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Peconic, LLC

State College, Pennsylvania, US

Peconic provides high quality and cost-effective ChIP-exo and ChIP-seq laboratory and data analysis methods to the epigenomic research community.

Epigenomics, the science of gene regulation on a global scale, is rapidly growing and has been called the new frontier of biotechnology and personalized medicine. Understanding why and how genes are regulated has significant value in medical research, drug development, bioproduct development, and many other fields. By offering ChIP-exo and ChIP-seq as services, Peconic aims to broaden the tools available to researchers while also reducing their costs and risk.

With years of experience performing and optimizing our ChIP assays, we have developed effective and efficient ChIP-exo and ChIP-seq procedures. Assays we conduct provide high resolution data, helping our customers drive towards new knowledge and solutions. Our results are presented in an easy-to-use and interpret... Show more »

Peconic provides high quality and cost-effective ChIP-exo and ChIP-seq laboratory and data analysis methods to the epigenomic research community.

Epigenomics, the science of gene regulation on a global scale, is rapidly growing and has been called the new frontier of biotechnology and personalized medicine. Understanding why and how genes are regulated has significant value in medical research, drug development, bioproduct development, and many other fields. By offering ChIP-exo and ChIP-seq as services, Peconic aims to broaden the tools available to researchers while also reducing their costs and risk.

With years of experience performing and optimizing our ChIP assays, we have developed effective and efficient ChIP-exo and ChIP-seq procedures. Assays we conduct provide high resolution data, helping our customers drive towards new knowledge and solutions. Our results are presented in an easy-to-use and interpret format, enabling our customers to quickly disseminate new knowledge.

From sample preparation to data construction, our many quality controls help us provide our customers with high quality data. However, as with any such lab technique, there is no guarantee that the DNA samples and antibodies are experimentally compatible. Our low-priced validation service assesses the ChIP-exo and/or ChIP-seq compatibility of submitted DNA and antibodies. Researchers then have the option to acquire the bioinformatics reports of their choosing. Our goal is to help researchers solve some of the most complex biological problems that currently exist while reducing the risk associated with experimental procedures.

We have worked with many academic researchers throughout the world to create new knowledge in the area of epigenomics.

Selected Publications

  • The Paf1 complex factors Leo1 and Paf1 promote local histone turnover to modulate chromatin states in fission yeast. Sadeghi L, Prasad P, Ekwall K, Cohen A, Svensson JP. (2015) EMBO Rep 16:1673-1687.
  • ChIP-exo signal associated with DNA-binding motifs provides insight into the genomic binding of the glucocorticoid receptor and cooperating transcription factors. Starick SR, Ibn-Salem J, Jurk M, Hernandez C, Love MI, Chung HR, . . . Meijsing SH. (2015) Genome Res 25:825-835.
  • A nucleosome turnover map reveals that the stability of histone H4 Lys20 methylation depends on histone recycling in transcribed chromatin. Svensson JP, Shukla M, Menendez-Benito V, Norman-Axelsson U, Audergon P, Sinha I, . . . Ekwall K. (2015) Genome research doi:10.1101/gr.188870.114.
  • ATF4 Gene Network Mediates Cellular Response to the Anticancer PAD Inhibitor YW3-56 in Triple-Negative Breast Cancer Cells. Wang S, Chen XA, Hu J, Jiang JK, Li Y, Chan-Salis KY, . . . Wang Y. (2015) Mol Cancer Ther 14:877-888.
  • Genome-Wide Analysis of Drosophila RBf2 Protein Highlights the Diversity of RB Family Targets and Possible Role in Regulation of Ribosome Biosynthesis. Wei Y, Mondal SS, Mouawad R, Wilczynski B, Henry RW, Arnosti DN. (2015) G3 (Bethesda) 5:1503-1515.
  • Genomic Targets and Features of BarA-UvrY (-SirA) Signal Transduction Systems. Zere TR, Vakulskas CA, Leng Y, Pannuri A, Potts AH, Dias R, . . . Romeo T. (2015) PLoS One 10:e0145035.
  • Genome-Wide Organization of GATA1 and TAL1 Determined at High Resolution. Han GC, Vinayachandran V, Bataille AR, Park B, Chan-Salis KY, Keller CA, . . . Pugh BF. (2016) Mol Cell Biol 36:157-172.
  • Genomic Organization of Human Transcription Initiation Complexes. Pugh BF, Venters BJ. (2016) PLoS One 11:e0149339.
  • Transcriptome regulation and chromatin occupancy by E2F3 and MYC in mice. Tang X, Liu H, Srivastava A, Pecot T, Chen Z, Wang Q, . . . Leone G. (2016) Sci Data 3:160008.
  • Deciphering the regulon of a GntR family regulator via transcriptome and ChIP-exo analyses and its contribution to virulence in Xanthomonas citri. Zhou X, Yan Q, Wang N. (2016) Mol Plant Pathol doi:10.1111/mpp.12397.
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ChIP-Seq
Chromatin Immunoprecipitation Sequencing
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Peconic provides end-to-end ultra-high resolution ChIP-seq services. We start with your antibody and cell pellet and deliver >20 million paired-end reads per sample, along with controls, statistics, and data analysis at near single-bp resolution.

Peconic provides end-to-end ultra-high resolution ChIP-seq services. We start with your antibody and cell pellet and deliver >20 million paired-end reads per sample, along with controls, statistics, and data analysis at near single-bp resolution.

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DNA Libraries
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Bioinformatics
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ChIP-Exo
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Chromatin immunoprecipitation, or “ChIP”, is a means by which the genomic binding locations for a protein can be identified. This involves formaldehyde-based crosslinking of proteins to DNA to covalently trap proteins at their physiologically-bound locations in vivo. Genomic binding sites are separated from other sites by... Show more »

Chromatin immunoprecipitation, or “ChIP”, is a means by which the genomic binding locations for a protein can be identified. This involves formaldehyde-based crosslinking of proteins to DNA to covalently trap proteins at their physiologically-bound locations in vivo. Genomic binding sites are separated from other sites by sonication, which shears chromosomes into small fragments of ~200-1000 bp. The protein of interest is then purified using immobilized antibodies directed against the protein. The random cleavage of DNA by the sonication process limits mapping resolution to about ±100 bp. To improve this resolution, ChIP-exo employs lambda exonuclease to trim the randomly cleaved ends up to the point of where the protein is crosslinked to DNA, thereby diminishing the uncertainty to about a few base pairs. Since the trimming is exclusively in the 5’- 3’ direction, DNA sequences downstream (more 3’) of the exonuclease block site remain intact, and thus are sufficiently long to allow unique identification by deep sequencing.

​Details of the method can be found in a publication by H.S. Rhee and B.F. Pugh in Cell 2011, 147(6):1408-1419 titled “Comprehensive genome-wide protein-DNA interactions detected at single-nucleotide resolution.” It should be noted that ChIP-exo is an experimental method with many complicated steps that may fail for technical reasons, or because the protein of interest may not "ChIP" very well.

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Biology
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Biochemistry & Molecular Biology
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Biomolecular Interaction Analysis
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Protein-DNA Interaction Analysis
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Chromatin Immunoprecipitation (ChIP) Assays
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Nucleic Acid Services
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DNA Services
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Computational Modeling
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Biostatistics & Bioinformatics
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