Nipponbare - OmicsDI

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Genomics (515)
Unknown (412)
Transcriptomics (262)
Proteomics (38)
Methylation profiling (9)
Other (1)
Metabolomics (1)

Organisms

Oryza sativa (199)
Oryza sativa Japonica Group (85)
Chlamydomonas reinhardtii (31)
Pseudomonas canadensis (31)
Marchantia polymorpha subsp. ruderalis (31)
Methylocystis sp. (31)
Exiguobacterium sp. SH31 (31)
Porites pukoensis (31)
Bothrops insularis (31)
Bothrops jararaca (31)
Bothrops jararacussu (31)
Bothrops cotiara (31)
Dinosauria (31)
Streptomyces coelicolor (31)
Pseudomonas taiwanensis (31)
Burkholderia ubonensis MSMB22 (31)
Pseudomonas aeruginosa PA103 (31)
Artibeus jamaicensis (31)
Oryza sativa Indica Group (12)
Oryza rufipogon (4)
Arabidopsis thaliana (3)
Oryza nivara (3)
Azospirillum lipoferum 4B (2)
Azoarcus sp. (2)
Oryza sativa aus subgroup (2)
Oryza sativa Japonica Group x Oryza sativa Indica Group (1)
Oryza sativa Indica Group x Oryza sativa Japonica Group (1)
Hordeum vulgare (1)
Azoarcus olearius (1)
Cnaphalocrocis medinalis (1)

Organisms

Oryza sativa (249)
Oryza sativa Japonica Group (97)
unidentified (6)
Oryza sativa Indica Group (3)
Oryza (2)
Oryza rufipogon (2)
Oryza officinalis (2)
root metagenome (2)
Azospirillum lipoferum 4B (1)
Dinebra chinensis (1)
Oryza sativa Japonica Group x Oryza sativa Indica Group (1)
shoot metagenome (1)
Methylocystis iwaonis (1)
Azoarcus sp. (1)
Oryza sativa Japonica Group x Oryza rufipogon (1)
Oryza longistaminata (1)
Oryza australiensis (1)
plant metagenome (1)
metagenome (1)
rhizosphere metagenome (1)

Repository

ENA (491)
biostudies-arrayexpress (180)
geo (107)
pride (31)
ExpressionAtlas (7)
PAXDB (4)
iProX (3)
EVA (2)
MetaboLights (1)

Tissue

Leaf (16)
Plant cell (12)
Root (5)
Seed (4)
Embryo (3)
Whole body (3)
Root tip (1)
Callus (1)
Post-flowering panicle (1)
Pre-flowering panicle (1)
Shoot (1)
Plant embryo (1)
Early inflorescence (1)
Seed 5 days after pollination (1)
Emerging inflorescence (1)
Pistil (1)
Seed 10 days after pollination (1)
Anther (1)
Endosperm (1)
Meiotic cell (1)
Plant cell line (1)
Seedling (1)

Technology Type

Mass Spectrometry (31)
Shotgun proteomics (20)
Affinity purification coupled with mass spectrometry proteomics (7)
Data-dependent acquisition (3)
Bottom-up proteomics (3)
Proteogenomics (2)
Mass spectrometry (1)
HDMSE (1)
SWATH MS (1)

Instrument Platform

Illumina HiSeq 2000 (7)
Illumina Genome Analyzer IIx (4)
DNA Microarray Scanner BA [Agilent Technologies] (2)
Illumina HiSeq 1000 (2)
Illumina NovaSeq 6000 (2)
NextSeq 500 (2)
Hisat2 v2.0.5 (1)
DESeq (1)
Growthroom (1)
Illumina Novaseq platform (1)
NextSeq 2000 (1)
Illumina HiSeq 4000 (1)
Illumina HiSeq 2500 (1)
GCT Premier (Waters) (1)

Publication Date

2016 (36)
2012 (33)
2014 (31)
2013 (31)
2011 (27)
2015 (25)
2008 (21)
2010 (18)
2018 (17)
2019 (13)
2009 (13)
2021 (12)
2020 (10)
2024 (8)
2022 (8)
2017 (8)
2025 (7)
2023 (7)
2026 (5)
2007 (1)
2006 (1)
2004 (1)

UNIPROT ID/AC

FDH1_ORYSJ (3)
Q84TA1_ORYSJ (3)
Q6K241_ORYSJ (3)
ALFC1_ORYSJ (3)
A0A0P0XWA7_ORYSJ (3)
6PGL4_ORYSJ (3)
GSTF2_ORYSJ (3)
ALFC3_ORYSJ (3)
RS3A_ORYSJ (3)
Q5QMK7_ORYSJ (3)
Q94LR9_ORYSJ (3)
Q7X8A1_ORYSJ (3)
Q2QXL3_ORYSJ (3)
CLPC2_ORYSJ (3)
Q8H590_ORYSJ (3)
Q93X08_ORYSJ (3)
NIR_ORYSJ (3)
GLO1_ORYSJ (3)
UGDH3_ORYSJ (3)
Q6ZGJ8_ORYSJ (3)
Q651T8_ORYSJ (3)
Q9AS12_ORYSJ (3)
Q5NAM3_ORYSJ (3)
Q7XPR2_ORYSJ (3)
Q2QVC1_ORYSJ (3)
A0A0P0WKD6_ORYSJ (3)
Q6AVR6_ORYSJ (3)
GLO5_ORYSJ (3)
Q6K9T1_ORYSJ (3)
Q0DZE5_ORYSJ (3)

