Gene Expression
Nebulas
Gene Expression Nebulas| Download | Dataset ID | BioProject ID | Dataset Name | Species | Strategy | Sample Number | Biological Condition | Quality and Quantity | |||||||||
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| Baseline | Genetic | Phenotypic | Environmental | Spatial | Temporal | RNA Type | Median Mapping Quality | Median Coverage | Max Sequencing Length | Max Replicate# | |||||||
Download | Dataset ID | BioProject ID | Dataset Name | Species | Strategy | Sample Number | Biological Condition | Quality and Quantity | |||||||||
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Baseline | Genetic | Phenotypic | Environmental | Spatial | Temporal | RNA Type | Median Mapping Quality | Median Coverage | Max Sequencing Length | Max Replicate# | |||||||
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A Core Regulatory Pathway Controlling Rice Tiller Angle Mediated by the LAZY1-Dependent Asymmetric Distribution of Auxin.
Zhang N, Yu H, Yu H, Cai Y, Huang L, Xu C, Xiong G, Meng X, Wang J, Chen H, Liu G, Jing Y, Yuan Y, Liang Y, Li S, Smith SM, Li J, Wang Y.
Plant Cell. 2018-06-18; 30 (7)
PMID: 29915152 DOI: 10.1105/tpc.18.00063
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A heat stress responsive NAC transcription factor heterodimer plays key roles in rice grain filling.
Ren Y, Huang Z, Jiang H, Wang Z, Wu F, Xiong Y, Yao J.
J Exp Bot. 2021-04-01; 72 (8)
PMID: 33476364 DOI: 10.1093/jxb/erab027
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A lamin-like protein OsNMCP1 regulates drought resistance and root growth through chromatin accessibility modulation by interacting with a chromatin remodeller OsSWI3C in rice.
Yang J, Chang Y, Qin Y, Chen D, Zhu T, Peng K, Wang H, Tang N, Li X, Wang Y, Liu Y, Li X, Xie W, Xiong L.
New Phytol. 2020-04-13; 227 (1)
PMID: 32129897 DOI: 10.1111/nph.16518
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A mycorrhiza-associated receptor-like kinase with an ancient origin in the green lineage.
Montero H, Lee T, Pucker B, Ferreras-Garrucho G, Oldroyd G, Brockington SF, Miyao A, Paszkowski U.
Proc Natl Acad Sci U S A. 2021-06-01; 118 (25)
PMID: 34161289 DOI: 10.1073/pnas.2105281118
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A transcription activator-like effector from Xanthomonas oryzae pv. oryzicola elicits dose-dependent resistance in rice.
Hummel AW, Wilkins KE, Wang L, Cernadas RA, Bogdanove AJ.
Mol Plant Pathol. 2016-04-21; 18 (1)
PMID: 26821568 DOI: 10.1111/mpp.12377
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A viral protein promotes host SAMS1 activity and ethylene production for the benefit of virus infection.
Zhao S, Hong W, Wu J, Wu J, Wang Y, Ji S, Zhu S, Wei C, Zhang J, Li Y.
Elife. 2017-10-10; 6
PMID: 28994391 DOI: 10.7554/elife.27529
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Analysis of non-coding transcriptome in rice and maize uncovers roles of conserved lncRNAs associated with agriculture traits.
Wang H, Niu QW, Wu HW, Liu J, Ye J, Yu N, Chua NH.
Plant J. 2015-10-01; 84 (2)
PMID: 26387578 DOI: 10.1111/tpj.13018
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Co-overexpression of the Constitutively Active Form of OsbZIP46 and ABA-Activated Protein Kinase SAPK6 Improves Drought and Temperature Stress Resistance in Rice.
Chang Y, Nguyen BH, Xie Y, Xiao B, Tang N, Zhu W, Mou T, Xiong L.
Front Plant Sci. 2017-06-26; 8
PMID: 28694815 DOI: 10.3389/fpls.2017.01102
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Comparative transcriptome analysis of transporters, phytohormone and lipid metabolism pathways in response to arsenic stress in rice (Oryza sativa).
Yu LJ, Luo YF, Liao B, Xie LJ, Chen L, Xiao S, Li JT, Hu SN, Shu WS.
