Tag Archives: ChIP-Seq

Semiconductor-based DNA sequencing of histone modification states

October 2013 Authors: Christine S. Cheng, Kunal Rai, Manuel Garber, Andrew Hollinger, Dana Robbins, Scott Anderson, Alyssa Macbeth, Austin Tzou, Mauricio O. Carneiro, Raktima Raychowdhury, Carsten Russ, Nir Hacohen, Jeffrey E. Gershenwald, Niall Lennon, Chad Nusbaum, Lynda Chin, Aviv Regev … more »

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Selective Inhibition of Tumor Oncogenes by Disruption of Super-Enhancers

April 2013 Authors: Jakob Love, Heather A. Hoke, Charles Y. Lin, Ashley Lau, David A. Orlando, Christopher R. Vakoc, James E. Bradner, Tong Ihn Lee, and Richard A. Young Info: The Pippin Prep was used to size-select ChIP-seq libraries. Citation: … more »

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At Iowa Core Lab, Pippin Sizing Is Essential for MicroRNA Studies

Kevin Knudtson’s DNA Facility at the University of Iowa acquired a Pippin Prep almost a year ago, and in the time since, the automated size selection tool has become an integral part of the core lab’s microRNA pipeline. “Pippin is … more »

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SATB1-mediated functional packaging of chromatin into loops

November 2012 Authors: Terumi Kohwi-Shigematsu, Yoshinori Kohwi, Keiko Takahashi, Hunter W. Richards, Stephen D. Ayers, Hye-Jung Han, Shutao Cai Info: Among other things, this paper outlines methods for mapping all DNA binding sites for a global chromatin organizing protein, SATB1. … more »

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Cell Paper Offers New Understanding of Myc Mechanism in Cancer

A big paper came out of Richard Young’s lab at the Whitehead Institute last month in Cell describing the mechanism through which the c-Myc transcription factor causes elevated expression in tumor cells. We were happy to see that the Pippin … more »

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Transcriptional Amplification in Tumor Cells with Elevated c-Myc

September 2012 Authors: Charles Y. Lin, Jakob Loven,Peter B. Rahl, Ronald M. Paranal, Christopher B. Burge, James E. Bradner, Tong Ihn Lee, and Richard A. Young Info: This high impact study completely revises knowledge on how c-myc gene is involved … more »

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ChIP-Seq sample prep tip – Interpreting the apparent presence of a secondary band in size-selected DNA

ChIP-Seq analysis is used to study the control of gene expression by identifying DNA regions that are associated  with chromatin at the time of cellular analysis. The ChIP-Seq procedure typically involves cross-linking DNA to the associated chromatin proteins, sonication to … more »

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