Data access for the 1,000 Plants (1KP) project.
Naim Matasci,Ling-Hong Hung,Zhixiang Yan,Eric J. Carpenter,Norman J. Wickett,Siavash Mirarab,Nam Nguyen,Tandy Warnow,Saravanaraj Ayyampalayam,Michael S. Barker,J. G. Burleigh,Matthew A. Gitzendanner,Eric K. Wafula,Joshua P. Der,Claude W. dePamphilis,Béatrice Roure,Hervé Philippe,Hervé Philippe,Brad R. Ruhfel,Brad R. Ruhfel,Nicholas W. Miles,Sean W. Graham,Sarah Mathews,Barbara Surek,Michael Melkonian,Douglas E. Soltis,Pamela S. Soltis,Carl J. Rothfels,Carl J. Rothfels,Lisa Pokorny,Lisa Pokorny,Jonathan Shaw,Lisa DeGironimo,Dennis W. Stevenson,Juan Carlos Villarreal,Tao Chen,Toni M. Kutchan,Megan Rolf,Regina S. Baucom,Michael K. Deyholos,Ram Samudrala,Zhijian Tian,Xiaolei Wu,Xiao Sun,Yong Zhang,Jun Wang,Jim Leebens-Mack,Gane Ka-Shu Wong,Gane Ka-Shu Wong +48 more
TL;DR: How to access the data used in a phylogenomics analysis of the first 85 species, and how to visualize the gene and species trees of the 1KP project.
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Abstract: The 1,000 plants (1KP) project is an international multi-disciplinary consortium that has generated transcriptome data from over 1,000 plant species, with exemplars for all of the major lineages across the Viridiplantae (green plants) clade. Here, we describe how to access the data used in a phylogenomics analysis of the first 85 species, and how to visualize our gene and species trees. Users can develop computational pipelines to analyse these data, in conjunction with data of their own that they can upload. Computationally estimated protein-protein interactions and biochemical pathways can be visualized at another site. Finally, we comment on our future plans and how they fit within this scalable system for the dissemination, visualization, and analysis of large multi-species data sets.
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References
Independent optical excitation of distinct neural populations
Nathan C. Klapoetke,Yasunobu Murata,Sung Soo Kim,Stefan R. Pulver,Amanda Birdsey-Benson,Yong Ku Cho,Tania K. Morimoto,Amy S. Chuong,Eric J. Carpenter,Zhijian Tian,Jun Wang,Yinlong Xie,Zhixiang Yan,Yong Zhang,Brian Y. Chow,Barbara Surek,Michael Melkonian,Vivek Jayaraman,Martha Constantine-Paton,Gane Ka-Shu Wong,Edward S. Boyden +20 more
TL;DR: Two channelrhodopsins, Chronos and Chrimson, are described, discovered through sequencing and physiological characterization of opsins from over 100 species of alga, that enable two-color activation of neural spiking and downstream synaptic transmission in independent neural populations without detectable cross-talk in mouse brain slice.
Phylotranscriptomic analysis of the origin and early diversification of land plants
Norman J. Wickett,Siavash Mirarab,Nam Nguyen,Tandy Warnow,Eric J. Carpenter,Naim Matasci,Saravanaraj Ayyampalayam,Michael S. Barker,J. Gordon Burleigh,Matthew A. Gitzendanner,Brad R. Ruhfel,Brad R. Ruhfel,Eric K. Wafula,Joshua P. Der,Sean W. Graham,Sarah Mathews,Michael Melkonian,Douglas E. Soltis,Douglas E. Soltis,Pamela S. Soltis,Pamela S. Soltis,Nicholas W. Miles,Carl J. Rothfels,Carl J. Rothfels,Lisa Pokorny,Lisa Pokorny,A. Jonathan Shaw,Lisa DeGironimo,Dennis W. Stevenson,Barbara Surek,Juan Carlos Villarreal,Béatrice Roure,Hervé Philippe,Hervé Philippe,Claude W. dePamphilis,Tao Chen,Michael K. Deyholos,Regina S. Baucom,Toni M. Kutchan,Megan M. Augustin,Jun Wang,Yong Zhang,Zhijian Tian,Zhixiang Yan,Xiaolei Wu,Xiao Sun,Gane Ka-Shu Wong,Jim Leebens-Mack +47 more
TL;DR: Strong and robust support is found for a sister-group relationship between land plants and one group of streptophyte green algae, the Zygnematophyceae, and suggests that phylogenetic hypotheses used to understand the evolution of fundamental plant traits should be reevaluated.
Independent optical excitation of distinct neural populations
Nathan C. Klapoetke,Yasunobu Murata,Sung Soo Kim,Stefan R. Pulver,Amanda Birdsey-Benson,Yong Ku Cho,Tania K. Morimoto,Amy S. Chuong,Eric J. Carpenter,Zhijian Tian,Jun Wang,Yinlong Xie,Zhixiang Yan,Yong Zhang,Brian Y. Chow,Barbara Surek,Michael Melkonian,Vivek Jayaraman,Martha Constantine-Paton,Gane Ka-Shu Wong,Edward S. Boyden +20 more
- 01 Feb 2014
TL;DR: Chronos and Chrimson as mentioned in this paper have been shown to enable two-color activation of neural spiking and downstream synaptic transmission in independent neural populations without detectable cross-talk in mouse brain slice.
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SOAPdenovo-Trans: de novo transcriptome assembly with short RNA-Seq reads
Yinlong Xie,Yinlong Xie,Gengxiong Wu,Jingbo Tang,Ruibang Luo,Jordan Patterson,Shanlin Liu,Weihua Huang,Guangzhu He,Shengchang Gu,Shengkang Li,Xin Zhou,Tak-Wah Lam,Yingrui Li,Xun Xu,Gane Ka-Shu Wong,Jun Wang +16 more
TL;DR: The conclusion is that SOAPdenovo-Trans provides higher contiguity, lower redundancy and faster execution, compared with two other popular transcriptome assemblers.
•Posted Content
SOAPdenovo-Trans: De novo transcriptome assembly with short RNA-Seq reads
Yinlong Xie,Yinlong Xie,Gengxiong Wu,Jingbo Tang,Ruibang Luo,Jordan Patterson,Shanlin Liu,Weihua Huang,Guangzhu He,Shengchang Gu,Shengkang Li,Xin Zhou,Tak-Wah Lam,Yingrui Li,Xun Xu,Gane Ka-Shu Wong,Jun Wang +16 more
TL;DR: SOAPdenovo-Trans as mentioned in this paper is a de novo transcriptome assembler designed specifically for RNA-Seq that provides higher contiguity, lower redundancy, and faster execution.
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