ChIP-Atlas
A data-mining suite for exploring epigenomic landscapes by fully integrating 428,000 ChIP-seq, ATAC-seq and Bisulfite-seq experiments. This work is supported by NIG Supercomputer system and JST NBDC JPMJND2202. All data and analysis tools provided by ChIP-Atlas are licensed under CC-BY 4.0 .
ChIP sequencing - Wikipedia
ChIP-sequencing, also known as ChIP-seq, is a method used to analyze protein interactions with DNA. ChIP-seq combines chromatin immunoprecipitation (ChIP) with massively parallel DNA sequencing to identify the binding sites of DNA-associated proteins.
Basics of ChIP-seq data analysis - Bioconductor
This vignette describes steps of a basic analysis of ChIP-seq data. To exemplify this tutorial, we use ChIP-seq data for the lysine 27 acetylation of the histone H3 (i.e H3K27ac).
ChIP-Seq - Expasy
The ChIP-Seq Web Server provides access to a set of useful tools performing common ChIP-seq data analysis tasks, including positional correlation analysis, peak detection, and genome partitioning into signal-rich and signal-poor regions.
Chromatin Immunoprecipitation Sequencing (ChIP-Seq)
ChIP-Seq identifies the binding sites of DNA-associated proteins and can be used to map global binding sites for a given protein. ChIP-Seq typically starts with crosslinking of DNA-protein complexes. Samples are then fragmented and treated with an exonuclease to trim unbound oligonucleotides.
Practical Guidelines for the Comprehensive Analysis of ChIP-seq Data
We address all the major steps in the analysis of ChIP-seq data: sequencing depth selection, quality checking, mapping, data normalization, assessment of reproducibility, peak calling, differential binding analysis, controlling the false discovery rate, peak annotation, visualization, and motif analysis.
ChIP‐Atlas: a data‐mining suite powered by full integration of …
ChIP‐Atlas is able to show alignment and peak‐call results for all public ChIP‐seq and DNase‐seq data archived in the NCBI Sequence Read Archive (SRA), which encompasses data derived from GEO, ArrayExpress, DDBJ, ENCODE, Roadmap Epigenomics, and the scientific literature.
ChIP-qPCR analysis of RNApolII enrichment in GAPDH promoters in MBD-231 cells chromatin using High-sensitivity ChIP Kit (ab185913). Library obtained from 0.2 ng of human placenta DNA using High Sensitivity DNA Library Preparation Kit (ab185905). Size distribution of …
Methods for ChIP-seq analysis: A practical workflow and …
Mar 1, 2021 · In this review, we first present a typical ChIP-seq analysis workflow, from quality assessment to chromatin-state annotation. We focus on practical, rather than theoretical, approaches for biological studies.
ChIP-Seq Analysis | Bioinformatics Lab | UT Southwestern, Dallas, …
Our ChIP-Seq Analysis Workflow. Our ChIP-Seq analysis pipeline integrates state-of-the-art tools and algorithms to ensure precise results and actionable insights. The key steps in our workflow include: Pre-processing: Quality control (QC) of raw sequencing data using tools like FastQC. Read trimming and filtering to ensure high-quality input data.