Transcriptomics,Multiomics

Dataset Information

1K

Developmental gene expression of Xenopus laevis J strain [stage]


ABSTRACT: Comprehensive RNA-seq experiments to measure the expression of homoeologs across different developmental stages, as a part of the Xenopus laevis genome project. This work is funded by Agency Japanese Ministry of Education, Culture, Sports, Science and Technology (MEXT; "Genome Science" Grant ID 221S0002). Collect mRNA from whole embryos; two clutches were used (Taira dataset for one pair, Ueno dataset for the other pair)

OTHER RELATED OMICS DATASETS IN: PRJNA313213PRJNA306175PRJNA306102PRJNA306718

ORGANISM(S): Xenopus laevis  

SUBMITTER: Shuji Takahashi   Naoto Ueno  Masanori Taira  Atsushi Toyoda  Taejoon Kwon  Yutaka Suzuki 

PROVIDER: E-GEOD-73430 | ArrayExpress | 2016-10-24

SECONDARY ACCESSION(S): GSE73430SRP064186PRJNA296953

REPOSITORIES: GEO, ArrayExpress, ENA

Dataset's files

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Action DRS
E-GEOD-73430.additional.1.zip Other
E-GEOD-73430.idf.txt Idf
E-GEOD-73430.sdrf.txt Txt
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Publications

Genome evolution in the allotetraploid frog Xenopus laevis.

Session Adam M AM   Uno Yoshinobu Y   Kwon Taejoon T   Chapman Jarrod A JA   Toyoda Atsushi A   Takahashi Shuji S   Fukui Akimasa A   Hikosaka Akira A   Suzuki Atsushi A   Kondo Mariko M   van Heeringen Simon J SJ   Quigley Ian I   Heinz Sven S   Ogino Hajime H   Ochi Haruki H   Hellsten Uffe U   Lyons Jessica B JB   Simakov Oleg O   Putnam Nicholas N   Stites Jonathan J   Kuroki Yoko Y   Tanaka Toshiaki T   Michiue Tatsuo T   Watanabe Minoru M   Bogdanovic Ozren O   Lister Ryan R   Georgiou Georgios G   Paranjpe Sarita S SS   van Kruijsbergen Ila I   Shu Shengquiang S   Carlson Joseph J   Kinoshita Tsutomu T   Ohta Yuko Y   Mawaribuchi Shuuji S   Jenkins Jerry J   Grimwood Jane J   Schmutz Jeremy J   Mitros Therese T   Mozaffari Sahar V SV   Suzuki Yutaka Y   Haramoto Yoshikazu Y   Yamamoto Takamasa S TS   Takagi Chiyo C   Heald Rebecca R   Miller Kelly K   Haudenschild Christian C   Kitzman Jacob J   Nakayama Takuya T   Izutsu Yumi Y   Robert Jacques J   Fortriede Joshua J   Burns Kevin K   Lotay Vaneet V   Karimi Kamran K   Yasuoka Yuuri Y   Dichmann Darwin S DS   Flajnik Martin F MF   Houston Douglas W DW   Shendure Jay J   DuPasquier Louis L   Vize Peter D PD   Zorn Aaron M AM   Ito Michihiko M   Marcotte Edward M EM   Wallingford John B JB   Ito Yuzuru Y   Asashima Makoto M   Ueno Naoto N   Matsuda Yoichi Y   Veenstra Gert Jan C GJ   Fujiyama Asao A   Harland Richard M RM   Taira Masanori M   Rokhsar Daniel S DS  

Nature 20161001 7625


To explore the origins and consequences of tetraploidy in the African clawed frog, we sequenced the Xenopus laevis genome and compared it to the related diploid X. tropicalis genome. We characterize the allotetraploid origin of X. laevis by partitioning its genome into two homoeologous subgenomes, marked by distinct families of 'fossil' transposable elements. On the basis of the activity of these elements and the age of hundreds of unitary pseudogenes, we estimate that the two diploid progenitor  ...[more]

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