Results 41 to 50 of about 5,931 (188)

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

The transcription factor Spores Absent A is a PKA dependent inducer of Dictyostelium sporulation [PDF]

, 2018
Sporulation in Dictyostelium fruiting bodies evolved from amoebozoan encystation with both being induced by cAMP acting on PKA, but with downstream components still being unknown. Using tagged mutagenesis to find missing pathway components, we identified
A Kuspa, A Muller-Taubenberger, A Parikh, A Telser, AE Early, B Langmead, B Lardy, BN Mitra, C Anjard, C Schilde, CM West, CM West, DL Richardson, E Huang, ER Miranda, F Ronquist, G Glockner, G Loughran, G Shaulsky, I Takeuchi, J Faix, JG Williams, JL Dynes, KL Fosnaugh, KM Flick, LJ Zhu, M Fukuzawa, M Keim, NA Hopper, NA Hopper, P Schaap, P Schaap, P Zhang, Q Du, R Escalante, R Escalante, R Escalante, R Escalante, R Escalante, R Sucgang, S Veeranki, SKO Mann, SKO Mann, W Zimmerman, W-T Chang, WF Loomis, Y Kawabe, Y Yamada, Y Yamada, Y Zhang   +49 more
core   +2 more sources

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

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

Protocol to target a promoter region in human embryonic kidney cells using the CRISPR-dCas9 system for single-locus proteomics

STAR Protocols
Summary: The unbiased identification of less-abundant transcription factors, which direct the expression of a target gene, is technically challenging. Here, we present a protocol to analyze the locus-specific chromatin-regulating proteome using in situ ...
Reem Alkhayer, Viviane Ponath, Elke Pogge von Strandmann   +2 more
doaj   +1 more source

Computer analysis of co-localization of transcription factor binding sites in genome by ChIP-seq data

Вавиловский журнал генетики и селекции, 2017
Statistical features of the distribution of transcription factor binding sites in the mouse genome that are obtained by ChIP-seq experiments in embryonic stem cells have been considered. Clusters of sites that contain four or more different transcription
A. I. Dergilev, A. M. Spitsina, I. V. Chadaeva, A. V. Svichkarev, F. M. Naumenko, E. V. Kulakova, E. R. Galieva, E. E. Vityaev, M. Chen, Y. L. Orlov   +9 more
doaj   +1 more source

Transcriptional regulation of FoxO3 gene by glucocorticoids in murine myotubes. [PDF]

, 2016
Glucocorticoids and FoxO3 exert similar metabolic effects in skeletal muscle. FoxO3 gene expression was increased by dexamethasone (Dex), a synthetic glucocorticoid, both in vitro and in vivo.
Chau, Andy, Chen, Tzu-Chieh, Cheung, Edna, Kuo, Taiyi, Lee, Rebecca A, Lei, Cassandra, Liu, Patty H, New, Jenny, Tang, Yicheng, Wang, Jen-Chywan, Zhang, Danyun   +10 more
core   +1 more source

Nanolesions induced by heavy ions in human tissues: experimental and theoretical studies [PDF]

, 2012
The biological effects of energetic heavy ions are attracting increasing interest for their applications in cancer therapy and protection against space radiation.
Cathrin Wälzlein, Francesco Natale, Gisela Taucher-scholz, Igor Mishustin, Igor Pshenichnov, Iris Müller, Lucas Burigo, M. Huth, Marco Durante, Marcus Bleicher, Maren Herrlitz, Michael Krämer, Stefan Schramm   +12 more
core   +2 more sources

Shape-based peak identification for ChIP-Seq

BMC Bioinformatics, 2011
Background The identification of binding targets for proteins using ChIP-Seq has gained popularity as an alternative to ChIP-chip. Sequencing can, in principle, eliminate artifacts associated with microarrays, and cheap sequencing offers the ability to ...
Evans Steven N, Hower Valerie, Pachter Lior   +2 more
doaj   +1 more source

Chromatin Immunoprecipitation dataset of H3ac and H3K27me3 histone marks followed by DNA sequencing of Medicago truncatula embryos during control and heat stress conditions to decipher epigenetic regulation of desiccation tolerance acquisition

Data in Brief, 2022
Desiccation tolerance (DT) is one of the most important processes that seeds need to acquire during seed maturation because it will ensure survival until seeds have favourable conditions for germinating.
Jaiana Malabarba, Zhijuan Chen, David Windels, Jerome Verdier   +3 more
doaj   +1 more source