Searching journal content for articles similar to Johnson et al. 18 (3): 393.

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  1. Method: Evaluation of affinity-based genome-wide DNA methylation data: Effects of CpG density, amplification bias, and copy number variation
    • Mark D. Robinson,
    • Clare Stirzaker,
    • Aaron L. Statham,
    • Marcel W. Coolen,
    • Jenny Z. Song,
    • Shalima S. Nair,
    • Dario Strbenac,
    • Terence P. Speed,
    • and Susan J. Clark
    Genome Res. December 2010 20: 1719-1729; Published in Advance November 2, 2010, doi:10.1101/gr.110601.110
    ...effect on transcript levels (Stranger et al. 2007). The effect is less clear in DNA methylome data, but the expectation is that genetically amplified (deleted) regions of the should be captured at a higher (lower) rate if the DNA is methylated. In the analysis of the ChIP-chip experiments, it is common...
  2. Article: Erythroid GATA1 function revealed by genome-wide analysis of transcription factor occupancy, histone modifications, and mRNA expression
    • Yong Cheng,
    • Weisheng Wu,
    • Swathi Ashok Kumar,
    • Duonan Yu,
    • Wulan Deng,
    • Tamara Tripic,
    • David C. King,
    • Kuan-Bei Chen,
    • Ying Zhang,
    • Daniela Drautz,
    • Belinda Giardine,
    • Stephan C. Schuster,
    • Webb Miller,
    • Francesca Chiaromonte,
    • Yu Zhang,
    • Gerd A. Blobel,
    • Mitchell J. Weiss,
    • and Ross C. Hardison
    Genome Res. December 2009 19: 2172-2184; Published in Advance November 3, 2009, doi:10.1101/gr.098921.109
    ...1 OSs in the nonintersection sets. Therefore, we made a union of the ChIP-seq and ChIP-chip peaks, followed by merging of overlaps to generate a set of 15,360 GATA1 OSs. This set of GATA1 OSs is highly accurate based on comparisons with previously characterized DNA segments occupied by GATA1...
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  3. LETTER: E2F in vivo binding specificity: Comparison of consensus versus nonconsensus binding sites
    • Alina Rabinovich,
    • Victor X. Jin,
    • Roman Rabinovich,
    • Xiaoqin Xu,
    • and Peggy J. Farnham
    Genome Res. November 2008 18: 1763-1777; Published in Advance October 3, 2008, doi:10.1101/gr.080622.108
    ...independent cultures of cells. Thus, the HA-tagged E2F1 (HA-wtE2F1) binds to the same targets as does the endogenous E2F1. We then performed the ChIP-chip assays using the HA tagged E2F1 DNA-binding domain mutant (HA-DBDmut E2F1). These arrays were analyzed in two ways. First, we selected the set of top...
  4. Resource: A ChIP-exo screen of 887 Protein Capture Reagents Program transcription factor antibodies in human cells
    • William K.M. Lai,
    • Luca Mariani,
    • Gerson Rothschild,
    • Edwin R. Smith,
    • Bryan J. Venters,
    • Thomas R. Blanda,
    • Prashant K. Kuntala,
    • Kylie Bocklund,
    • Joshua Mairose,
    • Sarah N. Dweikat,
    • Katelyn Mistretta,
    • Matthew J. Rossi,
    • Daniela James,
    • James T. Anderson,
    • Sabrina K. Phanor,
    • Wanwei Zhang,
    • Zibo Zhao,
    • Avani P. Shah,
    • Katherine Novitzky,
    • Eileen McAnarney,
    • Michael-C. Keogh,
    • Ali Shilatifard,
    • Uttiya Basu,
    • Martha L. Bulyk,
    • and B. Franklin Pugh
    Genome Res. September 2021 31: 1663-1679; Published in Advance August 23, 2021, doi:10.1101/gr.275472.121
    ...In a new window Figure 3. Cell type comparison of antibody performance. (A,B) ChIP-exo heatmap, composite, and DNA-sequence four-color plots are shown for the indicated number of bound motifs for the indicated targets, in the indicated cell types. The 5′ end of aligned sequence reads for each set...
  5. Methods: Detection of nonneutral substitution rates on mammalian phylogenies
    • Katherine S. Pollard,
    • Melissa J. Hubisz,
    • Kate R. Rosenbloom,
    • and Adam Siepel
    Genome Res. January 2010 20: 110-121; Published in Advance October 26, 2009, doi:10.1101/gr.097857.109
    ...-evolving segment is shown. Interestingly, cDNA data from other mammals suggest that this exon derives from a fusion of two ancestral exons, with the fast-evolving segment corresponding to the ancestral intron. Detection of nonneutral substitution rates Genome Research 117 www..org and methylation of cytosines...
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