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ChIP sequencing

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152: 269:-based ChIP methods, the precision of the ChIP-seq assay is not limited by the spacing of predetermined probes. By integrating a large number of short reads, highly precise binding site localization is obtained. Compared to ChIP-chip, ChIP-seq data can be used to locate the binding site within few tens of base pairs of the actual protein binding site. Tag densities at the binding sites are a good indicator of protein–DNA binding affinity, which makes it easier to quantify and compare binding affinities of a protein to different DNA sites. 383: 369: 341:
to call for broader peaks, spanning over kilobases to megabases in order to search for broader chromatin domains. SICER is more useful for histone marks spanning gene bodies. A mathematical more rigorous method BCP (Bayesian Change Point) can be used for both sharp and broad peaks with faster computational speed, see benchmark comparison of ChIP-seq peak-calling tools by Thomas
171:. However, the widespread use of this method has been limited by the lack of a sufficiently robust method to identify all of the enriched DNA sequences. The ChIP wet lab protocol contains ChIP and hybridization. There are essentially five parts to the ChIP protocol that aid in better understanding the overall process of ChIP. In order to carry out the ChIP, the first step is 327:
analysis pipeline as long as a high-quality genome sequence is available for read mapping and the genome doesn't have repetitive content that confuses the mapping process. ChIP-seq also has the potential to detect mutations in binding-site sequences, which may directly support any observed changes in protein binding and gene regulation.
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some of the transcription factors were also identified. Some of the transcription factors regulate genes that control other transcription factors. These genes are not regulated by other factors. Most transcription factors serve as both targets and regulators of other factors, demonstrating a network of regulation.
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pieces for ChIP analysis in the end. These fragments should be cut to become under 500 base pairs each to have the best outcome for genome mapping. The third step is called chromatin immunoprecipitation, which is what ChIP is short for. The ChIP process enhances specific crosslinked DNA-protein complexes using an
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To reduce spurious sites from ChIP-seq, multiple experimental controls can be used to detect binding sites from an IP experiment. Bay2Ctrls adopts a Bayesian model to integrate the DNA input control for the IP, the mock IP and its corresponding DNA input control to predict binding sites from the IP.
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methods have been developed. One of the most popular methods is MACS which empirically models the shift size of ChIP-Seq tags, and uses it to improve the spatial resolution of predicted binding sites. MACS is optimized for higher resolution peaks, while another popular algorithm, SICER is programmed
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against the protein of interest followed by incubation and centrifugation to obtain the immunoprecipitation. The immunoprecipitation step also allows for the removal of non-specific binding sites. The fourth step is DNA recovery and purification, taking place by the reversed effect on the cross-link
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to explore genome-wide binding sites of 22 transcription factors. Up to 20% of the annotated candidate genes were assigned to transcription factors. Several transcription factors were assigned to non-coding RNA regions and may be subject to developmental or environmental variables. The functions of
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using formaldehyde and large batches of the DNA in order to obtain a useful amount. The cross-links are made between the protein and DNA, but also between RNA and other proteins. The second step is the process of chromatin fragmentation which breaks up the chromatin in order to get high quality DNA
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Sensitivity of this technology depends on the depth of the sequencing run (i.e. the number of mapped sequence tags), the size of the genome and the distribution of the target factor. The sequencing depth is directly correlated with cost. If abundant binders in large genomes have to be mapped with
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After size selection, all the resulting ChIP-DNA fragments are sequenced simultaneously using a genome sequencer. A single sequencing run can scan for genome-wide associations with high resolution, meaning that features can be located precisely on the chromosomes. ChIP-chip, by contrast, requires
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ChIP-seq offers an alternative to ChIP-chip. STAT1 experimental ChIP-seq data have a high degree of similarity to results obtained by ChIP-chip for the same type of experiment, with greater than 64% of peaks in shared genomic regions. Because the data are sequence reads, ChIP-seq offers a rapid
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were shown to be more correlated with transcription factor motifs at promoters in comparison to RNA level. Hence author proposed that using histone modification ChIP-seq would provide more reliable inference of gene-regulatory networks in comparison to other methods based on expression.
