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

Datasets

Download Dataset ID BioProject ID Project ID Dataset Name Species Strategy Sample Number Tissue Cell Type Cell Line Healthy Condition Development Stage Case Detail Control Detail Cell Number Biological Condition Quality and Quantity
Baseline Genetic Phenotypic Environmental Spatial Temporal RNA Type Median Mapping Quality Median Coverage Max Sequencing Length Max Replicate#

Publications

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)
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)
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)
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)
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)
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
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)
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)
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)
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)
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)
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)
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)
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 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)
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)
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)
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)
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 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)
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)
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)
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)
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)