ArticleMethods in enzymology2015
ChIP-seq and RNA-seq methods to study circadian control of transcription in mammals.
Article in Methods in enzymology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed.
- Nonenzymatic detection and imaging of m6A-methylated RNA via proximity hybridization-initiated hybridization chain reaction with site-specific recognition.Analytical and bioanalytical chemistry · 2026Article
- Advances in monitoring mammalian circadian components and their rhythms using reporter systems.RSC chemical biology · 2026Review
- Super-enhancer-driven recruitment of C/EBPβ by SULT1B1 is implicated in metabolic dysfunction-associated steatotic liver disease progression.Clinical epigenetics · 2026Article
- Single-Cell Multiomic Analysis of Circadian Rhythmicity in Mouse Liver.bioRxiv : the preprint server for biology · 2025Article
- Roles of circadian clocks in macrophage metabolism: implications in inflammation and metabolism of lipids, glucose, and amino acids.American journal of physiology. Endocrinology and metabolism · 2025Review
- Loss ofZoological research · 2024Article
- Circadian alignment of early onset caloric restriction promotes longevity in male C57BL/6J mice.Science (New York, N.Y.) · 2022Article
- Combined glyoxalase 1 dysfunction and vitamin B6 deficiency in a schizophrenia model system causes mitochondrial dysfunction in the prefrontal cortex.Redox biology · 2021Article
- Gene-expression correlates of the oscillatory signatures supporting human episodic memory encoding.Nature neuroscience · 2021Article
- Disruption of Circadian Transcriptome in Lung by Acute Sleep Deprivation.Frontiers in genetics · 2021Article
- An Optimal Time for Treatment-Predicting Circadian Time by Machine Learning and Mathematical Modelling.Cancers · 2020Review
- Article
- The malaria parasite has an intrinsic clock.Science (New York, N.Y.) · 2020Article
- Dysregulated H3K27 Acetylation Is Implicated in Fatty Liver Hemorrhagic Syndrome in Chickens.Frontiers in genetics · 2020Article
- Accelerated evolution of oligodendrocytes in the human brain.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
- Improving Gene Regulatory Network Inference by Incorporating Rates of Transcriptional Changes.Scientific reports · 2017Article
- Foxp1 in Forebrain Pyramidal Neurons Controls Gene Expression Required for Spatial Learning and Synaptic Plasticity.The Journal of neuroscience : the official journal of the Society for Neuroscience · 2017Article
- HCFC2 is needed for IRF1- and IRF2-dependentThe Journal of experimental medicine · 2017Article
- Novel transcriptional networks regulated by CLOCK in human neurons.Genes & development · 2017Article
- Foxp1 regulation of neonatal vocalizations via cortical development.Genes & development · 2017Article
Corrections and comments
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Authors and funding
7 authors.
Funding
Abstract
Genome-wide analyses have revolutionized our ability to study the transcriptional regulation of circadian rhythms. The advent of next-generation sequencing methods has facilitated the use of two such technologies, ChIP-seq and RNA-seq. In this chapter, we describe detailed methods and protocols for these two techniques, with emphasis on their usage in circadian rhythm experiments in the mouse liver, a major target organ of the circadian clock system. Critical factors for these methods are highlighted and issues arising with time series samples for ChIP-seq and RNA-seq are discussed. Finally, detailed protocols for library preparation suitable for Illumina sequencing platforms are presented.
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