CHEBI ID

CHEBI:31006 (1)
CHEBI:141071 (1)
CHEBI:141070 (1)
CHEBI:141095 (1)
CHEBI:141093 (1)
CHEBI:141092 (1)
CHEBI:141091 (1)
CHEBI:141089 (1)
CHEBI:141088 (1)
CHEBI:141086 (1)
CHEBI:141085 (1)
CHEBI:141084 (1)
CHEBI:141083 (1)
CHEBI:141082 (1)
CHEBI:141081 (1)
CHEBI:141080 (1)
CHEBI:141079 (1)
CHEBI:141076 (1)
CHEBI:17030 (1)
CHEBI:1307 (1)
CHEBI:141061 (1)
CHEBI:47771 (1)
CHEBI:43619 (1)
CHEBI:16148 (1)
CHEBI:141090 (1)
CHEBI:141094 (1)
CHEBI:141078 (1)
CHEBI:141072 (1)
CHEBI:140958 (1)
CHEBI:140951 (1)

Metabolite Name

Triacontane (1)
Lauryl laurate(C12:0_C12:0) (1)
C9:0 (1)
C8:0 (1)
C7:0 (1)
C23:0 ME (1)
C22:1(13Z) ME (1)
C22:0 ME (1)
C21:0 ME (1)
C21:0 (1)
C20:1(11Z) ME (1)
C20:0 ME (1)
C18:2 ME (1)
C18:1 ME (1)
C18:0 ME (1)
C17:0 ME (1)
C17:0 (1)
C16:1(9Z) ME (1)
C16:0 ME (1)
C15:0 ME (1)
C14:0 ME (1)
C12:0 ME (1)
C12:0 (1)
C11:0 ME (1)
Cycloartenol (1)
3beta-24-Methylenecycloartan-3-ol (1)
C13:0 (1)
C15:0 (1)
Undecane (1)
C23:0 (1)

First Public Date

2014 (81)
2017 (50)
2025 (46)
2024 (46)
2018 (38)
2019 (34)
2022 (32)
2020 (28)
2026 (26)
2015 (26)
2023 (22)
2021 (22)
2013 (22)
2016 (16)
2011 (1)
2010 (1)

Study type

Transcription profiling by array (116)
RNA-seq of coding RNA (35)
RNA-seq of non coding RNA (11)
Transcription profiling by tiling array (5)
ChIP-seq (5)
Unknown experiment type (4)
Plant - Two-color microarray (1)
ChIP-chip by tiling array (1)
Comparative genomic hybridization by array (1)
Other (1)

Release Date

2014 (48)
2016 (47)
2022 (42)
2020 (41)
2013 (36)
2025 (34)
2015 (34)
2019 (34)
2021 (33)
2012 (32)
2023 (31)
2011 (30)
2018 (29)
2017 (29)
2010 (24)
2024 (21)
2008 (18)
2009 (12)
2026 (5)
2007 (5)
2005 (2)
2002 (2)
2004 (1)
2001 (1)
2000 (1)

Lab affiliation

National Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, China (2)
State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China (2)
Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou 225009, China (2)
State Key Lab of Plant Genomics Institute of Genetics and Developmental Biology Chinese Academy of Sciences, Beijing 100101, China Chaoyang District, Beichen West Road, Campus #1, No. 2 (2)
China national rice research institute (1)
Department of Molecular Systems Biology at Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran (1)
China National Rice Research Institute (1)
Biological Sciences and Health Center, University of Taquari Valley - Univates, Lajeado, RS, Brazil (1)
Department of Molecular Sciences, Macquarie University, Australia (1)
Department of Molecular Sciences, Faculty of Science and Engineering, Macquarie University, NSW 2109, Australia (1)
Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Coupure links 653, B-9000 Ghent, Belgium (1)
Instituto de Agricultura Sostenible-CSIC Av. Menéndez Pidal s/n Campus Alameda del Obispo Apartado 4084, 14080 Córdoba, Spain (1)
Plant Stress Physiology and Proteomics Laboratory, College of General Education, Kookmin University, Seoul, South Korea (1)
National Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University,China (1)
Professor at School of Natural Sciences in Macquarie University (1)
Principal Research Officer Malaysian Agricultural Research & Development Institute (MARDI), 43300 Serdang, Selangor, Malaysia (1)
Department of Molecular Sciences, Macquarie University, North Ryde, NSW, Australia (1)
Key Laboratory of Plant Germplasm Enhancement and Speciality Agriculture, Wuhan Botanical Garden, Sino-African Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China (1)
NARO Institute of Crop Science (1)
Chemistry and Biomolecular Sciences, Faculty of Science and Engineering, Macquarie University (1)
1. School of Life Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China 2. Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong SAR, China (1)
Jian Zhang Ph.D and Professor China National Rice Research Institute 28 shuidaosuo road Fuyang, Hangzhou P.R.China 311400 Office: +86 571 63370277 Cell: +86 13656661382 Email: zhangjian@caas.cn (1)
Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, the Chinese Academy of Sciences (1)
Wuhan Botanical Garden, CAS (1)
Department of Molecular Sciences, Macquarie University, North Ryde, NSW 2109, Australia (1)
Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou 225009,China (1)
Department of Chemistry and Biomolecular Sciences, Faculty of Science and Engineering, Macquarie University (1)

