Erosion of human X chromosome inactivation causes major remodeling of the iPSC proteome.
Alejandro Brenes,Harunori Yoshikawa,Dalila Bensaddek,Bogdan Mirauta,Daniel D Seaton,Jens L. Hukelmann,Hao Jiang,Oliver Stegle,Angus I. Lamond +8 more
TLDR
In this article, a proteomic analysis of human induced pluripotent stem cells (iPSCs) derived from female donors identified that low levels of XIST RNA correlated strongly with erosion of XCI.About:
This article is published in Cell Reports.The article was published on 2021-04-27 and is currently open access. It has received 15 citations till now. The article focuses on the topics: XIST & X-inactivation.read more
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Genetic variation at mouse and human ribosomal DNA influences associated epigenetic states
Francisco Rodríguez-Algarra,Robert A. Seaborne,Amy F. Danson,Selin Yildizoglu,Harunori Yoshikawa,Pui Pik Law,Zakaryya Ahmad,Victoria A Maudsley,Ama Brew,Nadine Holmes,Mateus Ochôa,Alan Hodgkinson,Sarah J. Marzi,Madapura M. Pradeepa,Matthew Loose,Michelle L. Holland,Vardhman K. Rakyan +16 more
TL;DR: Using a combination of long-and short-read sequencing, this paper established that 45S rDNA units in the C57BL/6J mouse strain exist as distinct genetic haplotypes that influence the epigenetic state and transcriptional output of any given unit.
Journal ArticleDOI
Genetic variation at mouse and human ribosomal DNA influences associated epigenetic states
Francisco Rodríguez-Algarra,Robert A. Seaborne,Amy F. Danson,Selin Yildizoglu,Harunori Yoshikawa,Pui Pik Law,Zakaryya Ahmad,Victoria A Maudsley,Ama Brew,Nadine Holmes,Mateus Ochôa,Alan Hodgkinson,Sarah J. Marzi,Madapura M. Pradeepa,Matthew Loose,Michelle L. Holland,Vardhman K. Rakyan +16 more
TL;DR: Using a combination of long-and short-read sequencing, this paper established that 45S rDNA units in the C57BL/6J mouse strain exist as distinct genetic haplotypes that influence the epigenetic state and transcriptional output of any given unit.
Journal ArticleDOI
Inherent genomic properties underlie the epigenomic heterogeneity of human induced pluripotent stem cells
Shihori Yokobayashi,Yukihiro Yabuta,Masato Nakagawa,Keisuke Okita,Bo Hu,Bo Hu,Yusuke Murase,Tomonori Nakamura,Guillaume Bourque,Guillaume Bourque,Jacek Majewski,Takuya Yamamoto,Mitinori Saitou +12 more
TL;DR: In this article, the authors show that seven human induced pluripotent stem cells (hiPSC) lines with variable germline potential exhibit substantial epigenomic heterogeneity, despite their uniform transcriptomes.
Journal ArticleDOI
Tissue of Origin, but Not XCI State, Influences Germ Cell Differentiation from Human Pluripotent Stem Cells.
Yolanda W Chang,Arend W Overeem,Celine M Roelse,Xueying Fan,Christian Freund,Christian Freund,Susana M. Chuva de Sousa Lopes,Susana M. Chuva de Sousa Lopes +7 more
TL;DR: In this paper, the authors investigated whether differences in X chromosome inactivation (XCI) in female pluripotent stem cells could contribute to the variability of hPGCLC differentiation efficiency during embryoid body (EB) formation.
Journal ArticleDOI
The Immunological Proteome Resource
Alejandro Brenes,Jens L. Hukelmann,Laura Spinelli,Andrew J. M. Howden,Julia M. Marchingo,Linda V. Sinclair,Christina M. Rollings,Olivia J. James,Iain R. Phair,Stephen P. Matthews,Sarah H. Ross,J. Simon C. Arthur,Mahima Swamy,David K. Finlay,Angus I. Lamond,Doreen A. Cantrell +15 more
TL;DR: The Immunological Proteome Resource is an open access public resource integrating proteomic data generated by large-scale mass-spectrometry analysis of murine hematopoietic populations with analysis of copy numbers per cell of > 10,000 proteins, enabling new understanding of lymphocyte phenotypes.
References
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Alexander Dobin,Carrie A. Davis,Felix Schlesinger,Jorg Drenkow,Chris Zaleski,Sonali Jha,Philippe Batut,Mark Chaisson,Thomas R. Gingeras +8 more
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KEGG: Kyoto Encyclopedia of Genes and Genomes
Minoru Kanehisa,Susumu Goto +1 more
TL;DR: The Kyoto Encyclopedia of Genes and Genomes (KEGG) as discussed by the authors is a knowledge base for systematic analysis of gene functions in terms of the networks of genes and molecules.
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Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors.
TL;DR: Induction of pluripotent stem cells from mouse embryonic or adult fibroblasts by introducing four factors, Oct3/4, Sox2, c-Myc, and Klf4, under ES cell culture conditions is demonstrated and iPS cells, designated iPS, exhibit the morphology and growth properties of ES cells and express ES cell marker genes.
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limma powers differential expression analyses for RNA-sequencing and microarray studies
Matthew E. Ritchie,Belinda Phipson,Di Wu,Yifang Hu,Charity W. Law,Wei Shi,Gordon K. Smyth,Gordon K. Smyth +7 more
TL;DR: The philosophy and design of the limma package is reviewed, summarizing both new and historical features, with an emphasis on recent enhancements and features that have not been previously described.