Category Ranking
98%
Total Visits
921
Avg Visit Duration
2 minutes
Citations
20
Article Abstract
ATAC-seq (assay for transposase-accessible chromatin using sequencing) enables high resolution mapping of chromatin accessibility, providing critical insights into gene regulatory mechanisms in neuroscience research. This protocol presents an optimized approach for applying ATAC-seq to neural tissues and cells, addressing the unique challenges of preserving chromatin integrity in these delicate samples. We detail the key steps of tissue processing, nuclear isolation, transposition reactions, and library preparation specifically adapted for neural applications. The method requires minimal starting material (20,000-50,000 cells) while maintaining high sensitivity for detecting regulatory elements involved in neural development, plasticity, and neurological disorders. This tailored protocol facilitates robust investigation of neuroepigenomic regulation in diverse experimental contexts.
Download full-text PDF |
Source |
|---|---|
| http://dx.doi.org/10.1007/s12565-025-00850-5 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
Optimized ChIP-exo for mammalian cells and patterned sequencing flow cells.
bioRxiv
August 2025
Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA.
By combining chromatin immunoprecipitation (ChIP) with an exonuclease digestion of protein-bound DNA fragments, ChIP-exo characterizes genome-wide protein-DNA interactions at near base-pair resolution. However, the widespread adoption of ChIP-exo has been hindered by several technical challenges, including lengthy protocols, the need for multiple custom reactions, and incompatibilities with recent Illumina sequencing platforms. To address these barriers, we systematically optimized and adapted the ChIP-exo library construction protocol for the unique requirements of mammalian cells and current sequencing technologies.
View Article and Find Full Text PDFAutomated chromatin profiling with spa-ChIP seq uncovers the impacts of condition variations.
bioRxiv
August 2025
Department of Medicine, Division of Genomics & Precision Medicine, University of California San Diego, La Jolla, CA.
Chromatin immunoprecipitation followed by sequencing (ChIP-seq) is a well-established method for studying the genomic localization of DNA-associated proteins. Yet, while useful, most ChIP-seq protocols include multiple manual steps that can introduce inconsistency and make it burdensome to analyze large sample sets, limiting the inclusion of appropriate replicates and other controls. Although some of these challenges were addressed by incorporation of liquid handling platforms, most of those previous efforts have automated only a subset of the ChIP-seq steps.
View Article and Find Full Text PDFA 17.1 kb duplication downstream GATA6 is strongly associated with egg weight in chicken.
BMC Genomics
August 2025
Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, Huazhong Agricultural University, Wuhan, Hubei Province, 430070, China.
Egg weight (EW) is one of the most economically important traits in chickens. Recent statistics show that the EWs of most yellow-feathered chickens in China fall within the 40 ~ 50 g range, while, Danzhou (DZH) chickens exhibit significantly lower EW compared to this range. Here, we aim to identify candidate genes and regulatory variants involved in EW control by conducting a genome-wide association study (GWAS) with high-density SNPs obtained from whole-genome sequencing (WGS).
View Article and Find Full Text PDFChrom-Sig: de-noising 1-dimensional genomic profiles by signal processing methods.
bioRxiv
August 2025
Gilbert S. Omenn Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA.
Motivation: Modern genomic research is driven by next-generation sequencing experiments such as ChIP-seq, CUT&Tag, and CUT&RUN that generate coverage files for transcription factor binding, as well as ATAC-seq that yield coverage files for chromatin accessibility. Due to the inherent technical noise present in the experimental protocols, researchers need statistically rigorous and computational efficient methods to extract true biological signal from a mixture of signal and noise. However, existing approaches are often computationally demanding or require input or spike-in controls.
View Article and Find Full Text PDFProtocol for measuring endogenous 24(S),25-epoxycholesterol and inducing innate immune memory in mouse macrophages.
STAR Protoc
August 2025
Hainan Academy of Medical Sciences, Hainan Medical University, Haikou, P.R. China. Electronic address:
Multiple metabolic pathways and metabolites are involved in innate immune memory induction of macrophages; however, protocols for in vitro-trained immunity assays induced by metabolites in mouse macrophages are limited. Here, we present a protocol for measuring endogenous 24(S),25-epoxycholesterol and inducing innate immune memory in mouse macrophages. We describe steps for sample preparation, measurement of 24(S),25-epoxycholesterol, and establishment of an in vitro-trained immunity model.
View Article and Find Full Text PDF