Chromatin immunoprecipitation sequencing(Ch IP-seq)and the Assay for Transposase-Accessible Chromatin with high-throughput sequencing(ATAC-seq)have become essential technologies to effectively measure protein–DNA int...Chromatin immunoprecipitation sequencing(Ch IP-seq)and the Assay for Transposase-Accessible Chromatin with high-throughput sequencing(ATAC-seq)have become essential technologies to effectively measure protein–DNA interactions and chromatin accessibility.However,there is a need for a scalable and reproducible pipeline that incorporates proper normalization between samples,correction of copy number variations,and integration of new downstream analysis tools.Here we present Containerized Bioinformatics workflow for Reproducible Ch IP/ATAC-seq Analysis(Co BRA),a modularized computational workflow which quantifies Ch IP-seq and ATAC-seq peak regions and performs unsupervised and supervised analyses.Co BRA provides a comprehensive state-of-the-art Ch IP-seq and ATAC-seq analysis pipeline that can be used by scientists with limited computational experience.This enables researchers to gain rapid insight into protein–DNA interactions and chromatin accessibility through sample clustering,differential peak calling,motif enrichment,comparison of sites to a reference database,and pathway analysis.Co BRA is publicly available online at https://bitbucket.org/cfce/cobra.展开更多
The Cistrome Data Browser(DB)at the website(cistrome.org/db)provides about 56,000 published human and mouse ChlP-seq,DNase-seq,and ATAC-seq chromatin profiles,which we have processed using uniform analysis and quality...The Cistrome Data Browser(DB)at the website(cistrome.org/db)provides about 56,000 published human and mouse ChlP-seq,DNase-seq,and ATAC-seq chromatin profiles,which we have processed using uniform analysis and quality control pipelines.The Cistrome DB Toolkit at the website(dbtoolkit.cistrome.org)was developed to allow users to investigate fundamental questions using this data collection.In this tutorial,we describe how to use the Cistrome DB to search for publicly available chromatin profiles,to assess sample quality,to access peak results,to visualize signal intensities,to explore DNA sequence motifs,and to identify putative target genes・We also describe the use of the Toolkit module to seek the factors most likely to regulate a gene of interest,the factors that bind to a given genomic interval(enhancer,SNP,etc.),and samples that have significant peak overlaps with user-defined peak sets.This tutorial guides biomedical researchers in the use of Cistrome DB resources to rapidly obtain valuable insights into gene regulatory questions.展开更多
基金funding from the National Institutes of Health,United States(Grant Nos.2PO1CA163227 and P01CA250959)。
文摘Chromatin immunoprecipitation sequencing(Ch IP-seq)and the Assay for Transposase-Accessible Chromatin with high-throughput sequencing(ATAC-seq)have become essential technologies to effectively measure protein–DNA interactions and chromatin accessibility.However,there is a need for a scalable and reproducible pipeline that incorporates proper normalization between samples,correction of copy number variations,and integration of new downstream analysis tools.Here we present Containerized Bioinformatics workflow for Reproducible Ch IP/ATAC-seq Analysis(Co BRA),a modularized computational workflow which quantifies Ch IP-seq and ATAC-seq peak regions and performs unsupervised and supervised analyses.Co BRA provides a comprehensive state-of-the-art Ch IP-seq and ATAC-seq analysis pipeline that can be used by scientists with limited computational experience.This enables researchers to gain rapid insight into protein–DNA interactions and chromatin accessibility through sample clustering,differential peak calling,motif enrichment,comparison of sites to a reference database,and pathway analysis.Co BRA is publicly available online at https://bitbucket.org/cfce/cobra.
基金The authors would like to acknowledge Dr.Zhiping Weng for providing the backup of the Cistrome DB and Dr.Ting Wang for the Wash U Epigenome Gateway BrowserThis work is supported by National Institutes of Health of US(U24 CA237617).
文摘The Cistrome Data Browser(DB)at the website(cistrome.org/db)provides about 56,000 published human and mouse ChlP-seq,DNase-seq,and ATAC-seq chromatin profiles,which we have processed using uniform analysis and quality control pipelines.The Cistrome DB Toolkit at the website(dbtoolkit.cistrome.org)was developed to allow users to investigate fundamental questions using this data collection.In this tutorial,we describe how to use the Cistrome DB to search for publicly available chromatin profiles,to assess sample quality,to access peak results,to visualize signal intensities,to explore DNA sequence motifs,and to identify putative target genes・We also describe the use of the Toolkit module to seek the factors most likely to regulate a gene of interest,the factors that bind to a given genomic interval(enhancer,SNP,etc.),and samples that have significant peak overlaps with user-defined peak sets.This tutorial guides biomedical researchers in the use of Cistrome DB resources to rapidly obtain valuable insights into gene regulatory questions.
