Chip sequencing databases

Author: jrqc

August undefined, 2024

Web13 rows · Recent advances in chromatin immunoprecipitation followed by sequencing ( … WebCaenorhabditis elegans, a free-living soil nematode, is widely used as a model organism. It is transparent, and consists of 959 somatic cells. This easily cultured worm provides a model for complex organ systems, as well as developmental biology and genetics. Caenorhabditis elegans was the first multicellular eukaryotic genome to be completely ...

The analysis of ChIP-Seq data - PubMed

Web10 years recent experience on high throughput NGS sequencing data analysis: genome assembly, annotation, Chip-seq, single-cell, and bulk RNA-seq, RRBS methylation, variation discovery. WebApr 7, 2024 · Transcription factors (TFs) play central roles in regulating gene expression. With the rapid growth in the use of high-throughput sequencing methods, there is a need to develop a comprehensive data processing and analyzing framework for inferring influential TFs based on ChIP-seq/ATAC-seq datasets. Here, we introduce FindIT2 (Find … chip b vimeo

RetSeq Database

WebChIP-sequencing, also known as ChIP-seq, is a method used to analyze protein interactions with DNA. ... Massively parallel sequence analyses are used in conjunction with whole-genome sequence databases to analyze … WebChIP-Seq Data The primary data for published Broad Institute ChIP-Seq experiments have been deposited to the NCBI GEO database under the following accessions: Mikkelsen et … WebGenome-wide association studies have identified over 150 risk loci that increase prostate cancer risk. However, few causal variants and their regulatory mechanisms have been characterized. In this study, we utilized our previously developed single-nucleotide polymorphisms sequencing (SNPs-seq) technology to test allele-dependent protein … grantheatingelectricalrepa

ChIPSummitDB: a ChIP-seq-based database of human …

Database for Plant Transcription Factor Binding Sites

WebThe 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, … WebJan 8, 2024 · The database was annotated with potential functions of super-enhancers in the gene regulation. The current version of SEdb documented a total of 331 601 super-enhancers from 542 samples. Especially, unlike existing super-enhancer databases, we manually curated and classified 410 available H3K27ac samples from >2000 ChIP-seq … chip butty sandwich menu ukhttp://rna.sysu.edu.cn/chipbase/ chip butty wikipedia

"WebWe also explored the ChIP-seq data in the Cistrome database to identify the relationship between FOXA1 and GJB1. Based on this analysis of the ChIP-seq data, we found that FOXA1 could bind to the GJB1 promoter . Furthermore, we performed ChIP-qPCR in cells of the OC cell lines A2780 or SKOV3 to further determine whether FOXA1 directly binds to ... " - Chip sequencing databases

Chip sequencing databases

WebJan 14, 2024 · The ChIP-seq peaks and the protein-binding DNA motifs under them can be further analyzed, and the resulted data can be integrated into a higher level database, … WebChIP-Atlas: Peak Browser Visualizes protein binding on given genomic loci with IGV genome browser Tutorial movies H.sapiens (hg38) H. sapiens (hg19) M. musculus …

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http://rna.sysu.edu.cn/chipbase/ WebFeb 27, 2024 · ChIPSummitDB – A ChIP-seq-based database of human transcription factor binding sites and the topological arrangements of the proteins bound to them ; ChIPSummitDB contains ~4,000 uniformly processed human ChIP-seq data sets and determines the cistrome for 292 TFs together with the distances between the TF binding …

WebOct 4, 2024 · ChIP-Atlas An integrative, comprehensive database to explore public Epigenetic dataset, including ChIP-Seq, DNase-Seq, ATAC-Seq, and Bisulfite-Seq data: ChIP-Atlas covers almost all public data archived in Sequence Read Archive of NCBI, … ChIP-Atlas: Peak Browser Visualizes protein binding on given genomic loci … ChIP-Atlas: Target Genes Predict target genes bound by given transcription … ChIP-Atlas: Colocalization Predict partner proteins colocalizing with given … ChIP-Atlas: Enrichment Analysis Predict proteins bound to given genomic loci … The list of publications that used ChIP-Atlas database. Toggle navigation ChIP-Atlas … ChIP-Atlas: Dataset Search Search for data by keywords Simple search Detailed … WebChIPBase v3.0 identified ~151,187,000 regulatory relationships between ~171,600 genes and ~3,000 regulators by analyzing ~55,000 ChIP-seq datasets, which represent a 30-fold expansion. Moreover, we de novo identified ~29,000 motif matrices of transcription factors. In addition, we constructed a novel “Enhancer” module to predict ~1,837,200 regulation …

WebTips. Check what factors regulate your gene of interest, what factors bind in your interval or have a significant binding overlap with your peak set. Have a try at CistromeDB Toolkit. If you have a T ranscription Cistrome-GO help you predict the function of this TF. Please help us curate the samples which has incorrect meta-data annotation by ... WebDec 7, 2015 · 9 years of close collaboration with scientists in cancer genomic research, routinely working on varieties of next generation …

WebSep 7, 2024 · Chromatin immunoprecipitation (ChIP) has ushered in a new era of scientific discovery by allowing new insights into DNA-protein interactions. ChIP is used to …

WebOct 21, 2024 · Plant ChIP-seq Database (PCBase) is a sub-database integrated into PlantPAN. PCBase collects plant ChIP-seq experimental data derived from the Gene … chip buxton urbanna vaWebThe accumulated data of chromatin immunoprecipitation sequencing (ChIP-seq) provide great opportunities to discover the TF-target regulations across different conditions. In this study, we constructed a database named hTFtarget, which integrated huge human TF target resources (7190 ChIP-seq samples of 659 TFs and high-confidence binding sites ... chip byWebThis database of transcription factor (TF) to target gene interactions was constructed by combining: 1) human genome sequence, 2) ... ChIP-seq with antibodies specific to a particular TF provides a means to empirically determine the genome-wide binding locations for a specific TF. We compare our predicted TF to target gene interactions to ... grant heating and cooling systemsWebAbstract Chromatin immunoprecipitation coupled with ultra-high-throug put parallel DNA sequencing (ChIP-seq) is an effective technology for the investigation of genome-wide … chip butty song sheffield utdWebJan 14, 2024 · ChIP-seq data collection from public databases. We searched for human ChIP-seq experiments in the NCBI SRA database according to its status as per 1 November 2024. We used the NCBI’s run selector feature to download all available metadata associated with the selected experiments . A custom PERL script was used to … grant heard wifeWebHowever, because of the complex, multistaged analysis workflow, it is still difficult for an experimental investigator to conduct the analysis of his or her own ChIP-seq data. In this chapter, we review the basic design of ChIP-seq experiments and provide an in-depth tutorial on how to prepare, to preprocess, and to analyze ChIP-seq datasets. grant heartsWebThe 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. ... (MGA) database. MGA-Search: Fast full-text search of our local collection of publicly available datasets ... chip buyers