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Xenbase: a genomic, epigenomic and transcriptomic model organism database

Kamran Karimi, Joshua D Fortriede, Vaneet S Lotay, Kevin A Burns, Dong Zhou Wang, Malcom E Fisher, Troy J Pells, Christina James-Zorn, Ying Wang, V G Ponferrada, Stanley Chu, Praneet Chaturvedi (+2 others)
2017 Nucleic Acids Research  
Xenbase ( is an online resource for researchers utilizing Xenopus laevis and Xenopus tropicalis, and for biomedical scientists seeking access to data generated with these model systems.  ...  Content is aggregated from a variety of external resources and also generated by in-house curation of scientific literature and bioinformatic analyses.  ...  and Facebase.  ... 
doi:10.1093/nar/gkx936 pmid:29059324 pmcid:PMC5753396 fatcat:yrmnbwipgffc5c5ncaqi2bc2bi

From whole-mount to single-cell spatial assessment of gene expression in 3D

Lisa N. Waylen, Hieu T. Nim, Luciano G. Martelotto, Mirana Ramialison
2020 Communications Biology  
, and improving medical diagnostics.  ...  These approaches digitally reconstruct patterns of embryonic expression in three dimensions, and have successfully identified novel domains of expression, cell types, and tissue features.  ...  The Australian Regenerative Medicine Institute is supported by grants from the State Government of Victoria and the Australian Government.  ... 
doi:10.1038/s42003-020-01341-1 pmid:33097816 fatcat:zdbbtgfiufhihc7nldbcxgnoxm

Four novel, immortal cell lines derived from embryos of Xenopus tropicalis [article]

Gary J Gorbsky, John R Daum, Hem Sapkota, Katja Summala, Hitoshi Yoshida, Constantin Georgescu, Jonathan D Wren, Leonid Peshkin, Marko E Horb
2022 bioRxiv   pre-print
The diploid anuran, Xenopus tropicalis, has emerged as a key research model in cell and developmental biology.  ...  Transcriptome analysis indicated that the four lines were distinct lineages.  ...  LP has been supported by grant # R01HD073104 from the National Institute of Child Health and Development.  ... 
doi:10.1101/2022.03.01.482505 fatcat:cbrsgu3urvgjxgvticimvwxvie

Derivedness Index for Estimating Degree of Phenotypic Evolution of Embryos: A Study of Comparative Transcriptomic Analyses of Chordates and Echinoderms

Jason Cheok Kuan Leong, Yongxin Li, Masahiro Uesaka, Yui Uchida, Akihito Omori, Meng Hao, Wenting Wan, Yang Dong, Yandong Ren, Si Zhang, Tao Zeng, Fayou Wang (+6 others)
2021 Frontiers in Cell and Developmental Biology  
Finally, we highlight technical concerns that may influence the measured transcriptomic derivedness, such as read depth and library preparation protocols, for further improvement of our method through  ...  This approach creates a major barrier, especially when quantifying the degree of phenotypic evolution or degree of derivedness, since it focuses only on commonly shared traits, and newly acquired or lost  ...  A., Segerdell, E., Jarabek, C. J., Azam, K., Zorn, A. M., et al. (2010). Xenbase: Gene Expression and Improved Integration.  ... 
doi:10.3389/fcell.2021.749963 pmid:34900995 pmcid:PMC8661034 fatcat:vliupbvv3nhalezcky2pqcr6j4

DNA methylation clocks for clawed frogs reveal evolutionary conservation of epigenetic ageing [article]

Joseph A Zoller, Eleftheria Parasyraki, Ake T Lu, Amin Haghani, Christof Niehrs, Steve Horvath
2022 bioRxiv   pre-print
to employ Xenopus as a model organism to study development and ageing.  ...  We generated DNA methylation data from African clawed frogs (Xenopus laevis) and Western clawed frogs (Xenopus tropicalis), from adult tissues, whole embryos, and tadpoles.  ...  Allen Frontiers Group (PI SH) and Open Philanthropy (SH). We thank the European Xenopus Resource Centre (EXRC) for DNA samples.  ... 
doi:10.1101/2022.08.02.502561 fatcat:wcfopdxldvewrkxzmvswrq6v6u

NCBP2-mediated apoptosis contributes to developmental defects of the schizophrenia-associated 3q29 deletion [article]

Mayanglambam Dhruba Singh, Matthew Jensen, Micaela Lasser, Emily Huber, Tanzeen Yusuff, Lucilla Pizzo, Brian Lifschutz, Inshya Desai, Alexis Kubina, Sneha Yennawar, Sydney Kim, Janani Iyer (+3 others)
2019 bioRxiv   pre-print
In particular, NCBP2 synergistically enhanced the phenotypes of other 3q29 homologs in both Drosophila and X. laevis, leading to significant increases in apoptosis that disrupt cellular organization and  ...  Here, we used quantitative methods to assay Drosophila melanogaster and Xenopus laevis models with knockdown of individual 3q29 homologs in different tissues.  ...  Karimi K, et al. (2018) Xenbase: a genomic, epigenomic and transcriptomic model 20 organism database. Nucleic Acids Res 46(D1):D861-D868.  ... 
doi:10.1101/614750 fatcat:eks2qhef3bgfdo5xf2etoxceli