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Developing endosperm: Nipponbare vs NIL(TGW6)

Gene expression profoling of developping endosperm at 3 and 6 days after flowering (DAH): Nipponbare vs NIL(TGW6) We used two rice varieties, NIL(TGW6) and Nipponbare.NIL(TGW6) is a nearly isogenic line containing the thousand grain weight qTGW6. For samples used three stages: 3 and 6 DAH endosperm ...

ORGANISM(S): Oryza sativa

2013-02-12 | E-GEOD-44223 | biostudies-arrayexpress

Host transcriptional reprogramming across diverse strains of the rice bacterial leaf streak pathogen Xanthomonas oryzae pv.oryzicola

We performed RNA-Seq of leaves of Oryza sativa L. ssp. japonica cv. Nipponbare 48 hours after inoculation with 10 geographically diverse strains of Xanthomonas oryzae pv. oryzicola, the causal agent of bacterial leaf streak. Results provide insight into the molecular basis of bacterial leaf streak, ...

ORGANISM(S): Oryza sativa Japonica Group

2015-05-01 | E-GEOD-67588 | biostudies-arrayexpress

Transcriptome and methylome interactions in rice hybrids

This research reports genome-wide measurements of genetic and epigenetic patterns of inheritance through an integrative analysis of BS-seq, RNA-seq, and siRNA-seq data in two inbred parents of the Nipponbare (NPB) and Indica (93-11) variety of rice and their hybrid offspring. We generated integrativ...

ORGANISM(S): Oryza sativa Indica Group

2012-07-10 | E-GEOD-38480 | biostudies-arrayexpress

Microarray analysis of strain EG4 vs. Nipponbare

In the japonica rice strain Gimbozu EG4, the DNA transposon mPing is actively transposing to attain over 1,000 copies, whereas in Nipponbare, where this element is virtually silent and has only 50 copies. To analyze the impact of such a massive amplification of transposable element on gene regulatio...

ORGANISM(S): Oryza sativa Japonica Group

2010-06-20 | E-GEOD-15021 | biostudies-arrayexpress

Oryza sativa, Nipponbare RNA-Seq - Conserved Poaceae Specific Genes Project

Illumina RNA Sequencing (RNA-Seq) of Oryza sativa, Nipponbare for the Conserved Poaceae Specific Genes project. Authors: Robin Buell, Ning Jiang, Haining Lin, Rebecca Davidson, Malali Gowda, John Hamilton, Brieanne Vaillancourt

ORGANISM(S): Oryza sativa Japonica Group

2012-04-04 | E-MTAB-2039 | biostudies-arrayexpress

Oryza sativa strain:Nipponbare

Oryza sativa Nipponbare Genome sequencing

PRJNA238421 | ENA

Response to salt stress treatment over time in Oryza sativa L. Japonica Nipponbare, RNA-seq dataset

Oryza sativa L. Japonica nipponbare seedlings were treated with 300mM NaCl or water, and then samples were taken after one hour, five hours and 24 hours, to assess which genes are differentially expressed over time during salt stress treatment. The results from this dataset are also compared with th...

ORGANISM(S): Oryza sativa Japonica Group

2015-08-25 | E-MTAB-1625 | biostudies-arrayexpress

Response to salt stress treatment over time in Oryza sativa L. Japonica Nipponbare, microarray dataset

ORGANISM(S): Oryza sativa Japonica Group

2015-12-04 | E-MTAB-1624 | biostudies-arrayexpress

Oryza sativa cv. Nipponbare and Oryza barthii as unexpected tolerance and susceptibility sources against Schizotetranychus oryzae (Acari: Tetranychidae) mite infestation

Cultivated rice (Oryza sativa L.) is frequently exposed to multiple stresses, including Schizotetranychus oryzae mite infestation. Rice domestication has narrowed the genetic diversity of the species, leading to a wide susceptibility. This work aimed to observe the response of two wild rice species ...

ORGANISM(S): Oryza barthii Oryza sativa (Rice)

2021-09-09 | PXD020940 | Pride

Oryza sativa Japonica Group strain:Nipponbare

Update of genome assembly of Oryza sativa L. Nipponbare (Os-Nipponbare-Reference-IRGSP-1.0)

PRJDB1747 | ENA

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