Model-based Analysis of ChIP-Seq (MACS)
Yong Zhang,Tao Liu,Clifford A. Meyer,Jérôme Eeckhoute,David S. Johnson,Bradley E. Bernstein,Bradley E. Bernstein,Chad Nusbaum,Richard M. Myers,Myles Brown,Wei Li,X. Shirley Liu +11 more
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This work presents Model-based Analysis of ChIP-Seq data, MACS, which analyzes data generated by short read sequencers such as Solexa's Genome Analyzer, and uses a dynamic Poisson distribution to effectively capture local biases in the genome, allowing for more robust predictions.Abstract:
We present Model-based Analysis of ChIP-Seq data, MACS, which analyzes data generated by short read sequencers such as Solexa's Genome Analyzer. MACS empirically models the shift size of ChIP-Seq tags, and uses it to improve the spatial resolution of predicted binding sites. MACS also uses a dynamic Poisson distribution to effectively capture local biases in the genome, allowing for more robust predictions. MACS compares favorably to existing ChIP-Seq peak-finding algorithms, and is freely available.read more
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Opposing macrophage polarization programs show extensive epigenomic and transcriptional cross-talk
Viviana Piccolo,Alessia Curina,Marco Genua,Serena Ghisletti,Marta Simonatto,Arianna Sabò,Bruno Amati,Bruno Amati,Renato Ostuni,Gioacchino Natoli,Gioacchino Natoli +10 more
TL;DR: It is found that IFN-γ and IL-4 mutually inhibited the epigenomic and transcriptional changes induced by each cytokine alone, providing a core mechanistic framework for the integration of signals that control macrophage activation in complex environmental conditions.
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Selectivity of ORC binding sites and the relation to replication timing, fragile sites, and deletions in cancers.
TL;DR: The origin recognition complex (ORC) binds sites from which DNA replication is initiated, and mapping binding sites in human cells shows that ORC binds selectively to open (DNase I-hypersensitive) regions containing active chromatin marks such as H3 acetylation and H3K4 methylation.
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Single cell RNA-seq and ATAC-seq analysis of cardiac progenitor cell transition states and lineage settlement
Guangshuai Jia,Jens Preussner,Xi Chen,Stefan Guenther,Xuejun Yuan,Michail Yekelchyk,Carsten Kuenne,Mario Looso,Yonggang Zhou,Sarah A. Teichmann,Sarah A. Teichmann,Thomas P. Braun +11 more
TL;DR: It is shown that CPC fate transitions are associated with distinct open chromatin states critically depending on Isl1 and Nkx2-5, and provides a model of transcriptional and epigenetic regulations during cardiac progenitor cell fate decisions at single-cell resolution.
Journal ArticleDOI
Efficient derivation of stable primed pluripotent embryonic stem cells from bovine blastocysts.
Y. S. Bogliotti,Jun Wu,Jun Wu,Jun Wu,Marcela Vilarino,Daiji Okamura,Delia Alba Soto,Cuiqing Zhong,Masahiro Sakurai,Masahiro Sakurai,Masahiro Sakurai,R. V. Sampaio,Keiichiro Suzuki,Juan Carlos Izpisua Belmonte,Pablo J. Ross +14 more
TL;DR: It is reported that stable bovine ESCs can be efficiently derived in a culture condition based on Wnt-pathway inhibition and these well-characterized ESC lines will enrich the understanding of pluripotency programs in the ungulate species but also will provide a useful resource for the creation of transgenic ungulates models of human diseases.
Journal ArticleDOI
Shark genomes provide insights into elasmobranch evolution and the origin of vertebrates
Yuichiro Hara,Kazuaki Yamaguchi,Koh Onimaru,Mitsutaka Kadota,Mitsumasa Koyanagi,Sean D. Keeley,Kaori Tatsumi,Kaori Tanaka,Fumio Motone,Yuka Kageyama,Ryo Nozu,Noritaka Adachi,Osamu Nishimura,Reiko Nakagawa,Chiharu Tanegashima,Itsuki Kiyatake,Rui Matsumoto,Kiyomi Murakumo,Kiyonori Nishida,Akihisa Terakita,Shigeru Kuratani,Keiichi Sato,Susumu Hyodo,Shigehiro Kuraku +23 more
TL;DR: A thorough genome annotation revealed Hox C genes previously hypothesized to have been lost, as well as distinct gene repertories of opsins and olfactory receptors that would be associated with adaptation to unique underwater niches, and provided insights on the molecular basis of adaptation to underwater lifestyle and the evolutionary origins of vertebrates.
References
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Genome-wide location and function of dna binding proteins
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