Amour,, J., Liu,, S., Hudson,, M., Chen,, C., Karimi,, M. M., & Lorincz,, M. C. (2015). An ultra‐low‐input native ChIP‐seq protocol for genome‐wide profiling of rare cell populations. Nature Communications, 6, 6033. http://doi.org/10.1038/ncomms7033
Buenrostro,, J. D., Giresi,, P. G., Zaba,, L. C., Chang,, H. Y., & Greenleaf,, W. J. (2013). Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA‐binding proteins and nucleosome position. Nature Methods, 10, 1213–1218.
Cao,, Z., Chen,, C., He,, B., Tan,, K., & Lu,, C. (2015). A microfluidic device for epigenomic profiling using 100 cells. Nature Methods, 12(10), 959–962.
Cejas,, P., Li,, L., O`Neill,, N. K., Duarte,, M., Rao,, P., Bowden,, M., … Long,, H. W. (2016). Chromatin immunoprecipitation from fixed clinical tissues reveals tumor‐specific enhancer profiles. Nature Medicine, 22, 685–691. http://doi.org/10.1038/nm.4085
Clark,, S. J., Smallwood,, S. A., Lee,, H. J., Krueger,, F., Reik,, W., & Kelsey,, G. (2017). Genome‐wide base‐resolution mapping of DNA methylation in single cells using single‐cell bisulfite sequencing (scBS‐seq). Nature Protocols, 12, 534–547.
Crawford,, G. E., Holt,, I. E., Whittle,, J., Webb,, B. D., Tai,, D., Davis,, S., … Collins,, F. S. (2006). Genome‐wide mapping of DNase hypersensitive sites using massively parallel signature sequencing (MPSS). Genome Research, 16(1), 123–131.
Dahl,, J. A., & Collas,, P. (2007). Q 2ChIP, a quick and quantitative chromatin immunoprecipitation assay, unravels epigenetic dynamics of developmentally regulated genes in human carcinoma cells. Stem Cells, 25(4), 1037–1046. http://doi.org/10.1634/stemcells.2006-0430
Dahl,, J. A., & Collas,, P. (2008a). A rapid micro chromatin immunoprecipitation assay (ChIP). Nature Protocols, 3, 1032–1045.
Dahl,, J. A., & Collas,, P. (2008b). MicroChIP—A rapid micro chromatin immunoprecipitation assay for small cell samples and biopsies. Nucleic Acids Research, 36(3), e15–e15. http://doi.org/10.1093/nar/gkm1158
Dahl,, J. A., Jung,, I., Aanes,, H., Greggains,, G. D., Manaf,, A., Lerdrup,, M., … Klungland,, A. (2016). Broad histone H3K4me3 domains in mouse oocytes modulate maternal‐to‐zygotic transition. Nature, 537(7621), 548–552. http://doi.org/10.1038/nature19360
Dahl,, J. A., & Klungland,, A. (2015). Micro chromatin immunoprecipitation (μChIP) from early mammalian embryos. Methods in Molecular Biology (Clifton, N.J.), 1222(Chapter 17), 227–245. http://doi.org/10.1007/978-1-4939-1594-1_17
Dahl,, J. A., Reiner,, A. H., & Collas,, P. (2009). Fast genomic muChIP‐chip from 1,000 cells. Genome Biology, 10(2), R13. http://doi.org/10.1186/gb-2009-10-2-r13
Dahl,, J. A., Reiner,, A. H., Klungland,, A., Wakayama,, T., & Collas,, P. (2010). Histone H3 lysine 27 methylation asymmetry on developmentally‐regulated promoters distinguish the first two lineages in mouse preimplantation embryos. PLoS One, 5(2), e9150. http://doi.org/10.1371/journal.pone.0009150
Davies,, J. O. J., Oudelaar,, A. M., Higgs,, D. R., & Hughes,, J. R. (2017). How best to identify chromosomal interactions: A comparison of approaches. Nature Methods, 14(2), 125–134. http://doi.org/10.1038/nmeth.4146
Day,, N., Hemmaplardh,, A., Thurman,, R. E., Stamatoyannopoulos,, J. A., & Noble,, W. S. (2007). Unsupervised segmentation of continuous genomic data. Bioinformatics, 23(11), 1424–1426. http://doi.org/10.1093/bioinformatics/btm096
Dekker,, J., Rippe,, K., Dekker,, M., & Kleckner,, N. (2002). Capturing chromosome conformation. Science, 295(5558), 1306.
