Protocol for using heterologous spike-ins to normalize for technical variation in chromatin immunoprecipitation [PDF]
STAR Protocols, 2021 Summary: Quantifying differential genome occupancy by chromatin immunoprecipitation (ChIP) remains challenging due to variation in chromatin fragmentation, immunoprecipitation efficiencies, and intertube variability. In this protocol, we add heterologous
Franziska Greulich +1 more
exaly +4 more sources
Protocol for chromatin immunoprecipitation of histone modifications in frozen adipose tissue [PDF]
STAR ProtocolsSummary: Chromatin immunoprecipitation (ChIP) combined with sequencing has revolutionized our understanding of gene regulation; however, its application to frozen adipose tissue presents unique challenges due to the high levels of lipid content. Here, we
Matthias Blüher
exaly +4 more sources
Protocol to investigate bivalent histone modification dynamics via chromatin immunoprecipitation followed by re-chromatin immunoprecipitation [PDF]
STAR ProtocolsSummary: Epigenetic modifications play key roles in regulating transcription by altering chromatin structure and accessibility in response to internal cues or external stimuli.
Zhengyao Shao, Hong Qiao
doaj +2 more sources
An optimized two-step chromatin immunoprecipitation protocol to quantify the associations of two separate proteins and their common target DNA [PDF]
STAR Protocols, 2021 Summary: Sequential chromatin immunoprecipitation (ChIP) is commonly used to investigate DNA-protein and protein-protein interactions to a specific genomic region. However, it can be tricky to achieve a robust and reproducible signal with sequential ChIP.
Lingli He +3 more
doaj +2 more sources
Cell-free chromatin immunoprecipitation to detect molecular pathways in heart transplantation [PDF]
Life Science Alliance, 2023 Cell-free DNA chromatin immunoprecipitation detects molecular pathways and profiles the sources of tissue injury in heart transplant patients. Existing monitoring approaches in heart transplantation lack the sensitivity to provide deep molecular ...
Moon Kyoo Jang +5 more
doaj +2 more sources
Optimized protocols for chromatin immunoprecipitation of exogenously expressed epitope-tagged proteins [PDF]
STAR Protocols, 2023 Summary: Chromatin immunoprecipitation (ChIP) assay is widely used for investigating the interaction between DNA and DNA-binding proteins such as transcription factors, co-factors, or chromatin-associated proteins.
Wentong Fang, Chengheng Liao, Qing Zhang
doaj +2 more sources
Protocol for in vivo chromatin immunoprecipitation on purified chromatin isolated from mouse liver nuclei [PDF]
STAR ProtocolsSummary: Chromatin immunoprecipitation (ChIP) is used to investigate genome binding by transcription factors, but it can be problematic. We present a protocol to isolate fixed DNA-protein complexes from mouse liver prior to chromatin shearing.
Lei Li, May G. Akl, Scott B. Widenmaier
doaj +2 more sources
An Optimized Chromatin Immunoprecipitation Protocol for Quantification of Protein-DNA Interactions [PDF]
STAR Protocols, 2020 Summary: Transcription factors are important regulators of cell fate and function. Knowledge about where transcription factors are bound in the genome is crucial for understanding their function.
Wim J. de Jonge +3 more
doaj +2 more sources
A low-input high resolution sequential chromatin immunoprecipitation method captures genome-wide dynamics of bivalent chromatin [PDF]
Epigenetics & ChromatinBackground Bivalent chromatin is an exemplar of epigenetic plasticity. This co-occurrence of active-associated H3K4me3 and inactive-associated H3K27me3 histone modifications on opposite tails of the same nucleosome occurs predominantly at promoters that ...
Janith A. Seneviratne +3 more
doaj +2 more sources
A Computational Model of Quantitative Chromatin Immunoprecipitation (ChIP) Analysis
Cancer Informatics, 2008 Chromatin immunoprecipitation (ChIP) analysis is widely used to identify the locations in genomes occupied by transcription factors (TFs). The approach involves chemical cross-linking of DNA with associated proteins, fragmentation of chromatin by ...
Jingping Xie +2 more
exaly +4 more sources