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 BYU 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 UCLA 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
|
6 |
|
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 Missouri STACEYG AT missouri DOT edu |
Medicago truncatula |
yes |
- Root, leaf varied by nitrogen source
- Symbiotic conditions for root, nodules, leaf
|
35 |
Gary Stacey Missouri STACEYG AT missouri DOT edu |
Phaseolus vulgaris |
no |
- Root, nodule, stem, young trifoliates, leaf
- Young pod, green mature pod
- Budding and mature flower
|
11 |
|
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 Marburg 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 .
|