Dennis,, G., Sherman,, B. T., Hosack,, D. A., Yang,, J., Gao,, W., Lane,, H. C., & Lempicki,, R. A. (2003). DAVID: Database for annotation, visualization, and integrated discovery. Genome Biology, 4(9), R60.
Dingwall,, C., Lomonossoff,, G. P., & Laskey,, R. A. (1981). High sequence specificity of micrococcal nuclease. Nucleic Acids Research, 9(12), 2659–2673.
Dunham,, I., Kundaje,, A., Aldred,, S. F., Collins,, P. J., Davis,, C. A., Francis,, D., … Birney,, E. (The ENCODE Project Consortium). (2012). An integrated encyclopedia of DNA elements in the human genome. Nature, 489, 57–74.
Ernst,, J., & Kellis,, M. (2010). Discovery and characterization of chromatin states for systematic annotation of the human genome. Nature Biotechnology, 28(8), 817–825.
Ernst,, J., & Kellis,, M. (2012). ChromHMM: Automating chromatin state discovery and characterization. Nature Methods, 9(3), 215–216.
Falconer,, E., Hills,, M., Naumann,, U., Poon,, S. S. S., Chavez,, E. A., Sanders,, A. D., … Lansdorp,, P. M. (2012). DNA template strand sequencing of single‐cells maps genomic rearrangements at high resolution. Nature Methods, 9(11), 1107–1112.
Frommer,, M., McDonald,, L. E., Millar,, D. S., Collis,, C. M., Watt,, F., Grigg,, G. W., … Paul,, C. L. (1992). A genomic sequencing protocol that yields a positive display of 5‐methylcytosine residues in individual DNA strands. Proceedings of the National Academy of Sciences of the United States of America, 89(5), 1827–1831.
Gahurova,, L., Tomizawa,, S.‐I., Smallwood,, S. A., Stewart‐Morgan,, K. R., Saadeh,, H., Kim,, J., … Kelsey,, G. (2017). Transcription and chromatin determinants of de novo DNA methylation timing in oocytes. Epigenetics %26 Chromatin, 10(1), 25.
Gerstein,, M. B., Kundaje,, A., Hariharan,, M., Landt,, S. G., Yan,, K.‐K., Cheng,, C., … Snyder,, M. (2012). Architecture of the human regulatory network derived from ENCODE data. Nature, 489(7414), 91–100.
Gilfillan,, G. D., Hughes,, T., Sheng,, Y., Hjorthaug,, H. S., Straub,, T., Gervin,, K., … Lyle,, R. (2012). Limitations and possibilities of low cell number ChIP‐seq. BMC Genomics, 13, 645–645.
Gilmour,, D. S., & Lis,, J. T. (1984). Detecting protein‐DNA interactions in vivo: Distribution of RNA polymerase on specific bacterial genes. Proceedings of the National Academy of Sciences of the United States of America, 81(14), 4275–4279.
Ginzinger,, D. G. (2002). Gene quantification using real‐time quantitative PCR. Experimental Hematology, 30(6), 503–512. http://doi.org/10.1016/S0301-472X(02)00806-8
Grosselin,, K., Durand,, A., Marsolier,, J., Poitou,, A., Marangoni,, E., Nemati,, F., … Gérard,, A. (2019). High‐throughput single‐cell ChIP‐seq identifies heterogeneity of chromatin states in breast cancer. Nature Genetics, 51(6), 1060–1066.
