Gene Expression Nebulas
A data portal of transcriptomic profiles across multiple species

Gene Expression Nebulas

A data portal of transcriptome profiles across multiple species

Basic Information

Latin Name: Oryza sativa
Common Name: Rice
Kingdom: Plantae
Division: Plants and Fungi
Taxonomy ID: 4530
Parent Taxonomy ID: 4527


Data Resource Project ID BioProject ID Title Strategy Species Tissue Cell Type Cell Line Disease Sample Number Summary Overall Design PMID Release Date Submission Date Update Date


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)
The Rice Annotation Project Database (RAP-DB): 2008 update.
Rice Annotation Project, Tanaka T, Antonio BA, Kikuchi S, Matsumoto T, Nagamura Y, Numa H, Sakai H, Wu J, Itoh T, Sasaki T, Aono R, Fujii Y, Habara T, Harada E, Kanno M, Kawahara Y, Kawashima H, Kubooka H, Matsuya A, Nakaoka H, Saichi N, Sanbonmatsu R, Sato Y, Shinso Y, Suzuki M, Takeda J, Tanino M, Todokoro F, Yamaguchi K, Yamamoto N, Yamasaki C, Imanishi T, Okido T, Tada M, Ikeo K, Tateno Y, Gojobori T, Lin YC, Wei FJ, Hsing YI, Zhao Q, Han B, Kramer MR, McCombie RW, Lonsdale D, O'Donovan CC, Whitfield EJ, Apweiler R, Koyanagi KO, Khurana JP, Raghuvanshi S, Singh NK, Tyagi AK, Haberer G, Fujisawa M, Hosokawa S, Ito Y, Ikawa H, Shibata M, Yamamoto M, Bruskiewich RM, Hoen DR, Bureau TE, Namiki N, Ohyanagi H, Sakai Y, Nobushima S, Sakata K, Barrero RA, Sato Y, Souvorov A, Smith-White B, Tatusova T, An S, An G, OOta S, Fuks G, Fuks G, Messing J, Christie KR, Lieberherr D, Kim H, Zuccolo A, Wing RA, Nobuta K, Green PJ, Lu C, Meyers BC, Chaparro C, Piegu B, Panaud O, Echeverria M.
Nucleic Acids Res. 2007-12-17; 36 (Database issue)
Alternative Splicing Plays a Critical Role in Maintaining Mineral Nutrient Homeostasis in Rice (Oryza sativa).
Dong C, He F, Berkowitz O, Liu J, Cao P, Tang M, Shi H, Wang W, Li Q, Shen Z, Whelan J, Zheng L.
Plant Cell. 2018-09-25; 30 (10)
Cell fixation and preservation for droplet-based single-cell transcriptomics.
Alles J, Karaiskos N, Praktiknjo SD, Grosswendt S, Wahle P, Ruffault PL, Ayoub S, Schreyer L, Boltengagen A, Birchmeier C, Zinzen R, Kocks C, Rajewsky N.
BMC Biol. 2017-05-19; 15 (1)
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)
Network-based feature selection reveals substructures of gene modules responding to salt stress in rice.
Du Q, Campbell M, Yu H, Liu K, Walia H, Zhang Q, Zhang C.
Plant Direct. 2019-08-12; 3 (8)
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)
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)
Rice nucleosome patterns undergo remodeling coincident with stress-induced gene expression.
Zhang Q, Oh DH, DiTusa SF, RamanaRao MV, Baisakh N, Dassanayake M, Smith AP.
BMC Genomics. 2018-01-26; 19 (1)
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)
Integrated Analysis of the Transcriptome and Metabolome Revealed the Molecular Mechanisms Underlying the Enhanced Salt Tolerance of Rice Due to the Application of Exogenous Melatonin.
Xie Z, Wang J, Wang W, Wang Y, Xu J, Li Z, Zhao X, Fu B.
Front Plant Sci. 2020-01-01; 11
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)
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)
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)
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)
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
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
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)
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)
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)
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)
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)
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
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)
Genomic basis of geographical adaptation to soil nitrogen in rice.
Liu Y, Wang H, Jiang Z, Wang W, Xu R, Wang Q, Zhang Z, Li A, Liang Y, Ou S, Liu X, Cao S, Tong H, Wang Y, Zhou F, Liao H, Hu B, Chu C.
Nature. 2021-01-06; 590 (7847)
Characterization of the transcriptional divergence between the subspecies of cultivated rice (Oryza sativa).
Campbell MT, Du Q, Liu K, Sharma S, Zhang C, Walia H.
BMC Genomics. 2020-06-08; 21 (1)
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)
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)
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)
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)
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)