Analysis of ChIP-Seq data identifies CzcR regulon
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA645690 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR12203059_1.fastq.gz | Fastqsanger.gz | |||
| SRR12203059_2.fastq.gz | Fastqsanger.gz | |||
| SRR12203060_1.fastq.gz | Fastqsanger.gz | |||
| SRR12203060_2.fastq.gz | Fastqsanger.gz | |||
| SRR12203061_1.fastq.gz | Fastqsanger.gz |
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Project description:Analysis of ChIP-Seq data identifies BfmR regulon
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Project description:Analysis of ChIP-Seq data identifies BfmR and CzcR regulons
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Project description:Purpose:To identify the direct targets and regulatory mechanism of CzcR in Pseudomonas aeruginosa, we performed chromatin immunoprecipitation (ChIP) followed by high-throughput sequencing (Seq). Methods: In the experiment, chromatin bound CzcR was crosslinked, sheared, bound to antibody, nonspecific proteins and nucleic acids removed, purified and sequenced. The sequencing data were obtained from several independent ChIP samples and then located on the p. aeruginosa genome. The MACS (Model-based Analysis for ChIP-Seq) software was used to call peak for sequence reads. Results: We identified 108 enriched loci (p-value≤1e-5; fold enrichment>1) containing CzcR binding peak in the P. aeruginosa genome. In accordance with the previous studies, oprD, phzA1 promoters were significantly enriched compared to input DNA (80, 76-fold, respectively).
2021-04-13 | GSE154265 | GEO
Project description:Purpose:To identify the direct targets and regulatory mechanism of BfmR in Pseudomonas aeruginosa, we performed chromatin immunoprecipitation (ChIP) followed by high-throughput sequencing (Seq). Methods: In the experiment, chromatin bound BfmR was crosslinked, sheared, bound to antibody, nonspecific proteins and nucleic acids removed, purified and sequenced. The sequencing data were obtained from several independent ChIP samples and then located on the p. aeruginosa genome. The MACS (Model-based Analysis for ChIP-Seq) software was used to call peak for sequence reads. Results: We identified 141 enriched loci (p-value≤1e-5; fold enrichment>3) containing BfmR binding peak in the P. aeruginosa genome. In accordance with the previous studies, bfmR, PA4103 promoters were significantly enriched compared to input DNA (49, 60-fold, respectively), had the highest degree of enrichment in all peaks.
2021-04-13 | GSE154264 | GEO
Project description:SarA regulon in S. aureus (ChIP-seq)
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Project description:Arabidopsis thaliana CHIP, CHIP [Source:UniProtKB/TrEMBL;Acc:A0A178VGJ7], is differentially expressed in 100 experiment(s);
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Project description:Arabidopsis thaliana CHIP, CHIP [Source:UniProtKB/TrEMBL;Acc:A0A178VGJ7], is expressed in 13 baseline experiment(s);
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Project description:MotivationAlthough chromatin immunoprecipitation coupled with high-throughput sequencing (ChIP-seq) or tiling array hybridization (ChIP-chip) is increasingly used to map genome-wide-binding sites of transcription factors (TFs), it still remains difficult to generate a quality ChIPx (i.e. ChIP-seq or ChIP-chip) dataset because of the tremendous amount of effort required to develop effective antibodies and efficient protocols. Moreover, most laboratories are unable to easily obtain ChIPx data for one or more TF(s) in more than a handful of biological contexts. Thus, standard ChIPx analyses primarily focus on analyzing data from one experiment, and the discoveries are restricted to a specific biological context.ResultsWe propose to enrich this existing data analysis paradigm by developing a novel approach, ChIP-PED, which superimposes ChIPx data on large amounts of publicly available human and mouse gene expression data containing a diverse collection of cell types, tissues and disease conditions to discover new biological contexts with potential TF regulatory activities. We demonstrate ChIP-PED using a number of examples, including a novel discovery that MYC, a human TF, plays an important functional role in pediatric Ewing sarcoma cell lines. These examples show that ChIP-PED increases the value of ChIPx data by allowing one to expand the scope of possible discoveries made from a ChIPx experiment.Availabilityhttp://www.biostat.jhsph.edu/~gewu/ChIPPED/
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Project description:Chromatin immunoprecipitation (ChIP) followed by microarray hybridization (ChIP-chip) or high-throughput sequencing (ChIP-seq) allows genome-wide discovery of protein-DNA interactions such as transcription factor bindings and histone modifications. Previous reports only compared a small number of profiles, and little has been done to compare histone modification profiles generated by the two technologies or to assess the impact of input DNA libraries in ChIP-seq analysis. Here, we performed a systematic analysis of a modENCODE dataset consisting of 31 pairs of ChIP-chip/ChIP-seq profiles of the coactivator CBP, RNA polymerase II (RNA PolII), and six histone modifications across four developmental stages of Drosophila melanogaster.Both technologies produce highly reproducible profiles within each platform, ChIP-seq generally produces profiles with a better signal-to-noise ratio, and allows detection of more peaks and narrower peaks. The set of peaks identified by the two technologies can be significantly different, but the extent to which they differ varies depending on the factor and the analysis algorithm. Importantly, we found that there is a significant variation among multiple sequencing profiles of input DNA libraries and that this variation most likely arises from both differences in experimental condition and sequencing depth. We further show that using an inappropriate input DNA profile can impact the average signal profiles around genomic features and peak calling results, highlighting the importance of having high quality input DNA data for normalization in ChIP-seq analysis.Our findings highlight the biases present in each of the platforms, show the variability that can arise from both technology and analysis methods, and emphasize the importance of obtaining high quality and deeply sequenced input DNA libraries for ChIP-seq analysis.
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