Gutiérrez,, G., Millán‐Zambrano,, G., Medina,, D. A., Jordán‐Pla,, A., Pérez‐Ortín,, J. E., Peñate,, X., & Chávez,, S. (2017). Subtracting the sequence bias from partially digested MNase‐seq data reveals a general contribution of TFIIS to nucleosome positioning. Epigenetics %26 Chromatin, 10(1), 58–58.
Hainer,, S. J., Bošković,, A., McCannell,, K. N., Rando,, O. J., & Fazzio,, T. G. (2019). Profiling of pluripotency factors in single cells and early embryos. Cell, 177(5), 1319–1329.
Hajkova,, P., Ancelin,, K., Waldmann,, T., Lacoste,, N., Lange,, U. C., Cesari,, F., … Surani,, M. A. (2008). Chromatin dynamics during epigenetic reprogramming in the mouse germ line. Nature, 452(7189), 877–881. https://doi.org/10.1038/nature06714
Halbritter,, F., Kousa,, A. I., & Tomlinson,, S. R. (2014). GeneProf data: A resource of curated, integrated and reusable high‐throughput genomics experiments. Nucleic Acids Research, 42(Database issue), D851–D858.
Handyside,, A. H., & Hunter,, S. (1986). Cell division and death in the mouse blastocyst before implantation. Roux`s Archives of Developmental Biology, 195(8), 519–526.
Hanna,, C. W., Taudt,, A., Huang,, J., Gahurova,, L., Kranz,, A., Andrews,, S., … Kelsey,, G. (2018). MLL2 conveys transcription‐independent H3K4 trimethylation in oocytes. Nature Structural %26 Molecular Biology, 25(1), 73–82.
Hebbes,, T. R., Thorne,, A. W., & Crane‐Robinson,, C. (1988). A direct link between core histone acetylation and transcriptionally active chromatin. The EMBO Journal, 7(5), 1395–1402.
Henikoff,, J. G., Belsky,, J. A., Krassovsky,, K., MacAlpine,, D. M., & Henikoff,, S. (2011). Epigenome characterization at single base‐pair resolution. Proceedings of the National Academy of Sciences of the United States of America, 108(45), 18318–18323.
Ho,, J. W., Bishop,, E., Karchenko,, P. V., Nègre,, N., White,, K. P., & Park,, P. J. (2011). ChIP‐chip versus ChIP‐seq: Lessons for experimental design and data analysis. BMC Genomics, 12, 134–134.
Hoffman,, E. A., Frey,, B. L., Smith,, L. M., & Auble,, D. T. (2015). Formaldehyde crosslinking: A tool for the study of chromatin complexes. The Journal of Biological Chemistry, 290(44), 26404–26411.
Howe,, F. S., Fischl,, H., Murray,, S. C., & Mellor,, J. (2016). Is H3K4me3 instructive for transcription activation? BioEssays, 39(1), e201600095. http://doi.org/10.1002/bies.201600095
Iyer,, V. R., Horak,, C. E., Scafe,, C. S., Botstein,, D., Snyder,, M., & Brown,, P. O. (2001). Genomic binding sites of the yeast cell‐cycle transcription factors SBF and MBF. Nature, 409, 533 EP.
Jakobsen,, J. S., Bagger,, F. O., Hasemann,, M. S., Schuster,, M. B., Frank,, A.‐K., Waage,, J., … Porse,, B. T. (2015). Amplification of pico‐scale DNA mediated by bacterial carrier DNA for small‐cell‐number transcription factor ChIP‐seq. BMC Genomics, 16(1), 46.
Jin,, C., Zang,, C., Wei,, G., Cui,, K., Peng,, W., Zhao,, K., & Felsenfeld,, G. (2009). H3.3/H2A.Z double variant‐containing nucleosomes mark “nucleosome‐free regions” of active promoters and other regulatory regions in the human genome. Nature Genetics, 41(8), 941–945.