New Phytol. 2012-04-27; 195 (1)
PMID: 22537016 DOI: 10.1111/j.1469-8137.2012.04154.x
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Diversity in the complexity of phosphate starvation transcriptomes among rice cultivars based on RNA-Seq profiles.
Oono Y, Kawahara Y, Yazawa T, Kanamori H, Kuramata M, Yamagata H, Hosokawa S, Minami H, Ishikawa S, Wu J, Antonio B, Handa H, Itoh T, Matsumoto T.
Plant Mol Biol. 2013-07-16; 83 (6)
PMID: 23857470 DOI: 10.1007/s11103-013-0106-4
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Dynamic and rapid changes in the transcriptome and epigenome during germination and in developing rice (Oryza sativa) coleoptiles under anoxia and re-oxygenation.
Narsai R, Secco D, Schultz MD, Ecker JR, Lister R, Whelan J.
Plant J. 2017-02-11; 89 (4)
PMID: 27859855 DOI: 10.1111/tpj.13418
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Dynamics and functional interplay of histone lysine butyrylation, crotonylation, and acetylation in rice under starvation and submergence.
Lu Y, Xu Q, Liu Y, Yu Y, Cheng ZY, Zhao Y, Zhou DX.
Genome Biol. 2018-09-25; 19 (1)
PMID: 30253806 DOI: 10.1186/s13059-018-1533-y
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Enhancing rice grain production by manipulating the naturally evolved cis-regulatory element-containing inverted repeat sequence of OsREM20.
Wu X, Liang Y, Gao H, Wang J, Zhao Y, Hua L, Yuan Y, Wang A, Zhang X, Liu J, Zhou J, Meng X, Zhang D, Lin S, Huang X, Han B, Li J, Wang Y.
Mol Plant. 2021-03-16; 14 (6)
PMID: 33741527 DOI: 10.1016/j.molp.2021.03.016
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Gene regulatory networks shape developmental plasticity of root cell types under water extremes in rice.
Reynoso MA, Borowsky AT, Pauluzzi GC, Yeung E, Zhang J, Formentin E, Velasco J, Cabanlit S, Duvenjian C, Prior MJ, Akmakjian GZ, Deal RB, Sinha NR, Brady SM, Girke T, Bailey-Serres J.
Dev Cell. 2022-05-02; 57 (9)
PMID: 35504287 DOI: 10.1016/j.devcel.2022.04.013
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Genome Wide Analysis of the Transcriptional Profiles in Different Regions of the Developing Rice Grains.
Wu TY, Müller M, Gruissem W, Bhullar NK.
Rice (N Y). 2020-09-07; 13 (1)
PMID: 32894395 DOI: 10.1186/s12284-020-00421-4
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Genome-wide disruption of gene expression in allopolyploids but not hybrids of rice subspecies.
Xu C, Bai Y, Lin X, Zhao N, Hu L, Gong Z, Wendel JF, Liu B.
Mol Biol Evol. 2014-02-27; 31 (5)
PMID: 24577842 DOI: 10.1093/molbev/msu085
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Genome-Wide Identification of SNAC1-Targeted Genes Involved in Drought Response in Rice.
Li X, Chang Y, Ma S, Shen J, Hu H, Xiong L.
Front Plant Sci. 2019-07-26; 10
PMID: 31402926 DOI: 10.3389/fpls.2019.00982
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Genome-wide screening and functional analysis identify a large number of long noncoding RNAs involved in the sexual reproduction of rice.
Zhang YC, Liao JY, Li ZY, Yu Y, Zhang JP, Li QF, Qu LH, Shu WS, Chen YQ.
Genome Biol. 2014-12-03; 15 (12)
PMID: 25517485 DOI: 10.1186/s13059-014-0512-1
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Genome-wide transcriptome analysis reveals that cadmium stress signaling controls the expression of genes in drought stress signal pathways in rice.
Oono Y, Yazawa T, Kawahara Y, Kanamori H, Kobayashi F, Sasaki H, Mori S, Wu J, Handa H, Itoh T, Matsumoto T.
