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RNA-Seq data from Phytozome.
Current data
mRNA Expression Data

Phytozome hosts a collection of RNA-seq expression studies acquired from several internal and external sources. Next-generation sequencing reads are aligned to reference genomes, and gene- and transcript-level expression values are determined using Cufflinks or DSeq2. The set covered in Phytozome v13 includes:

organism Gene Atlas? tissues / conditions # of expts permissions / contact
Arachis hypogaea no
  • Dry condition mixed
  • Floral
  • Green cotyledon
  • Immature seed
  • Maturing seed
  • Leaf
  • Root
  • Stem
8 P. Jeff Maughan
Jeff_Maughan AT byu DOT edu
Arabidopsis thaliana yes
  • Root, leaf varied by nitrogen source
6 Jeremy Schmutz
JGI / HudsonAlpha
jschmutz AT hudsonalpha DOT org
Brachypodium distachyon yes
  • Above ground tissues grown for 20 days / 18 hours of light, varied for harvesting time between 1 and 24 hours and by cold, heat, drought, salt treatment
  • Shoots grown for 29 through 31 days / 12 hours of light, sample series varied by day and hour of harvest
  • Root, leaf varied by nitrogen source
  • Young and mature leaf
  • Gradient young leaf tissues
  • Floral
  • Base, mixed and tip tissues of stem
65 Todd Mockler
Danforth Center
tmockler AT danforthcenter DOT org
Chlamydomonas reinhardtii yes
  • Anaerobiosis
  • Bilin signaling
  • Cu deficiency photoautotrophic
  • Fe deficiency
  • H2O2 treatment
  • N concentration
  • Heterotrophic, photoheterotrophic and phototrophic cultures varied by light exposure, nitrogen source and harvesting time
133 Sabeeha Merchant
merchant AT chem DOT ucla DOT edu

Jeremy Schmutz
JGI / HudsonAlpha
jschmutz AT hudsonalpha DOT org
Eucalyptus grandis no From a E. grandis × E. urophylla hybrid:

  • Mature leaf
  • Young leaf
  • Phloem
  • Shoot tips
  • Xylem
  • Immature xylem
Glycine max yes
  • Root, lateral root, root tip, root hairs, nodules, shoot tip, apical metristem shoot, leaf, flower, seed in a series of developmental stages
  • Root, leaf varied by nitrogen source
  • Opened, unopened flower
  • Symbiotic conditions for root, nodules, leaf
26 Gary Stacey
STACEYG AT missouri DOT edu
Medicago truncatula yes
  • Root, leaf varied by nitrogen source
  • Symbiotic conditions for root, nodules, leaf
35 Gary Stacey
STACEYG AT missouri DOT edu
Phaseolus vulgaris no
  • Root, nodule, stem, young trifoliates, leaf
  • Young pod, green mature pod
  • Budding and mature flower
Physcomitrella patens yes
  • Gametophores, varied by medium, (de/re)hydration, treatment with NAA
  • Detached leaflets from gametophores
  • Protonema, varied by medium with wide variety of treatments, light conditions
  • Protoplasts from protonema
  • Spores
  • Green and brown sporophytes
32 Stefan Rensing
stefan DOT rensing AT biologie DOT uni-marburg DOT de

Jeremy Schmutz
JGI / HudsonAlpha
jschmutz AT hudsonalpha DOT org
Setaria italica yes
  • Etiolated seedling, germinating root, germinating shoot
  • Multiple runs of leaf tissue in high light
  • Root, shoot, panicle
  • Root varied by nitrogen source, amount of H2O
  • Mixed above-ground tissue varied by light condition
22 Thomas Brutnell
Danforth Center
tbrutnell AT danforthcenter DOT org
Sorghum bicolor yes
  • Wide variety of root, stem and leaf structures, panicle and peduncle when juvenile, vegetative and at anthesis, floral initiation and grain maturity
  • Dry and imbibed seed at grain maturity
  • Root, shoot varied by nitrogen source, control with full fertilization, with H2O only
48 John Mullet
Texas A&M
jmullet AT tamu DOT edu
Vigna unguiculata no
  • Seeds at different stages of germination
  • Root, stem, leaf and pod tissue samples
9 Stefano Lonardi
UC Riverside
stelo AT cs DOT ucr DOT edu,

Timothy Close
UC Riverside
timothy DOT close AT ucr DOT edu,

and Maria Munoz-Amatriain

The JGI Plant Gene Atlas Project is a multi-laboratory collaboration that seeks to produce a standardized expression atlas across diverse tissues and time courses from JGI Plant Flagship organisms. More detail about the Plant Flagship Genomes can be found here. JGI users can submit proposals to have tissues and conditions of interest included in the Plant Atlas through the JGI Community Science Program .

The data included in the Atlas is unpublished. As a public service, the Department of Energy's Joint Genome Institute (JGI) is making the RNA-seq expression data available before scientific publication according to the Ft. Lauderdale Accord. This balances the imperative of the DOE and the JGI that the data from its sequencing projects be made available as soon and as completely as possible with the desire of contributing scientists and the JGI to reserve a reasonable period of time to publish on analysis without concerns about preemption by other groups.

At the present time, we request that anyone intending to download Gene Atlas data for use in any analysis to email contacts as noted with individual organisms. The overall project lead is Jeremy Schmutz at JGI / HudsonAlpha, email: jschmutz AT hudsonalpha DOT org. To be kept informed on the progress of the JGI Gene Atlas project, changes in the data usage policy, or to ask questions, please subscribe to the project mailing list by sending a blank email with the Subject line subscribe jgi-gene_atlas FirstName LastName to [email protected].

Bulk download
Bulk data files for gene expression data for non-Gene Atlas experiments are available for download from individual organisms folders at the JGI Genome Portal .
Related template queries

Expression score for all genes in an organism

Expression score for all mRNAs in an organism

Expression score for one specific gene

Query starting points

These links will take you to the Query Builder pages which allow you to make new queries and create template queries of your own