Johnson,, D. S., Mortazavi,, A., Myers,, R. M., & Wold,, B. (2007). Genome‐wide mapping of in vivo protein‐DNA interactions. Science, 316(5830), 1497.
Kaya‐Okur,, H. S., Wu,, S. J., Codomo,, C. A., Pledger,, E. S., Bryson,, T. D., Henikoff,, J. G., … Henikoff,, S. (2019). CUT%26tag for efficient epigenomic profiling of small samples and single cells. Nature Communications, 10(1), 1930–1930.
Kent,, W. J., Sugnet,, C. W., Furey,, T. S., Roskin,, K. M., Pringle,, T. H., Zahler,, A. M., & Haussler,, A. D. (2002). The human genome browser at UCSC. Genome Research, 12(6), 996–1006.
Kind,, J., Pagie,, L., de Vries,, S. S., Nahidiazar,, L., Dey,, S. S., Bienko,, M., … van Steensel,, B. (2015). Genome‐wide maps of nuclear lamina interactions in single human cells. Cell, 163(1), 134–147.
Ku,, W. L., Nakamura,, K., Gao,, W., Cui,, K., Hu,, G., Tang,, Q., … Zhao,, K. (2019). Single‐cell chromatin immunocleavage sequencing (scChIC‐seq) to profile histone modification. Nature Methods, 16(4), 323–325.
Kuleshov,, M. V., Jones,, M. R., Rouillard,, A. D., Fernandez,, N. F., Duan,, Q., Wang,, Z., … Ma`ayan,, A. (2016). Enrichr: A comprehensive gene set enrichment analysis web server 2016 update. Nucleic Acids Research, 44(Web Server issue), W90–W97.
Lara‐Astiaso,, D., Weiner,, A., Lorenzo‐Vivas,, E., Zaretsky,, I., Jaitin,, D. A., David,, E., … Amit,, I. (2014). Chromatin state dynamics during blood formation. Science, 345(6199), 943–949.
Lavender,, C. A., Shapiro,, A. J., Burkholder,, A. B., Bennett,, B. D., Adelman,, K., & Fargo,, D. C. (2017). ORIO (online resource for integrative omics): A web‐based platform for rapid integration of next generation sequencing data. Nucleic Acids Research, 45(10), 5678–5690. http://doi.org/10.1093/nar/gkx270
Lerdrup,, M., Johansen,, J. V., Agrawal‐Singh,, S., & Hansen,, K. (2016). An interactive environment for agile analysis and visualization of ChIP‐sequencing data. Nature Structural %26 Molecular Biology, 23(4), 349–357. http://doi.org/10.1038/nsmb.3180
Libbrecht,, M. W., & Noble,, W. S. (2015). Machine learning in genetics and genomics. Nature Reviews. Genetics, 16(6), 321–332.
Lieb,, J. D., Liu,, X., Botstein,, D., & Brown,, P. O. (2001). Promoter‐specific binding of Rap1 revealed by genome‐wide maps of protein–DNA association. Nature Genetics, 28, 327–334.
Limbach,, M., Saare,, M., Tserel,, L., Kisand,, K., Eglit,, T., Sauer,, S., … Peterson,, P. (2016). Epigenetic profiling in CD4+ and CD8+ T cells from Graves` disease patients reveals changes in genes associated with T cell receptor signaling. Journal of Autoimmunity, 67, 46–56.
Liu,, J., Zhu,, Y., Luo,, G.‐Z., Wang,, X., Yue,, Y., Wang,, X., … He,, C. (2016). Abundant DNA 6mA methylation during early embryogenesis of zebrafish and pig. Nature Communications, 7, 13052.
Liu,, T., Ortiz,, J. A., Taing,, L., Meyer,, C. A., Lee,, B., Zhang,, Y., … Liu,, X. S. (2011). Cistrome: An integrative platform for transcriptional regulation studies. Genome Biology, 12(8), R83.