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in parallel using novel fluorescently labelled reversible terminator nucleotides. Templates are sequenced base-by-base during each read. Then, the data collection and analysis software aligns sample sequences to a known genomic sequence to identify the ChIP-DNA fragments.
107:. ChIP produces a library of target DNA sites bound to a protein of interest. Massively parallel sequence analyses are used in conjunction with whole-genome sequence databases to analyze the interaction pattern of any protein with DNA, or the pattern of any epigenetic 357:
This approach is particularly effective for complex samples such as whole model organisms. In addition, the analysis indicates that for complex samples mock IP controls substantially outperform DNA input controls probably due to the active genomes of the samples.
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Another relevant computational problem is differential peak calling, which identifies significant differences in two ChIP-seq signals from distinct biological conditions. Differential peak callers segment two ChIP-seq signals and identify differential peaks using
100:. This introduces some bias, as an array is restricted to a fixed number of probes. Sequencing, by contrast, is thought to have less bias, although the sequencing bias of different sequencing technologies is not yet fully understood. 2002:: GeneProf is a freely accessible, easy-to-use analysis environment for ChIP-seq and RNA-seq data and comes with a large database of ready-analysed public experiments, e.g. for transcription factor binding and histone modifications. 225:
substrate to create clusters of approximately 1000 clonal copies each. The resulting high density array of template clusters on the flow cell surface is sequenced by a genome analyzing program. Each template cluster undergoes
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As with many high-throughput sequencing approaches, ChIP-seq generates extremely large data sets, for which appropriate computational analysis methods are required. To predict DNA-binding sites from ChIP-seq read count data,
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Jung, Youngsook L.; Luquette, Lovelace J.; Ho, Joshua W. K.; Ferrari, Francesco; Tolstorukov, Michael; Minoda, Aki; Issner, Robbyn; Epstein, Charles B.; Karpen, Gary H.; Kuroda, Mitzi I.; Park, Peter J. (May 2014).
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S3 cells which are clones of the HeLa line that are used for analysis of cell populations. The performance of ChIP-seq was then compared to the alternative protein–DNA interaction methods of ChIP-PCR and ChIP-chip.
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Xu, Jinrui; Kudron, Michelle M; Victorsen, Alec; Gao, Jiahao; Ammouri, Haneen N; Navarro, Fabio C P; Gevirtzman, Louis; Waterston, Robert H; White, Kevin P; Reinke, Valerie; Gerstein, Mark (21 December 2020).
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Robertson G, Hirst M, Bainbridge M, Bilenky M, Zhao Y, Zeng T, et al. (August 2007). "Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing".
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Chen, Yiwen; Negre, Nicolas; Li, Qunhua; Mieczkowska, Joanna O.; Slattery, Matthew; Liu, Tao; Zhang, Yong; Kim, Tae-Kyung; He, Housheng Hansen; Zieba, Jennifer; Ruan, Yijun (June 2012).
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high sensitivity, costs are high as an enormously high number of sequence tags will be required. This is in contrast to ChIP-chip in which the costs are not correlated with sensitivity.
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Using ChIP-seq, it was determined that Yeast genes seem to have a minimal nucleosome-free promoter region of 150bp in which RNA polymerase can initiate transcription.
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ChIP-seq was used to compare conservation of TFs in the forebrain and heart tissue in embryonic mice. The authors identified and validated the heart functionality of
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between DNA and protein to separate them and cleaning DNA with an extraction. The fifth and final step is the analyzation step of the ChIP protocol by the process of
2030: 463: 218: 128: 301:, and determined that transcription enhancers for the heart are less conserved than those for the forebrain during the same developmental stage. 426:, antibody-targeted controlled cleavage by micrococcal nuclease instead of ChIP, allowing for enhanced signal-to-noise ratio during sequencing. 487: 432:, antibody-targeted controlled cleavage by transposase Tn5 instead of ChIP, allowing for enhanced signal-to-noise ratio during sequencing. 1724:
Allhoff M, Seré K, Chauvistré H, Lin Q, Zenke M, Costa IG (December 2014). "Detecting differential peaks in ChIP-seq signals with ODIN".
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analysis of regulatory elements from +2800 ChIP-seq datasets, giving a catalogue of 80 million peaks from 485 transcription regulators.