Maternal and zygotic factors sequentially shape the tissue regionalization of chromatin landscapes in early vertebrate embryos [article]

Kitt D. Paraiso, Ira L. Blitz, Ken W.Y. Cho
2021 bioRxiv   pre-print
Maternal pioneer transcription factors (TFs) bind to the regulatory regions of the embryonic genome prior to zygotic genome activation and initiate germ layer specification.  ...  Establishment of these enhancers requires a sequential function of maternal and zygotic TFs.  ...  We thank Xenbase for genomic and community resources (, RRID: SCR_003280), and the University of California, Irvine High Performance Computing Cluster (  ... 
doi:10.1101/2021.04.14.439777 fatcat:orqbdsxa3ver7lwbvaqjnrvcqy

Physiological effects of KDM5C on neural crest migration and eye formation during vertebrate development

Youni Kim, Youngeun Jeong, Kujin Kwon, Tayaba Ismail, Hyun-Kyung Lee, Chowon Kim, Jeen-Woo Park, Oh-Shin Kwon, Beom-Sik Kang, Dong-Seok Lee, Tae Joo Park, Taejoon Kwon (+1 others)
2018 Epigenetics & Chromatin  
Furthermore, transcriptome analysis indicated the significance of KDM5C in morphogenesis and organogenesis.  ...  KDM5C is expressed in the brain and skeletal muscles of humans and is associated with various biologically significant processes.  ...  Background Embryonic organ development is a highly organized and complex process involving the temporal and spatial expression of genes that control differentiation, maturation, and survival of organs  ... 
doi:10.1186/s13072-018-0241-x pmid:30522514 pmcid:PMC6282277 fatcat:5kajsn2ihfao3iackoqwnzplwa

Fluid mechanics of mosaic ciliated tissues [article]

Francesco Boselli, Jerome Jullien, Eric Lauga, Raymond E. Goldstein
2021 bioRxiv   pre-print
to a single MCC, they best shear the tissue at low area coverage, a result that mirrors findings for other sparse distributions such as cell receptors and leaf stomata.  ...  A coarse-grained model that self-consistently couples bundles to the ambient flow reveals that hydrodynamic interactions between MCCs limit their rate of work so that when the system size is large compared  ...  Wang, et al., Xenbase: A genomic, epigenomic and transcriptomic model organism database, Nucleic Acids Research 46, (D1) (2018). [22] J. Faber and P.D.  ... 
doi:10.1101/2021.03.31.437829 fatcat:pfvyyqnx5zbznht6fikispwj6u

The nucleoporin Nup50 activates the Ran guanyl-nucleotide exchange factor RCC1 to promote mitotic NPC assembly [article]

Guillaume Holzer, Paola De Magistris, Cathrin Gramminger, Ruchika Sachdev, Adriana Magalska, Allana Schooley, Anja Scheufen, Birgitt Lennartz, Marianna Tatarek-Nossol, Hongqi Lue, Monika I Linder, Ulrike Kutay (+3 others)
2021 bioRxiv   pre-print
We define a conserved central region of 46 residues in Nup50 that is crucial for Nup153 and MEL28/ELYS binding, and NPC interaction.  ...  We show here that Nup50 plays a crucial role in NPC assembly that is independent of its well-established function in nuclear transport.  ...  ., Xenbase: a genomic, epigenomic and transcriptomic model organism database. 677 Nucleic Acids Res, 2018. 46(D1): p. D861-d868. 678 58.  ... 
doi:10.1101/2021.03.31.437874 fatcat:lpor5ndylfdkdjnux4m3rgnxgq

Xbp1 and Brachyury establish an evolutionarily conserved subcircuit of the notochord gene regulatory network

Yushi Wu, Arun Devotta, Diana S José-Edwards, Jamie E Kugler, Lenny J Negrón-Piñeiro, Karina Braslavskaya, Jermyn Addy, Jean-Pierre Saint-Jeannet, Anna Di Gregorio
2022 eLife  
Gene regulatory networks coordinate the formation of organs and structures that compose the evolving body plans of different organisms.  ...  We are using a simple chordate model, the Ciona embryo, to investigate the essential gene regulatory network that orchestrates morphogenesis of the notochord, a structure necessary for the proper development  ...  reported to participate in the UPR in other model organisms.  ... 
doi:10.7554/elife.73992 pmid:35049502 pmcid:PMC8803312 fatcat:lun7t3eqirbb3bfw744qgdz45a

The Methylome of the Marbled Crayfish Procambarus virginalis

Cassandra Falckenhayn
Aufgrund des großen Genoms von P. virginalis wurde das Transkriptom assembliert.  ...  Das Ziel dieser Arbeit war es, das Methylom des Mamorkrebses auf dem Auflösungsvermögen einzelner Basen mittels Whole-Genome Bisulfite Sequencing zu charakterisieren, um neue Einblicke in die Methylierung  ...  Thus, the marbled crayfish has the necessary attributes to be a laboratory model organism.  ... 
doi:10.11588/heidok.00022489 fatcat:4czxambne5brbpg7ef22t73s7q