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Escherichia coli

ABSTRACT: Data Exploration, Quality Control and Statistical Analysis of ChIP-exo/nexus Experiments

PROVIDER: PRJNA338159 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR4011420.fastq.gz	Fastqsanger.gz
	SRR4011421.fastq.gz	Fastqsanger.gz
	SRR4011423.fastq.gz	Fastqsanger.gz
	SRR4011425.fastq.gz	Fastqsanger.gz
	SRR4011416.fastq.gz	Fastqsanger.gz

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Data Exploration, Quality Control and Statistical Analysis of ChIP-exo/nexus Experiments

Project description:ChIP-exo/nexus experiments present modifications on the commonly used ChIP-seq protocol for high resolution mapping of transcription factor binding sites. Although many aspects of the ChIP-exo data analysis are similar to those of ChIP-seq, these high throughput experiments pose a number of unique quality control and analysis challenges. We develop a statistical quality control pipeline and accompanying R package, ChIPexoQual, to enable exploration and analysis of ChIP-exo and related experiments. ChIPexoQual evaluates a number of key issues including strand imbalance, library complexity, and signal enrichment of data. Assessment of these features are facilitated through diagnostic plots and summary statistics calculated over regions of the genome with varying levels of coverage. We evaluated our QC pipeline with both large collections of public ChIP-exo/nexus data and multiple, new ChIP-exo datasets from E. coli. ChIPexoQual analysis of these datasets resulted in guidelines for using these QC metrics across a wide range of sequencing depths and provided further insights for modelling ChIP-exo data. Finally, although ChIP-exo experiments have been compared to ChIP-seq experiments with single-end (SE) sequencing, we provide, for the first time, comparisons with paired-end (PE) ChIP-seq experiments. We illustrate that, at fixed sequencing depths, ChIP-exo provides higher sensitivity, specificity, and spatial resolution than PE ChIP-seq and both significantly outperform their SE ChIP-seq counterpart.

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ena-DATASET-UH-tumor-30-04-2018-10:14:30:708-124 - samples

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Project description:Understanding how eukaryotic enhancers are bound and regulated by specific combinations of transcription factors is still a major challenge. To better map transcription factor binding genome-wide at nucleotide resolution in vivo, we have developed a robust ChIP-exo protocol called ChIP-nexus (chromatin immunoprecipitation experiments with nucleotide resolution through exonuclease, unique barcode and single ligation), which utilizes an efficient DNA self-circularization step during library preparation. Application of ChIP-nexus to four proteins—human TBP, Drosophila NFkB, Twist and Max—showed that it outperformed existing ChIP protocols in resolution and specificity, pinpointed relevant binding sites within enhancers containing multiple binding motifs, and allowed for the analysis of in vivo binding specificities. Notably, we show that Max frequently interacted with DNA sequences next to its motif, and that this binding pattern correlated with local DNA-sequence features such as DNA shape. ChIP-nexus will be broadly applicable to the study of in vivo transcription factor binding specificity and its relationship to cis-regulatory changes in humans and model organisms.

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Escherichia coli

Project description:Integrated analysis of molecular and systems level function of the Crp regulon [ChIP-exo]

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RNA Polymerase II CTD phosphatase Rtr1 restricts noncoding transcript termination by Nrd1

Project description:RNA Seq and ChIP-exo experiments related to this project

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