Browse plant experiments
Thanks to funding from the Gramene project, Expression Atlas contains 1026 plant experiments, studying e.g. Arabidopsis, rice, and maize.
The baseline experiments, are either RNA-seq or proteomics, and display expression levels of gene products under 'normal' conditions (e.g. normal rice tissues). Each experiment is manually curated to a high standard, and RNA expression levels are calculated using the iRAP pipeline.
The differential experiments in Atlas, containing both microarray and RNA-seq data, allows users to query which genes are up-/down-regulatedin different experimental conditions, e.g. 'in Arabidopsis shoots, what genes are upregulated in plants treated by X?'
Baseline experiments
Arabidopsis thaliana
- Adrian et al 2015 (11 assays)
- Ages - 10 Klepikova et al (30 assays)
- Arabidopsis silique development - Chua et al (4 assays)
- Arabidopsis thaliana - ARAPORT11 (116 assays)
- Ecotypes - 17 Clark et al (51 assays)
- Ecotypes - 19 Gan et al (42 assays)
- Ecotypes - 9 Kurlovs et al. (54 assays)
- Huang et al 2017 - Root sampling site (9 assays)
- Mergner et al., 2020 - Organism part (56 assays)
- Narsai et al., 2017 - Time series (30 assays)
- Romanowski et al., 2020 - Timeseries (24 assays)
- Tissues - 4 Liu et al (4 assays)
- Tissues, genotypes - Pignatta et al., 2014 (30 assays)
- Wang et al., 2015 - Ecotype (24 assays)
- Wang et al., 2015 - Ecotype (64 assays)
- Wendrich et al., 2017 - Sampling site (24 assays)
- Yang et al., 2016 - Ecotype (12 assays)
- arabidopsis2023_Tissues - Mergner J et al. 2020 (30 assays)
Brachypodium distachyon
Glycine max
- 4 Stages - Harada and Goldberg (273 assays)
- 8 Stages - Brown and Hudson (42 assays)
- Developmental Stages - 4 Goldberg et al (9 assays)
- Developmental Stages - 7 Goldberg et al (19 assays)
- Developmental Stages - 7 Jones and Vodkin (16 assays)
- Huang et al 2017 - Root sampling site (9 assays)
- Seed oil content - Goettel et al (9 assays)
- Seedling development - Jones et al (14 assays)
- Tissues - 9 Shen et al. (28 assays)
Hordeum vulgare subsp vulgare
Oryza sativa
Oryza sativa japonica group
- Huang et al 2017 - Root sampling sites (9 assays)
- Lee et al 2017 - Time (36 assays)
- Reynoso et al, 2018 - Fraction (8 assays)
- Tissues - 4 Zhang et al (4 assays)
- Tissues - 5 Hong et al.(2022) (14 assays)
- Tissues - 7 Sakai (28 assays)
- Tissues - 9 Davidson (11 assays)
- Tissues - Anderson et al (9 assays)
- Wang et al 2015 - Organism Part (single-end seq) (8 assays)
- Wang et al 2015 - Organism Parts (8 assays)
Solanum lycopersicum
Sorghum bicolor
- Cui et al., 2021 - Ecotype (18 assays)
- Dhaka et al., 2020 - Developmental stage (9 assays)
- Emms et al., 2016 - Cell type (6 assays)
- Kawa et al., 2021 - Cultivar (45 assays)
- Kebrom et al 2017 - Sampling site (12 assays)
- Thurber et al., 2015 - Organism part (4 assays)
- Tissues - 3 Makita et al. (9 assays)
- Tissues - Davidson et al (10 assays)
- Tissues - Olson et al (17 assays)
- Turco et al 2017 - Organism Part (12 assays)
- Wang et al., 2018 - Organism part (165 assays)
Triticum aestivum
Vitis vinifera
- Bagnaresi et al., 2020 - Cultivar (18 assays)
- Cramer et al., 2015 - Cultivar (84 assays)
- Cultivars - 10 Potenza et al (9 assays)
- Cultivars - 5 Palumbo et al. (60 assays)
- Da Silva et al., 2013 - Organism part (11 assays)
- Dal Santo et al 2018 - Cultivar (72 assays)
- Leaf development - Pervaiz et al (4 assays)
- Massonnet et al., 2019 - Developmental stage (16 assays)
- Tissues - Venturini et al (9 assays)
- Wang et al, 2019 - Developmental stage (12 assays)
Zea mays
- Cell Type - Nelson et al 2014 (12 assays)
- Cell Types - Seed Lloyd et al (4 assays)
- Chen et al., 2017 - Cell types (18 assays)
- Cruz et al., 2020 - Individual (92 assays)
- Cultivar - 2 inbred Regulski (6 assays)
- Cultivars - eight inbred lines (3 assays)
- Frey et al, 2015 - Cultivar (51 assays)
- Huang et al 2017 - Root sampling site (9 assays)
- Koch et al, 2016 - Organism part (12 assays)
- Lemmon et al, 2014 - Cultivar (440 assays)
- Meng et al, 2017 - Age (24 assays)
- Oka et al, 2017 - Sampling site (18 assays)
- Organism Part - Chang et al 2012 (4 assays)
- Pang et al., 2018 - Cultivar (291 assays)
- Reyes et al, 2017 - Cell type (8 assays)
- Sampling Time Points - Plant Systems Biology Uni Ghent (16 assays)
- Sampling sites - Li et al 2010 (12 assays)
- Seed development - Chen et al (65 assays)
- Seifert et al., 2018 - Cultivar (25 assays)
- Shuai Wang et al, 2014 - Organism part (6 assays)
- Thatcher et al., 2014 - Cultivar (94 assays)
- Tissues - 4 Chettoor et al (11 assays)
- Tissues - 5 Xu et al (5 assays)
- Tissues - 6 Wang (36 assays)
- Tissues - Stelpflug et al (267 assays)
- Tissues - Walley et al (68 assays)
- Wang et al 2014 - Sampling site (75 assays)
- Wang et al, 2018 - Cultivar (14 assays)
- Wang et al., 2018 - Organism part (36 assays)
- Want et al., 2020 - Cultivar (40 assays)