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ChIP-seq offers us a fast analysis, however, a quality control must be performed to make sure that the results obtained are reliable:
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Kumar, Vibhor; Muratani, Masafumi; Rayan, Nirmala Arul; Kraus, Petra; Lufkin, Thomas; Ng, Huck Hui; Prabhakar, Shyam (July 2013).
50: 131:. As an alternative to the dependence on specific antibodies, different methods have been developed to find the superset of all 1577:"Genome-wide localization of protein-DNA binding and histone modification by a Bayesian change-point method with ChIP-seq data" 246:: low-complexity regions should be removed as they are not informative and may interfere with mapping in the reference genome. 662:"DNase-seq: a high-resolution technique for mapping active gene regulatory elements across the genome from mammalian cells" 60:
of DNA-associated proteins. It can be used to map global binding sites precisely for any protein of interest. Previously,
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Ho, Joshua W. K.; Bishop, Eric; Karchenko, Peter V.; Nègre, Nicolas; White, Kevin P.; Park, Peter J. (28 February 2011).
719:"FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) isolates active regulatory elements from human chromatin" 182: 111:
modifications. This can be applied to the set of ChIP-able proteins and modifications, such as transcription factors,
2063:"ReMap 2018: an updated atlas of regulatory regions from an integrative analysis of DNA-binding ChIP-seq experiments" 643: 103:
Specific DNA sites in direct physical interaction with transcription factors and other proteins can be isolated by
2018: 528:"RNA-seq and ChIP-seq as Complementary Approaches for Comprehension of Plant Transcriptional Regulatory Mechanism" 17: 2189: 1685:"An HMM approach to genome-wide identification of differential histone modification sites from ChIP-seq data" 460:, same goal and first steps, but does not use cross linking methods and uses microarray instead of sequencing 104: 46: 1979: 2184: 193:
adaptors are then added to the small stretches of DNA that were bound to the protein of interest to enable
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Muhammad, Isiaka Ibrahim; Kong, Sze Ling; Akmar Abdullah, Siti Nor; Munusamy, Umaiyal (25 December 2019).
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data. It provides the most comprehensive ChIP-Seq data set for various cell/tissue types and conditions.
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Bernstein BE, Kamal M, Lindblad-Toh K, Bekiranov S, Bailey DK, Huebert DJ, et al. (January 2005).
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Giresi, Paul G.; Kim, Jonghwan; McDaniell, Ryan M.; Iyer, Vishwanath R.; Lieb, Jason D. (June 2007).
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is a powerful method to selectively enrich for DNA sequences bound by a particular protein in living
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ratio of reads that are located in peaks over reads that are located where there isn't a peak.
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and expression analysis. ChIP-seq technology is currently seen primarily as an alternative to
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Calling Cards, uses a transposase to mark the sequence where a transcription factor binds.
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is essential for fully understanding many biological processes and disease states. This
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Blow MJ, McCulley DJ, Li Z, Zhang T, Akiyama JA, Holt A, et al. (September 2010).
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Licatalosi DD, Mele A, Fak JJ, Ule J, Kayikci M, Chi SW, et al. (November 2008).
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Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein BE, et al. (2008).
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Niu W, Lu ZJ, Zhong M, Sarov M, Murray JI, Brdlik CM, et al. (February 2011).
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used in this sequencing step. Some technologies that analyze the sequences can use
1765:"To mock or not: a comprehensive comparison of mock IP and DNA input for ChIP-seq" 1483:
Kumar V, Muratani M, Rayan NA, Kraus P, Lufkin T, Ng HH, Prabhakar S (July 2013).
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Kim TH, Dekker J (April 2018). "Preparation of Cross-Linked Chromatin for ChIP".
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uses S9.6 antibody to precipitate three-stranded DND:RNA hybrids called R-loops.
135:-depleted or nucleosome-disrupted active regulatory regions in the genome, like 2110:
Bailey T, Krajewski P, Ladunga I, Lefebvre C, Li Q, Liu T, et al. (2013).
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was the most common technique utilized to study these protein–DNA relations.
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Chèneby J, Gheorghe M, Artufel M, Mathelier A, Ballester B (January 2018).
