GEO DataSets

(Submitter supplied) The goal of this study is to clarify the function of ZmTE1 in auxin signal pathway and regulting cell cycle related genes. We isolated total RNA from the three nodes together with internodes of 28-day-old B73 and ZmTE1 seedlings. New genes act downstream of ZmTE1 at the nodes, are discovered.

Organism:

Zea mays

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15463

6 Samples

Download data: XLS

(Submitter supplied) KNOTTED1(KN1)-like homeobox (KNOX) transcription factors function in plant meristems, self-renewing structures consisting of stem cells and their immediate daughters. Despite their importance for plant development, the genomic network targeted by KNOX proteins is poorly understood. Using ChIP-seq, we defined the KN1 cistrome in maize inflorescences and found that KN1 binds to several thousand loci. To understand how these binding occupancies correlate with changes in transcriptional regulation, we performed RNA-seq on immature ears and tassels, and compared expression profiles between normal and loss-of-function kn1 plants, in addition to immature leaves from normal and gain-of-function Kn1 plants. We found that 643 of the KN1 targets were modulated in one or multiple tissues, with a strong enrichment for transcription factors (including other homeobox genes) and genes participating in several hormonal pathways, most significantly auxin, implicating KN1 at the crossroads of plant hormone signaling. The loss-of-function kn1 phenotype is reminiscent of auxin mutants and kn1 mis-expression in leaves correlates with increased auxin signaling. Our results demonstrate that KN1 plays a key role in orchestrating the upper levels of a hierarchical gene regulatory network that impacts plant meristem identity and function.

Organism:

Zea mays

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL9361

6 Samples

Download data: BED

(Submitter supplied) KNOTTED1(KN1)-like homeobox (KNOX) transcription factors function in plant meristems, self-renewing structures consisting of stem cells and their immediate daughters. Despite their importance for plant development, the genomic network targeted by KNOX proteins is poorly understood. Using ChIP-seq, we defined the KN1 cistrome in maize inflorescences and found that KN1 binds to several thousand loci. To understand how these binding occupancies correlate with changes in transcriptional regulation, we performed RNA-seq on immature ears and tassels, and compared expression profiles between normal and loss-of-function kn1 plants, in addition to immature leaves from normal and gain-of-function Kn1 plants. We found that 643 of the KN1 targets were modulated in one or multiple tissues, with a strong enrichment for transcription factors (including other homeobox genes) and genes participating in several hormonal pathways, most significantly auxin, implicating KN1 at the crossroads of plant hormone signaling. The loss-of-function kn1 phenotype is reminiscent of auxin mutants and kn1 mis-expression in leaves correlates with increased auxin signaling. Our results demonstrate that KN1 plays a key role in orchestrating the upper levels of a hierarchical gene regulatory network that impacts plant meristem identity and function.

Organism:

Zea mays

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15463

20 Samples

Download data: DIFF, XLS

(Submitter supplied) BP and ER encode proteins that act synergistically to regulate Arabidopsis inflorescence architecture. To search for genes/proteins that influence the BP/ER signaling pathways, we conducted mutagenesis of the bp er double mutant and found that a mutation in FILAMENTOUS FLOWER (FIL) suppresses many of the morphological/developmental defects in bp er. Given that FIL encodes a Zn-finger containing transcription factor, microarray analysis was conducted on bp er vs. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL198

6 Samples

Download data: CEL

(Submitter supplied) Bioenergy sorghum accumulates 75% of shoot biomass in stem internodes. Grass stem internodes are formed during vegetative growth and elongate in response to developmental and environmental signals. To identify genes and molecular mechanisms that modulate the extent of internode growth, we conducted microscopic and transcriptomic analysis of four successive sub-apical vegetative internodes representing different stages of internode development of the bioenergy sorghum genotype R.07020.

Organism:

Sorghum bicolor

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21615

12 Samples

Download data: CSV

(Submitter supplied) Eighteen samples from the low, middle and high hybrid at three development stages were used for RNA sequencing.

Organism:

Zea mays

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15463

18 Samples

Download data: XLS

(Submitter supplied) The shoot apical meristem (SAM) contains undifferentiated stem cells that are responsible for the initiation of above-ground organs, and eventually the general architecture of the plant. To gain insight into the nature of genetic programs and the regulatory networks underlying SAM function in soybean, we have used Affymetrix soybean GeneChip® to investigate the transcript profiles associated with micro-dissected SAMs or axillary meristems (AMs). more...

Organism:

Glycine max

Type:

Expression profiling by array

Platform:

GPL4592

6 Samples

Download data: CEL, CHP