Liu,, X., Wang,, C., Liu,, W., Li,, J., Li,, C., Kou,, X., … Gao,, S. (2016). Distinct features of H3K4me3 and H3K27me3 chromatin domains in pre‐implantation embryos. Nature, 537(7621), 558–562. http://doi.org/10.1038/nature19362
McGhee,, J. D., & Felsenfeld,, G. (1983). Another potential artifact in the study of nucleosome phasing by chromatin digestion with micrococcal nuclease. Cell, 32(4), 1205–1215. http://doi.org/10.1016/0092-8674(83)90303‐3
Mikkelsen,, T. S., Ku,, M., Jaffe,, D. B., Issac,, B., Lieberman,, E., Giannoukos,, G., … Bernstein,, B. E. (2007). Genome‐wide maps of chromatin state in pluripotent and lineage‐committed cells. Nature, 448(7153), 553–560.
Ng,, J.‐H., Kumar,, V., Muratani,, M., Kraus,, P., Yeo,, J.‐C., Yaw,, L.‐P., … Ng,, H. H. (2013). In vivo Epigenomic profiling of germ cells reveals germ cell molecular signatures. Developmental Cell, 24(3), 324–333. http://doi.org/10.1016/j.devcel.2012.12.011
Okonechnikov,, K., Conesa,, A., & García‐Alcalde,, F. (2016). Qualimap 2: Advanced multi‐sample quality control for high‐throughput sequencing data. Bioinformatics, 32(2), 292–294.
Okonechnikov,, K., Golosova,, O., & Fursov,, M. (2012). Unipro UGENE: A unified bioinformatics toolkit. Bioinformatics, 28(8), 1166–1167. http://doi.org/10.1093/bioinformatics/bts091
O`Neill,, L. P., VerMilyea,, M. D., & Turner,, B. M. (2006). Epigenetic characterization of the early embryo with a chromatin immunoprecipitation protocol applicable to small cell populations. Nature Genetics, 38(7), 835–841. http://doi.org/10.1038/ng1820
Peng,, X., Wu,, J., Brunmeir,, R., Kim,, S.‐Y., Zhang,, Q., Ding,, C., … Xu,, F. (2015). TELP, a sensitive and versatile library construction method for next‐generation sequencing. Nucleic Acids Research, 43(6), e35.
Ramírez,, F., Dündar,, F., Diehl,, S., Grüning,, B. A., & Manke,, T. (2014). deepTools: A flexible platform for exploring deep‐sequencing data. Nucleic Acids Research, 42(Web Server issue), W187–W191.
Ren,, B., Robert,, F., Wyrick,, J. J., Aparicio,, O., Jennings,, E. G., Simon,, I., … Young,, R. A. (2000). Genome‐wide location and function of DNA binding proteins. Science, 290(5500), 2306–2309. http://doi.org/10.1126/science.290.5500.2306
Robinson,, J. T., Thorvaldsdóttir,, H., Winckler,, W., Guttman,, M., Lander,, E. S., Getz,, G., & Mesirov,, J. P. (2011). Integrative genomics viewer. Nature Biotechnology, 29(1), 24–26.
Rotem,, A., Ram,, O., Shoresh,, N., Sperling,, R. A., Goren,, A., Weitz,, D. A., & Bernstein,, B. E. (2015). Single‐cell ChIP‐seq reveals cell subpopulations defined by chromatin state. Nature Biotechnology, 33(11), 1165–1172.
Sachs,, M., Onodera,, C., Blaschke,, K., Ebata,, K. T., Song,, J. S., & Ramalho Santos,, M. (2013). Bivalent chromatin Marks developmental regulatory genes in the mouse embryonic germline in vivo. Cell Reports, 3(6), 1777–1784.
Schmid,, M., Durussel,, T., & Laemmli,, U. K. (2004). ChIC and ChEC: Genomic mapping of chromatin proteins. Molecular Cell, 16(1), 147–157.