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uses exonuclease treatment to achieve up to single base-pair resolution
266: 132: 112: 85: 2112:"Practical guidelines for the comprehensive analysis of ChIP-seq data" 1881:"HITS-CLIP: panoramic views of protein-RNA regulation in living cells" 1306: 1501: 1484: 792: 775: 475: 441: 140: 136: 108: 93: 77: 2033:: a tool for probabilistic pattern discovery on multiple normalized 1896: 950: 2044: 2043:: a tool for regression and peak prediction on multiple normalized 2034: 1993: 1989: 1983: 1485:"Uniform, optimal signal processing of mapped deep-sequencing data" 1402: 1217: 776:"Uniform, optimal signal processing of mapped deep-sequencing data" 497: 491: 481: 457: 451: 445: 435: 368: 177: 89: 1992:: a database for exploring transcription factor binding maps from 525: 506:, principally similar method to measure mRNA translation dynamics. 438:, identical to ChIP-Seq but skipping the immunoprecipitation step. 382: 1338:"ChIP-Seq data reveal nucleosome architecture of human promoters" 503: 38: 1636:"Features that define the best ChIP-seq peak calling algorithms" 995:"Systematic evaluation of factors influencing ChIP-seq fidelity" 2060: 1291: 2109: 935:"ChIP-seq: advantages and challenges of a maturing technology" 1387:"ChIP-Seq identification of weakly conserved heart enhancers" 863:
Kim TH, Dekker J (April 2018). "Formaldehyde Cross-Linking".
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Wang H, Mayhew D, Chen X, Johnston M, Mitra RD (May 2011).
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Johnson DS, Mortazavi A, Myers RM, Wold B (June 2007).
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Song, Lingyun; Crawford, Gregory E. (February 2010).
448:), for finding interactions with RNA rather than DNA. 1821: 1761: 1634:
Thomas R, Thomas S, Holloway AK, Pollard KS (2017).
1053:"Impact of sequencing depth in ChIP-seq experiments" 364: 27:
Method used to analyze protein interactions with DNA
2015:: Tutorial for differential peak calling with ODIN. 1384: 466:, a method for finding a consensus binding sequence 472:, to measure relative replacement dynamics on DNA. 76:and other chromatin-associated proteins influence 644:"Whole-Genome Chromatin IP Sequencing (ChIP-Seq)" 221:of adapter-ligated ChIP DNA fragments on a solid 2166: 1574: 1433: 839:"ChIP guide: epigenetics applications | Abcam" 146: 1683:Xu H, Wei CL, Lin F, Sung WK (October 2008). 494:to achieve up to single base-pair resolution. 1682: 1335: 659: 280:ChIP-seq was used to study STAT1 targets in 72:ChIP-seq is primarily used to determine how 532:International Journal of Molecular Sciences 2021:: Comprehensive analysis of ChIP-seq data. 1476: 307:ChIP-sequencing was completed on the worm 2145: 2135: 2086: 1953: 1904: 1855: 1798: 1780: 1700: 1659: 1610: 1600: 1551: 1541: 1526:"Model-based analysis of ChIP-Seq (MACS)" 1500: 1459: 1410: 1353: 1235: 1194: 1184: 1143: 1125: 1084: 1026: 966: 897: 862: 791: 750: 693: 561: 543: 330: 150: 2019:Bioinformatic analysis of ChIP-seq data 1878: 1575:Xing H, Mo Y, Liao W, Zhang MQ (2012). 14: 2167: 478:to measure RNA-bound DNA and proteins. 1757: 1755: 1336:Schmid CD, Bucher P (November 2007). 1166: 988: 986: 289:Nucleosome Architecture of Promoters: 1885:Wiley Interdisciplinary Reviews. RNA 1268:"HeLa S3 from ATCC | Biocompare.com" 932: 833: 831: 829: 827: 2000:GeneProf database and analysis tool 272: 189:(hybrid array) or ChIP sequencing. 24: 1752: 983: 649:. Illumina, Inc. 26 November 2007. 