Results 21 to 30 of about 3,719 (149)

Widespread misinterpretable ChIP-seq bias in yeast. [PDF]

PLoS ONE, 2013
Chromatin immunoprecipitation followed by sequencing (ChIP-seq) is widely used to detect genome-wide interactions between a protein of interest and DNA in vivo.
Daechan Park, Yaelim Lee, Gurvani Bhupindersingh, Vishwanath R Iyer   +3 more
doaj   +1 more source

Chromatin topology defines estradiol-primed progesterone receptor and PAX2 binding in endometrial cancer cells

eLife, 2022
Estrogen (E2) and Progesterone (Pg), via their specific receptors (ERalpha and PR), are major determinants in the development and progression of endometrial carcinomas, However, their precise mechanism of action and the role of other transcription ...
Alejandro La Greca, Nicolás Bellora, François Le Dily, Rodrigo Jara, Ana Silvina Nacht, Javier Quilez Oliete, José Luis Villanueva, Enrique Vidal, Gabriela Merino, Cristóbal Fresno, Inti Tarifa Reischle, Griselda Vallejo, Guillermo Vicent, Elmer Fernández, Miguel Beato, Patricia Saragüeta   +15 more
doaj   +1 more source

The classification of mRNA expression levels by the phosphorylation state of RNAPII CTD based on a combined genome-wide approach

BMC Genomics, 2011
Background Cellular function is regulated by the balance of stringently regulated amounts of mRNA. Previous reports revealed that RNA polymerase II (RNAPII), which transcribes mRNA, can be classified into the pausing state and the active transcription ...
Tachibana Taro, Maehara Kazumitsu, Yoshimi Tomohiko, Harada Akihito, Odawara Jun, Okada Seiji, Akashi Koichi, Ohkawa Yasuyuki   +7 more
doaj   +1 more source

Genome-wide Interrogation of Protein-DNA Interactions in Mammalian Cells Using ChIPmentation

STAR Protocols, 2020
Summary: Mapping the genomic locations of chromatin-associated proteins, such as transcription factors and histone modifications, is key to understanding the mechanisms of transcriptional regulation.
Wei Xu, Ying Ye, Andrew D. Sharrocks, Wensheng Zhang, Xi Chen   +4 more
doaj   +1 more source

Histone modification ChIP-seq on Arabidopsis thaliana Plantlets

Bio-Protocol, 2021
Characterizing the molecular mechanisms regulating gene expression is crucial for understanding the regulatory processes underlying physiological responses to environmental and developmental signals in eukaryotes.
Juan Ramirez-Prado, David Latrasse, Moussa Benhamed   +2 more
doaj   +1 more source

SeqBox: RNAseq/ChIPseq reproducible analysis on a consumer game computer

Bioinformatics, 2017
Abstract Summary Short reads sequencing technology has been used for more than a decade now. However, the analysis of RNAseq and ChIPseq data is still computational demanding and the simple access to raw data does not guarantee results reproducibility between laboratories. To address these two aspects,
BECCUTI, Marco, CORDERO, Francesca, ARIGONI, MADDALENA, PANERO, RICCARDO, AMPARORE, ELVIO GILBERTO, DONATELLI, Susanna, CALOGERO, Raffaele Adolfo   +6 more
openaire   +4 more sources

ChIP-Seq in Candida albicans

Bio-Protocol, 2014
Systems biology approaches can be used to study the regulatory interactions occurring between many components of the biological system at the whole-genome level and decipher the circuitries implicated in the regulation of cellular processes, including ...
Sadri Znaidi, Caroline PROUX, Sandra Weber, Simon Drouin, François Robert, Martine Raymond, Jean-Yves Coppée, Christophe d'Enfert   +7 more
doaj   +1 more source

Development and application of ChIPSeq: genome‐wide DNA binding by MyoD

The FASEB Journal, 2008
ChIPSeq is an application of high throughput direct sequencing (Solexa / Illumina) to assay for factor‐DNA binding sites retrieved by chromatin immunoprecipitation (ChIP). A goal was to achieve reliable identification of true binding sites throughout large genomes, without need for cloning or microarray.
Gordon Kwan, Sandra B Sharp, Barbara J Wold   +2 more
openaire   +1 more source

ChIPseqR: analysis of ChIP-seq experiments

BMC Bioinformatics, 2011
Background The use of high-throughput sequencing in combination with chromatin immunoprecipitation (ChIP-seq) has enabled the study of genome-wide protein binding at high resolution.
Helliwell Chris A, Humburg Peter, Bulger David, Stone Glenn   +3 more
doaj   +1 more source

Defining pervasive transcription units using chromatin RNA-sequencing data

STAR Protocols, 2022
Summary: Pervasive transcripts (PTs) are difficult to detect by steady-state RNA-seq, because they are degraded immediately by the nuclear exosome complex.
Ziwei Guo, Xinhong Liu, Mo Chen
doaj   +1 more source