Schmidl,, C., Rendeiro,, A. F., Sheffield,, N. C., & Bock,, C. (2015). ChIPmentation: Fast, robust, low‐input ChIP‐seq for histones and transcription factors. Nature Methods, 12(10), 963–965. http://doi.org/10.1038/nmeth.3542
Schones,, D. E., Cui,, K., Cuddapah,, S., Roh,, T.‐Y., Barski,, A., Wang,, Z., … Zhao,, K. (2008). Dynamic regulation of nucleosome positioning in the human genome. Cell, 132(5), 887–898.
Seisenberger,, S., Peat,, J. R., Hore,, T. A., Santos,, F., Dean,, W., & Reik,, W. (2013). Reprogramming DNA methylation in the mammalian life cycle: Building and breaking epigenetic barriers. Philosophical Transactions of the Royal Society B: Biological Sciences, 368(1609), 20110330.
Seki,, Y., Yamaji,, M., Yabuta,, Y., Sano,, M., Shigeta,, M., Matsui,, Y., … Saitou,, M. (2007). Cellular dynamics associated with the genome‐wide epigenetic reprogramming in migrating primordial germ cells in mice. Development, 134(14), 2627–2638. http://doi.org/10.1242/dev.005611
Shah,, R. N., Grzybowski,, A. T., Cornett,, E. M., Johnstone,, A. L., Dickson,, B. M., Boone,, B. A., … Ruthenburg,, A. J. (2018). Examining the roles of H3K4 methylation states with systematically characterized antibodies. Molecular Cell, 72(1), 162.e7–177.e7.
Shankaranarayanan,, P., Mendoza‐Parra,, M.‐A., Walia,, M., Wang,, L., Li,, N., Trindade,, L. M., & Gronemeyer,, H. (2011). Single‐tube linear DNA amplification (LinDA) for robust ChIP‐seq. Nature Methods, 8, 565–567.
Skene,, P. J., & Henikoff,, S. (2017). An efficient targeted nuclease strategy for high‐resolution mapping of DNA binding sites. eLife, 6, e21856.
Smallwood,, S. A., Lee,, H. J., Angermueller,, C., Krueger,, F., Saadeh,, H., Peat,, J., … Kelsey,, G. (2014). Single‐cell genome‐wide bisulfite sequencing for assessing epigenetic heterogeneity. Nature Methods, 11(8), 817–820.
Solomon,, M. J., Larsen,, P. L., & Varshavsky,, A. (1988). Mapping proteinDNA interactions in vivo with formaldehyde: Evidence that histone H4 is retained on a highly transcribed gene. Cell, 53(6), 937–947. http://doi.org/10.1016/S0092-8674(88)90469‐2
Solomon,, M. J., & Varshavsky,, A. (1985). Formaldehyde‐mediated DNA‐protein crosslinking: A probe for in vivo chromatin structures. Proceedings of the National Academy of Sciences of the United States of America, 82(19), 6470–6474.
Steensel,, B. V., & Henikoff,, S. (2000). Identification of in vivo DNA targets of chromatin proteins using tethered dam methyltransferase. Nature Biotechnology, 18(4), 424–428.
Stewart,, K. R., Veselovska,, L., Kim,, J., Huang,, J., Saadeh,, H., Tomizawa,, S.‐I., … Kelsey,, G. (2015). Dynamic changes in histone modifications precede de novo DNA methylation in oocytes. Genes %26 Development, 29(23), 2449–2462.
Su,, Y., Shin,, J., Zhong,, C., Wang,, S., Roychowdhury,, P., Lim,, J., … Song,, H. (2017). Neuronal activity modifies the chromatin accessibility landscape in the adult brain. Nature Neuroscience, 20(3), 476–483.
