GEO DataSets

(Submitter supplied) Different plant species within the grasses were parallel targets of domestication, giving rise to crops with distinct evolutionary histories and traits. Key traits that distinguish these species are mediated by specialized cell types. Here, we compare the transcriptomes of root cells in three grass species—Zea mays (maize), Sorghum bicolor (sorghum), and Setaria viridis (Setaria). We first show that single-cell and single-nucleus RNA-seq provide complementary readouts of cell identity in both dicots and monocots, warranting a combined analysis. more...

Organism:

Setaria viridis; Zea mays; Sorghum bicolor; Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

4 related Platforms

22 Samples

Download data: CSV, RDATA

(Submitter supplied) Photosynthesis supports life on Earth but the regulatory architecture associated with photosynthesis gene expression is poorly understood. Most crops use either C3 or C4 photosynthesis with the latter allowing significantly higher efficiencies as well as improved water and nitrogen use. Here we use DNAse-SEQ to define >1 million transcription factor binding sites in leaves of grasses that either operate C3 or C4 photosynthesis and that are consistent with significant differences in the modes of gene regulation between the kingdoms of life. more...

Organism:

Brachypodium distachyon; Zea mays; Setaria italica; Sorghum bicolor

Type:

Genome binding/occupancy profiling by high throughput sequencing

4 related Platforms

20 Samples

Download data: BED, TXT

(Submitter supplied) Most plant roots have multiple cortex layers that make up the bulk of the organ and play key roles in physiology like flood tolerance and symbiosis. However, little is known about how cortical layers form outside the highly reduced anatomy of the model Arabidopsis. Here we use single-cell RNAseq to rapidly generate a cell-resolution map of the maize root, revealing an alternative configuration of the tissue-formative SHORT-ROOT (SHR) signaling pathway adjacent to the expanded cortex. more...

Organism:

Zea mays

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL20156 GPL25410 GPL17628

9 Samples

Download data: CSV, TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Zea mays

Type:

Expression profiling by high throughput sequencing

4 related Platforms

65 Samples

Download data

(Submitter supplied) Most plant roots have multiple cortex layers that make up the bulk of the organ and play key roles in physiology like flood tolerance and symbiosis. However, little is known about how cortical layers form outside the highly reduced anatomy of the model Arabidopsis. Here we use single-cell RNAseq to rapidly generate a cell-resolution map of the maize root, revealing an alternative configuration of the tissue-formative SHORT-ROOT (SHR) signaling pathway adjacent to the expanded cortex. more...

Organism:

Zea mays

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30012

24 Samples

Download data: CSV

(Submitter supplied) Most plant roots have multiple cortex layers that make up the bulk of the organ and play key roles in physiology like flood tolerance and symbiosis. However, little is known about how cortical layers form outside the highly reduced anatomy of the model Arabidopsis. Here we use single-cell RNAseq to rapidly generate a cell-resolution map of the maize root, revealing an alternative configuration of the tissue-formative SHORT-ROOT (SHR) signaling pathway adjacent to the expanded cortex. more...

Organism:

Zea mays

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20156

32 Samples

Download data: TXT

(Submitter supplied) Through domestication, humans have substantially altered the morphology of Zea mays ssp. parviglumis (teosinte) into the currently recognizable maize. A wealth of archeological and population genetic data has established maize as a model system for studying domestication , genome evolution and the genetics and evolution of complex traits. We used expression profiling of 18,242 genes for 38 diverse maize genotypes and 18 teosinte genotypes to examine how domestication has re-shaped the transcriptome of maize seedlings. more...

Organism:

Zea mays; Zea mays subsp. parviglumis

Type:

Expression profiling by array

Platform:

GPL13736

94 Samples

Download data: PAIR

(Submitter supplied) Setaria viridis, the wild ancestor of millet, exhibits strong repression of crown root growth in drought. We compare in gene expression in the S. viridis crown between drought vs watered treatments.

Organism:

Setaria viridis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21478

24 Samples

Download data: CSV

(Submitter supplied) We have characterized the transcriptional response in Maize under limiting and sufficient nitrogen conditions, and have identified a set of genes whose expression profiles can quantitatively assess the response of plants to those conditions.

Organism:

Zea mays

Type:

Expression profiling by array

Platform:

GPL14616

90 Samples

Download data: CEL

(Submitter supplied) The thk1 mutant, causing multiple aleurone layers, disrupts the NOT1 scaffolding subunit of the CCR4-NOT regulatory complex and dysregulates genes involved in cell division, signaling, differentiation and metabolism.

Organism:

Zea mays

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17628

9 Samples

Download data: TSV

(Submitter supplied) Iron (Fe) is an essential micronutrient for almost all organisms. However, Fe is frequently inaccessible to plants. To acquire insoluble Fe from soil, rice (Oryza sativa L.) plants employ a Combined Strategy, which is composed by all features of Strategy II, common to all Poaceae species, and some features of the Strategy I from non-Poaceae. To understand the evolution of Fe uptake mechanisms, we analyzed the root transcriptomic response to Fe deficiency in two species from the Oryza genus: O. more...

Organism:

Oryza sativa; Oryza rufipogon

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL15800 GPL13160

8 Samples

Download data: TSV

(Submitter supplied) We developed a method to synchronize the induction of lateral roots in primary and adventitious roots of Zea mays, and used it to perform a genome-wide transcriptome analysis of the pericycle cells in front of the phloem poles during lateral root initiation.

Organism:

Zea mays

Type:

Expression profiling by array

Platform:

GPL16941

30 Samples

Download data