PLoS One. 2014-05-09; 9 (5)
PMID: 24816929 DOI: 10.1371/journal.pone.0096946
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Identification of Key Genes for the Ultrahigh Yield of Rice Using Dynamic Cross-tissue Network Analysis.
Hu J, Zeng T, Xia Q, Huang L, Zhang Y, Zhang C, Zeng Y, Liu H, Zhang S, Huang G, Wan W, Ding Y, Hu F, Yang C, Chen L, Wang W.
Genomics Proteomics Bioinformatics. 2020-06-01; 18 (3)
PMID: 32736037 DOI: 10.1016/j.gpb.2019.11.007
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Initiation of scutellum-derived callus is regulated by an embryo-like developmental pathway in rice.
Guo F, Wang H, Lian G, Cai G, Liu W, Zhang H, Li D, Zhou C, Han N, Zhu M, Su Y, Seo PJ, Xu L, Bian H.
Commun Biol. 2023-04-25; 6 (1)
PMID: 37100819 DOI: 10.1038/s42003-023-04835-w
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Loss of function mutations in the rice chromomethylase OsCMT3a cause a burst of transposition.
Cheng C, Tarutani Y, Miyao A, Ito T, Yamazaki M, Sakai H, Fukai E, Hirochika H.
Plant J. 2015-09-01; 83 (6)
PMID: 26243209 DOI: 10.1111/tpj.12952
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Molecular bases for differential aging programs between flag and second leaves during grain-filling in rice.
Lee S, Jeong H, Lee S, Lee J, Kim SJ, Park JW, Woo HR, Lim PO, An G, Nam HG, Hwang D.
Sci Rep. 2017-08-18; 7 (1)
PMID: 28821707 DOI: 10.1038/s41598-017-07035-9
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Mutation of a major CG methylase in rice causes genome-wide hypomethylation, dysregulated genome expression, and seedling lethality.
Hu L, Li N, Xu C, Zhong S, Lin X, Yang J, Zhou T, Yuliang A, Wu Y, Chen YR, Cao X, Zemach A, Rustgi S, von Wettstein D, Liu B.
Proc Natl Acad Sci U S A. 2014-07-07; 111 (29)
PMID: 25002488 DOI: 10.1073/pnas.1410761111
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OsDCL3b affects grain yield and quality in rice.
Liao PF, Ouyang JX, Zhang JJ, Yang L, Wang X, Peng XJ, Wang D, Zhu YL, Li SB.
Plant Mol Biol. 2019-01-16; 99 (3)
PMID: 30652247 DOI: 10.1007/s11103-018-0806-x
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OsJAZ1 Attenuates Drought Resistance by Regulating JA and ABA Signaling in Rice.
Fu J, Wu H, Ma S, Xiang D, Liu R, Xiong L.
Front Plant Sci. 2017-12-11; 8
PMID: 29312378 DOI: 10.3389/fpls.2017.02108
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OsPRR37 confers an expanded regulation of the diurnal rhythms of the transcriptome and photoperiodic flowering pathways in rice.
Liu C, Qu X, Zhou Y, Song G, Abiri N, Xiao Y, Liang F, Jiang D, Hu Z, Yang D.
Plant Cell Environ. 2018-02-05; 41 (3)
PMID: 29314052 DOI: 10.1111/pce.13135
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Overlapping roles of spliceosomal components SF3B1 and PHF5A in rice splicing regulation.
Butt H, Bazin J, Alshareef S, Eid A, Benhamed M, Reddy ASN, Crespi M, Mahfouz MM.
Commun Biol. 2021-05-05; 4 (1)
PMID: 33953336 DOI: 10.1038/s42003-021-02051-y
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Retrogenes in rice (Oryza sativa L. ssp. japonica) exhibit correlated expression with their source genes.
Sakai H, Mizuno H, Kawahara Y, Wakimoto H, Ikawa H, Kawahigashi H, Kanamori H, Matsumoto T, Itoh T, Gaut BS.
Genome Biol Evol. 2011-10-31; 3
PMID: 22042334 DOI: 10.1093/gbe/evr111
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Rice diterpenoid phytoalexins are involved in defence against parasitic nematodes and shape rhizosphere nematode communities.