Sundaram,, A. Y. M., Hughes,, T., Biondi,, S., Bolduc,, N., Bowman,, S. K., Camilli,, A., … Gilfillan,, G. D. (2016). A comparative study of ChIP‐seq sequencing library preparation methods. BMC Genomics, 17(1), 134–112. http://doi.org/10.1186/s12864-016-3135-y
Tadros,, W., & Lipshitz,, H. D. (2009). The maternal‐to‐zygotic transition: A play in two acts. Development, 136(18), 3033–3042. http://doi.org/10.1242/dev.033183
Teytelman,, L., Özaydın,, B., Zill,, O., Lefrançois,, P., Snyder,, M., Rine,, J., & Eisen,, M. B. (2009). Impact of chromatin structures on DNA processing for genomic analyses. PLoS One, 4(8), e6700. http://doi.org/10.1371/journal.pone.0006700
Valensisi,, C., Liao,, J. L., Andrus,, C., Battle,, S. L., & Hawkins,, R. D. (2015). cChIP‐seq: A robust small‐scale method for investigation of histone modifications. BMC Genomics, 16(1), 1083.
van Galen,, P., Viny,, A. D., Ram,, O., Ryan,, R. J. H., Cotton,, M. J., Donohue,, L., … Bernstein,, B. E. (2016). A multiplexed system for quantitative comparisons of chromatin landscapes. Molecular Cell, 61(1), 170–180. http://doi.org/10.1016/j.molcel.2015.11.003
Weber,, M., Davies,, J. J., Wittig,, D., Oakeley,, E. J., Haase,, M., Lam,, W. L., & Schübeler,, D. (2005). Chromosome‐wide and promoter‐specific analyses identify sites of differential DNA methylation in normal and transformed human cells. Nature Genetics, 37(8), 853–862.
Whalen,, S., Truty,, R. M., & Pollard,, K. S. (2016). Enhancer‐promoter interactions are encoded by complex genomic signatures on looping chromatin. Nature Genetics, 48(5), 488–496.
Wreczycka,, K., Franke,, V., Uyar,, B., Wurmus,, R., & Akalin,, A. (2017). HOT or not: Examining the basis of high‐occupancy target regions. Nucleic Acids Research, 47(11), 5735–5745. https://doi.org/10.1093/nar/gkz460
Wu,, A. R., Hiatt,, J. B., Lu,, R., Attema,, J. L., Lobo,, N. A., Weissman,, I. L., … Quake,, S. R. (2009). Automated microfluidic chromatin immunoprecipitation from 2,000 cells. Lab on a Chip, 9(10), 1365–1370.
Wu,, A. R., & Quake,, S. R. (2016). Microfluidics technologies for low cell number chromatin immunoprecipitation. Cold Spring Harbor Protocols, 2016(4), 373–384.
Ye,, T., Krebs,, A. R., Choukrallah,, M.‐A., Keime,, C., Plewniak,, F., Davidson,, I., & Tora,, L. (2011). seqMINER: An integrated ChIP‐seq data interpretation platform. Nucleic Acids Research, 39(6), e35.
Yong,, W.‐S., Hsu,, F.‐M., & Chen,, P.‐Y. (2016). Profiling genome‐wide DNA methylation. Epigenetics %26 Chromatin, 9(1), 26.
Zentner,, G. E., & Henikoff,, S. (2014). High‐resolution digital profiling of the epigenome. Nature Reviews. Genetics, 15(12), 814–827. http://doi.org/10.1038/nrg3798
Zentner,, G. E., Kasinathan,, S., Xin,, B., Rohs,, R., & Henikoff,, S. (2015). ChEC‐seq kinetics discriminates transcription factor binding sites by DNA sequence and shape in vivo. Nature Communications, 6, 8733 EP.
Zhang,, B., Zheng,, H., Huang,, B., Li,, W., Xiang,, Y., Peng,, X., … Xie,, W. (2016). Allelic reprogramming of the histone modification H3K4me3 in early mammalian development. Nature, 537(7621), 553–557. http://doi.org/10.1038/nature19361
Zwart,, W., Koornstra,, R., Wesseling,, J., Rutgers,, E., Linn,, S., & Carroll,, J. S. (2013). A carrier‐assisted ChIP‐seq method for estrogen receptor‐chromatin interactions from breast cancer core needle biopsy samples. BMC Genomics, 14(1), 232.