Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Escherichia coli

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

PROVIDER: PRJNA338159 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			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

Items per page:

1 - 5 of 8

Similar Datasets

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.

2017-03-01 | GSE84830 | GEO

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

Project description:Chip-exo and Chip-nexus for FOXA1, HNF4A, KLF5, MYC, and TCF7L2 in colorectal cancer cell lines LoVo, GP5D, COLO320DM

| EGAD00001004099 | EGA

ChIP-nexus: a novel ChIP-exo protocol for improved detection of in vivo transcription factor binding footprints

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.

2014-12-02 | GSE55306 | GEO

Escherichia coli

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

| PRJNA272158 | ENA

In vivo probing of promoter overlapping between σ-factors in Escherichia coli (ChIP-Seq)

Project description:An alternative sigma factor (σ32) recognizes the unique set of promoters upon heat shock. Here, we determined 54 σ32 promoters at nucleotide resolution using ChIP-exo, enabling us to compare those with housekeeping σ70 promoters. The results elucidated the overarching principles of promoter overlapping between the two σ-factors, which are sequence-specific non-, half-, and full-shared modes with a perfect sequence conservativeness of −35 element as a key determinant of full-shared mode.

2020-08-12 | GSE60668 | GEO

In vivo probing of promoter overlapping between σ-factors in Escherichia coli (ChIP-exo)

2020-08-12 | GSE60667 | GEO

Optimized ChIP-exo for mammalian cells and patterned sequencing flow cells

Project description:By combining chromatin immunoprecipitation (ChIP) with an exonuclease that digests the ends 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. We introduce a Mammalian-Optimized ChIP-exo (MO-ChIP-exo) protocol that builds upon previous ChIP-exo protocols with systematic optimization of crosslinking, harvesting, and library construction. We validate MO-ChIP-exo by comparing it to previously published ChIP-exo protocols and demonstrate its adaptability to both suspension (K562) and adherent (HepG2, mESC) cell lines. This improved protocol provides a more robust and efficient method for generating high-quality ChIP-exo libraries from mammalian cells.

2025-08-14 | GSE305217 | GEO

Escherichia coli K-12

Project description:Quality control of single amplified genome information by using no template control sequence

| PRJDB4896 | ENA

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

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

2018-09-25 | GSE87657 | GEO