417: 295:Transcription factor conservation: 234: 25: 2201: 1973: 824: 1348:(5): 831–2, author reply 832–3. 381: 367: 88:information is complementary to 2103: 2054: 1921: 1872: 1717: 1676: 1627: 1568: 1517: 1427: 1378: 1329: 1285: 1260: 1211: 1160: 1101: 1043: 933:Park, Peter J. (October 2009). 926: 891: 856: 767: 710: 653: 636: 578: 519: 256: 37:, is a method used to analyze 13: 1: 1982:: An integrative and uniform 1738:10.1093/bioinformatics/btu722 1702:10.1093/bioinformatics/btn402 513: 316:Inferring regulatory network: 200: 195:massively parallel sequencing 105:chromatin immunoprecipitation 47:chromatin immunoprecipitation 2137:10.1371/journal.pcbi.1003326 1602:10.1371/journal.pcbi.1002613 900:Cold Spring Harbor Protocols 865:Cold Spring Harbor Protocols 666:Cold Spring Harbor Protocols 7: 1167:Jothi, et al. (2008). 412:Mammalian promoter database 360: 147:Workflow of ChIP-sequencing 10: 2206: 2116:PLOS Computational Biology 1355:10.1016/j.cell.2007.11.017 1237:10.1016/j.cell.2005.01.001 2006:Differential Peak Calling 117:transcriptional machinery 1543:10.1186/gb-2008-9-9-r137 1127:10.1186/1471-2164-12-134 939:Nature Reviews. Genetics 155:ChIP-sequencing workflow 614:10.1126/science.1141319 299:transcription enhancers 228:sequencing-by-synthesis 159: 67: 2067:Nucleic Acids Research 1769:Nucleic Acids Research 1057:Nucleic Acids Research 912:10.1101/pdb.prot082602 877:10.1101/pdb.prot082594 430:CUT&Tag sequencing 424:CUT&RUN sequencing 331:Computational analysis 278:STAT1 DNA association: 244:Non-redundant fraction 215:new sequencing methods 210:for lower resolution. 156: 1946:10.1101/gr.114850.110 1452:10.1101/gr.114587.110 906:(4): pdb.prot082602. 871:(4): pdb.prot082594. 305:Genome-wide ChIP-seq: 219:cluster amplification 154: 125:protein modifications 74:transcription factors 2190:Proteomic sequencing 1782:10.1093/nar/gkaa1155 1489:Nature Biotechnology 780:Nature Biotechnology 678:10.1101/pdb.prot5384 545:10.3390/ijms21010167 490:improved version of 351:Hidden Markov Models 320:Histone modification 45:. ChIP-seq combines 2185:Genomics techniques 2128:2013PLSCB...9E3326B 2079:10.1093/nar/gkx1092 2011:15 May 2021 at the 1879:Darnell RB (2010). 1848:10.1038/nature07488 1840:2008Natur.456..464L 1593:2012PLSCB...8E2613X 672:(2): pdb.prot5384. 606:2007Sci...316.1497J 318:ChIP-seq signal of 250:Fragments in peaks: 121:structural proteins 98:hybridization array 1652:10.1093/bib/bbw035 1272:www.biocompare.com 1186:10.1093/nar/gkn488 1069:10.1093/nar/gku178 1011:10.1038/nmeth.1985 735:10.1101/gr.5533506 600:(5830): 1497–502. 157: 51:massively parallel 41:interactions with 2073:(D1): D267–D275. 1990:ChIPBase database 1307:10.1038/nmeth1068 1179:(16): 5221–5231. 1173:Nucleic Acids Res 389:Technology portal 129:DNA modifications 96:which requires a 16:(Redirected from 2197: 2160: 2159: 2149: 2139: 2122:(11): e1003326. 2107: 2101: 2100: 2090: 2058: 2041:FullSignalRanker 1968: 1967: 1957: 1925: 1919: 1918: 1908: 1876: 1870: 1869: 1859: 1819: 1813: 1812: 1802: 1784: 1759: 1750: 1749: 1721: 1715: 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Index

Chip-sequencing
protein
DNA
chromatin immunoprecipitation
massively parallel
DNA sequencing
binding sites
ChIP-on-chip
transcription factors
phenotype
gene expression
epigenetic
genotype
ChIP-chip
hybridization array
chromatin immunoprecipitation
chromatin
polymerases
transcriptional machinery
structural proteins
protein modifications
DNA modifications
nucleosome
DNase-Seq
FAIRE-Seq

ChIP
cells
cross-linking
antibody

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