Epitope Tagging ChIP-Seq of DNA Binding Proteins Using CETCh-Seq.
Sign Up to like & getrecommendations! Published in 2020 at "Methods in molecular biology"
DOI: 10.1007/978-1-0716-0301-7_1
Abstract: Chromatin immunoprecipitation followed by next-generation DNA sequencing (ChIP-seq) has been used to identify transcription factor (TF) binding proteins throughout the genome. Unfortunately, this approach traditionally requires commercially available, ChIP-seq grade antibodies that frequently fail to… read more here.
Keywords: seq; chip seq; binding proteins; cetch seq ... See more keywords
User-Friendly and Interactive Analysis of ChIP-Seq Data Using EaSeq.
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DOI: 10.1007/978-1-0716-0301-7_2
Abstract: ChIP-seq is a central method to gain understanding of the regulatory networks in the genome of stem cells and during differentiation. Exploration and analysis of such genome-wide data often leads to unexpected discoveries and new… read more here.
Keywords: chip seq; using easeq; analysis; user friendly ... See more keywords
An Optimized ChIP-Seq Protocol to Determine Chromatin Binding of Estrogen Receptor Beta.
Sign Up to like & getrecommendations! Published in 2022 at "Methods in molecular biology"
DOI: 10.1007/978-1-0716-1920-9_13
Abstract: Estrogen regulates transcription through two nuclear receptors, ERα and ERβ, in a tissue and cellular-dependent manner. Both the receptors bind estrogen and activate transcription through direct or indirect interactions with DNA. Revealing their interactions with… read more here.
Keywords: seq protocol; estrogen; optimized chip; chip ... See more keywords
Native Chromatin Immunoprecipitation-Sequencing (ChIP-Seq) from Low Cell Numbers.
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DOI: 10.1007/978-1-4939-7380-4_14
Abstract: ChIP-seq is the current method of choice for genome-wide protein location analysis. Here, we present a native (non-cross-linked) ChIP procedure suitable for histone proteins, coupled with an efficient library preparation technique for subsequent next-generation sequencing.… read more here.
Keywords: chip seq; sequencing chip; chip; native chromatin ... See more keywords
Chromatin Immunoprecipitation Sequencing (ChIP-Seq) for Transcription Factors and Chromatin Factors in Arabidopsis thaliana Roots: From Material Collection to Data Analysis.
Sign Up to like & getrecommendations! Published in 2018 at "Methods in molecular biology"
DOI: 10.1007/978-1-4939-7747-5_18
Abstract: Chromatin immunoprecipitation combined with next-generation sequencing (ChIP-seq) is a powerful technique to investigate in vivo transcription factor (TF) binding to DNA, as well as chromatin marks. Here we provide a detailed protocol for all the… read more here.
Keywords: chip seq; chromatin; sequencing chip; chromatin immunoprecipitation ... See more keywords
Chromatin Immunoprecipitation and High-Throughput Sequencing (ChIP-Seq): Tips and Tricks Regarding the Laboratory Protocol and Initial Downstream Data Analysis.
Sign Up to like & getrecommendations! Published in 2018 at "Methods in molecular biology"
DOI: 10.1007/978-1-4939-7774-1_15
Abstract: Chromatin immunoprecipitation coupled with high-throughput sequencing (ChIP-seq) has become an essential tool for epigenetic scientists. ChIP-seq is used to map protein-DNA interactions and epigenetic marks such as histone modifications at the genome-wide level. Here we… read more here.
Keywords: chip seq; chip; sequencing chip; throughput sequencing ... See more keywords
How to Tackle Challenging ChIP-Seq, with Long-Range Cross-Linking, Using ATRX as an Example.
Sign Up to like & getrecommendations! Published in 2018 at "Methods in molecular biology"
DOI: 10.1007/978-1-4939-8663-7_6
Abstract: Chromatin immunoprecipitation coupled with high-throughput, next-generation DNA sequencing (ChIP-seq) has enabled researchers to establish the genome-wide patterns of chromatin modifications and binding of chromatin-associated proteins. Well-established protocols produce robust ChIP-seq data for many proteins by… read more here.
Keywords: chip seq; range; dna; chromatin ... See more keywords
Genome-Wide Profiling of Histone Modifications with ChIP-Seq.
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DOI: 10.1007/978-1-4939-9865-4_9
Abstract: Chromatin immunoprecipitation coupled with sequencing (ChIP-seq) is a widely used method for mapping the genome-wide locations of chromatin-associated proteins. This protocol has been developed and utilized to perform ChIP on histone covalent modifications in various… read more here.
Keywords: chip seq; genome wide; wide profiling; histone ... See more keywords
Identification of Rfx6 target genes involved in pancreas development and insulin translation by ChIP-seq.
Sign Up to like & getrecommendations! Published in 2019 at "Biochemical and biophysical research communications"
DOI: 10.1016/j.bbrc.2018.11.133
Abstract: Regulatory Factor X-box binding transcriptional factor 6 (Rfx6) plays an important role in the differentiation and development of pancreas in mammals. However, the direct target genes of Rfx6 to regulate this process were largely unknown.… read more here.
Keywords: chip seq; target genes; target; insulin translation ... See more keywords
CNN-Peaks: ChIP-Seq peak detection pipeline using convolutional neural networks that imitate human visual inspection
Sign Up to like & getrecommendations! Published in 2020 at "Scientific Reports"
DOI: 10.1038/s41598-020-64655-4
Abstract: ChIP-seq is one of the core experimental resources available to understand genome-wide epigenetic interactions and identify the functional elements associated with diseases. The analysis of ChIP-seq data is important but poses a difficult computational challenge,… read more here.
Keywords: chip seq; neural networks; convolutional neural; cnn peaks ... See more keywords
Enzymatic methods for genome-wide profiling of protein binding sites
Sign Up to like & getrecommendations! Published in 2018 at "Briefings in Functional Genomics"
DOI: 10.1093/bfgp/elx030
Abstract: Genome-wide mapping of protein-DNA interactions is a staple approach in many areas of modern molecular biology. Genome-wide profiles of protein-binding sites are most commonly generated by chromatin immunoprecipitation and high-throughput sequencing (ChIP-seq). Although ChIP-seq has… read more here.
Keywords: chip seq; genome wide; binding sites; protein binding ... See more keywords