Results 31 to 40 of about 5,931 (188)

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

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

High-resolution mapping of mitotic DNA synthesis under conditions of replication stress in cultured cells

STAR Protocols, 2023
Summary: Cells experiencing DNA replication stress enter mitosis with under-replicated DNA, which activates a repair mechanism known as mitotic DNA synthesis (MiDAS).
Florian J. Groelly, Rebecca A. Dagg, Jonathan Mailler, Thanos D. Halazonetis, Madalena Tarsounas   +4 more
doaj   +1 more source

HERV-H RNA is abundant in human embryonic stem cells and a precise marker for pluripotency [PDF]

, 2012
BACKGROUND: Certain post-translational modifications to histones, including H3K4me3, as well as binding sites for the transcription factor STAT1, predict the site of integration of exogenous gamma-retroviruses with great accuracy and cell-type ...
Federico A Santoni, Jeremy Luban, Jessica Guerra   +2 more
core   +2 more sources

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

Enforcement of developmental lineage specificity by transcription factor Oct1 [PDF]

, 2017
Embryonic stem cells co-express Oct4 and Oct1, a related protein with similar DNA-binding specificity. To study the role of Oct1 in ESC pluripotency and transcriptional control, we constructed germline and inducible-conditional Oct1-deficient ESC lines ...
Abranches, Azuara, Bain, Bellance, Bernstein, Boyer, Chen, Chen, De Los Angeles, Guo, Jiang, Jin, Kang, Kang, Kim, Ku, Love, Lu, Machanick, Maddox, Meissner, Molla Kazemiha, Morey, Nelakanti, Nichols, Nix, Okamoto, Pan, Reményi, Rosner, Sebastiano, Shakya, Shakya, Shakya, Shakya, Sridharan, Suh, Takahashi, Tantin, Tantin, Tantin, Theodorou, Tomilin, Verrijzer, Vázquez-Arreguín, Walker, Wang, Wang, Wang, Wang, Wen, Yeap, Yuan, Zylicz   +53 more
core   +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   +3 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

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

The Genomic Context and Corecruitment of SP1 Affect ERRα Coactivation by PGC-1α in Muscle Cells [PDF]

, 2016
The peroxisome proliferator-activated receptor-γ coactivator 1α (PGC-1α) coordinates the transcriptional network response to promote an improved endurance capacity in skeletal muscle, eg, by coactivating the estrogen-related receptor-α (ERRα) in the ...
Baresic, Mario, Handschin, Christoph, Kupr, Barbara, Salatino, Silvia, van Nimwegen, Erik   +4 more
core   +1 more source