Desmedt W, Kudjordjie EN, Chavan SN, Zhang J, Li R, Yang B, Nicolaisen M, Mori M, Peters RJ, Vanholme B, Vestergård M, Kyndt T.
New Phytol. 2022-04-23; 235 (3)
PMID: 35460590 DOI: 10.1111/nph.18152
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Rice germline-specific Argonaute MEL1 protein binds to phasiRNAs generated from more than 700 lincRNAs.
Komiya R, Ohyanagi H, Niihama M, Watanabe T, Nakano M, Kurata N, Nonomura K.
Plant J. 2014-04-15; 78 (3)
PMID: 24635777 DOI: 10.1111/tpj.12483
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Rice pyramided line IRBB67 (Xa4/Xa7) homeostasis under combined stress of high temperature and bacterial blight.
Dossa GS, Quibod I, Atienza-Grande G, Oliva R, Maiss E, Vera Cruz C, Wydra K.
Sci Rep. 2020-01-20; 10 (1)
PMID: 31959799 DOI: 10.1038/s41598-020-57499-5
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Rice SUB1A constrains remodelling of the transcriptome and metabolome during submergence to facilitate post-submergence recovery.
Locke AM, Barding GA, Sathnur S, Larive CK, Bailey-Serres J.
Plant Cell Environ. 2017-11-27; 41 (4)
PMID: 29094353 DOI: 10.1111/pce.13094
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Single-nucleus sequencing deciphers developmental trajectories in rice pistils.
Li C, Zhang S, Yan X, Cheng P, Yu H.
Dev Cell. 2023-04-06; 58 (8)
PMID: 37028425 DOI: 10.1016/j.devcel.2023.03.004
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Spatio-temporal transcript profiling of rice roots and shoots in response to phosphate starvation and recovery.
Secco D, Jabnoune M, Walker H, Shou H, Wu P, Poirier Y, Whelan J.
Plant Cell. 2013-11-18; 25 (11)
PMID: 24249833 DOI: 10.1105/tpc.113.117325
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Stress induced gene expression drives transient DNA methylation changes at adjacent repetitive elements.
Secco D, Wang C, Shou H, Schultz MD, Chiarenza S, Nussaume L, Ecker JR, Whelan J, Lister R.
Elife. 2015-07-21; 4
PMID: 26196146 DOI: 10.7554/elife.09343
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Stress-responsive regulation of long non-coding RNA polyadenylation in Oryza sativa.
Yuan J, Li J, Yang Y, Tan C, Zhu Y, Hu L, Qi Y, Lu ZJ.
Plant J. 2018-01-16; 93 (5)
PMID: 29265542 DOI: 10.1111/tpj.13804
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TAL effectors and activation of predicted host targets distinguish Asian from African strains of the rice pathogen Xanthomonas oryzae pv. oryzicola while strict conservation suggests universal importance of five TAL effectors.
Wilkins KE, Booher NJ, Wang L, Bogdanove AJ.
Front Plant Sci. 2015-07-21; 6
PMID: 26257749 DOI: 10.3389/fpls.2015.00536
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The evening complex integrates photoperiod signals to control flowering in rice.
Andrade L, Lu Y, Cordeiro A, Costa JMF, Wigge PA, Saibo NJM, Jaeger KE.
Proc Natl Acad Sci U S A. 2022-06-21; 119 (26)
PMID: 35733265 DOI: 10.1073/pnas.2122582119
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The Rice Serine/Arginine Splicing Factor RS33 Regulates Pre-mRNA Splicing during Abiotic Stress Responses.
Butt H, Bazin J, Prasad KVSK, Awad N, Crespi M, Reddy ASN, Mahfouz MM.
Cells. 2022-05-30; 11 (11)
PMID: 35681491 DOI: 10.3390/cells11111796
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Transcriptome Analysis Reveals Photoperiod-Associated Genes Expressed in Rice Anthers.
Sun S, Wang D, Li J, Lei Y, Li G, Cai W, Zhao X, Liang W, Zhang D.
Front Plant Sci. 2021-02-26; 12
PMID: 33719293 DOI: 10.3389/fpls.2021.621561
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