Chromatin immunoprecipitation and microarray-based analysis of protein location

By Tong Ihn Lee, Sarah E. Johnstone, Richard A. Young. Nature Protocols, 2006

789 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/e33782ae9206db98a59da8f210c73e4574a3f3ee

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Citations in the corpus

Whole-genome ChIP-chip analysis of Dorsal, Twist, and Snail suggests integration of diverse patterning processes in the Drosophila embryo. (2007, methodology): “The ChIP–chip protocol was developed based on protocols from the Young and Maschat laboratories (Chanas et al. 2004; Lee et al. 2006; see Supplemental Material).”
HSF1 drives a transcriptional program distinct from heat shock to support highly malignant human cancers. (2012, positive): “ChIP-Seq and ChIP-qPCR ChIP-qPCR and ChIP-Seq experiments were performed as described previously (Lee et al., 2006), with modifications detailed in Extended Experimental Procedures.”
Cell type-specific profiling of protein-DNA interactions without cell isolation using Targeted DamID with next-generation sequencing (2007, positive): “Currently, two techniques exist to determine the genomic binding patterns of DNA-interacting proteins: (1) chromatin immunoprecipitation combined with either microarray detection (‘‘ChIP-on-chip’’)1–4 or mass sequencing5 and (2) DamID, which is based on targeted adenine methylation6–9.”
Densely interconnected transcriptional circuits control cell states in human hematopoiesis (2011, positive): “The protocol for Chromatin Immunoprecipitation (ChIP) was performed as previously described (Lee et al., 2006).”
Distinct factors control histone variant H3.3 localization at specific genomic regions (2010, methodology): “ChIP and ChIP-Seq Crosslinking and native ChIP were performed as described (Barski et al., 2007; Lee et al., 2006), with minor modifications as detailed in the Extended Experimental Procedures.”
YY1 Is a Structural Regulator of Enhancer-Promoter Loops (2017, positive): “Chromatin Immunoprecipitation (ChIP)—ChIP was performed as described in (Lee et al., 2006) with a few adaptations.”
Dynamic and Coordinated Epigenetic Regulation of Developmental Transitions in the Cardiac Lineage (2012, neutral): “Chromatin immunoprecipitations were performed according to the Young lab protocol (Lee et al., 2006) with minor modification.”
PPARgamma and C/EBP factors orchestrate adipocyte biology via adjacent binding on a genome-wide scale. (2008, methodology): “(Lee et al. 2006), limited DNase I (Ambion) digestion to fragment DNA to average size of ∼200–300 bp, and labeling with”
Advances and Trends in Omics Technology Development (2022, methodology): “ChIP sequencing, coupling ChIP with NGS, outweighs ChIP-Chip by generating outputs with higher spatial resolution, dynamic range, and genomic coverage and, importantly, capable of exploring any species with a sequenced genome in principle (181, 182).”
Annotating non-coding regions of the genome (2010, methodology): “For instance, chromatin immunoprecipitation followed by microarray (ChIP–chip”
Poised chromatin at the ZEB1 promoter enables cell plasticity and enhances tumorigenicity (2013, positive): “ChiP-qPCR Chromatin immunoprecipitation was performed as previously described (Lee et al., 2006).”