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Links from GEO DataSets

Items: 16

1.

Pleiotropic and Non-redundant Effects of an Auxin Importer in Setaria and Maize

(Submitter supplied) Directional transport of auxin is critical for inflorescence and floral development in flowering plants, but the role of auxin influx carriers (AUX1 proteins) has been largely overlooked. Taking advantage of available AUX1 mutants in Setaria viridis and maize, we uncover previously unreported aspects of plant development that are affected by auxin influx, including higher order branches in the inflorescence, stigma branch number, and glume (floral bract) development, and plant fertility. more...
Organism:
Setaria viridis
Type:
Expression profiling by high throughput sequencing
Platform:
GPL23621
22 Samples
Download data: TXT
Series
Accession:
GSE193344
ID:
200193344
2.

The SvFUL2 transcription factor is required for inflorescence determinacy and timely flowering in Setaria viridis

(Submitter supplied) Inflorescence architecture in cereal crops directly impacts yield potential through regulation of seed number and harvesting ability. Extensive architectural diversity found in inflorescences of grass species is due to spatial and temporal activity and determinacy of meristems, which control the number and arrangement of branches and flowers, and underlie plasticity. Timing of the floral transition is also intimately associated with inflorescence development and architecture. more...
Organism:
Setaria viridis
Type:
Expression profiling by high throughput sequencing; Other
Platforms:
GPL23621 GPL29001
26 Samples
Download data: RDATA, TXT, XLSX
Series
Accession:
GSE156047
ID:
200156047
3.

Brassinosteroids modulate meristem fate and differentiation of unique inflorescence morphology in Setaria viridis

(Submitter supplied) RNA-seq was performed to profile the transcriptomes of inflorescence primordia hand-dissected from the bristleless1-1 (bsl1-1)mutant in Setaria viridis compared to wild-type controls sampled under the same conditions. Bsl1 encodes a rate limiting enzyme in BR biosynthesis, which is the ortholog of D11 from rice. Mutants are characterized by a homeotic conversion of sterile bristles to spikelets in the inflorescence.
Organism:
Setaria viridis
Type:
Expression profiling by high throughput sequencing
Platform:
GPL23621
5 Samples
Download data: TXT
Series
Accession:
GSE100423
ID:
200100423
4.

Regulatory Modules Controlling Maize Inflorescence Architecture

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Zea mays
Type:
Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms:
GPL15463 GPL9361
40 Samples
Download data: TXT
Series
Accession:
GSE51050
ID:
200051050
5.

Sporisorium reilianum Infection Changes Inflorescence and Branching Architectures of Maize

(Submitter supplied) S. reilianum triggered loss of organ and meristem identity, and loss of meristem determinacy in male and female inflorescences and flowers. Microarray analysis showed that these developmental changes were accompanied with transcriptional regulation of genes proposed to regulate floral organ and meristem identity, and meristem determinacy in maize.
Organism:
Zea mays
Type:
Expression profiling by array
Platform:
GPL4032
6 Samples
Download data: CEL, CHP
Series
Accession:
GSE29747
ID:
200029747
6.

The dicerlike1 homologue, fuzzy tassel, is required for the regulation of meristem determinacy in the inflorescence and vegetative growth in maize

(Submitter supplied) We have characterized a maize mutant, fuzzy tassel (fzt) with striking inflorescence and pleiotropic defects. fzt contains a mutation in the maize dicer-like1 homolog, a key enzyme required for microRNA (miRNA) biogenesis. By profiling the small RNA population in fzt mutants, we investigated the impact of fzt mutation on miRNA abundance in seedling and tassel primordia. We also investigated the transcript abundance of potential target genes of miRNA that were impacted in fzt mutant by transcriptome profiling. more...
Organism:
Zea mays
Type:
Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing
Platform:
GPL15463
26 Samples
Download data: TXT
Series
Accession:
GSE52879
ID:
200052879
7.

The founder-cell transcriptome in the Arabidopsis apetala1 cauliflower inflorescence meristem

(Submitter supplied) Although the pattern of lateral organ formation from apical meristems establishes species-specific plant architecture, the positional information that confers cell fate to cells as they transit to the meristem flanks where they differentiate, remains largely unknown. We have combined fluorescence-activated cell sorting and RNA-seq to characterise the cell-type-specific transcriptome at the earliest developmental time-point of lateral organ formation using DORNRĂ–SCHEN-LIKE::GFP to mark founder-cell populations at the periphery of the inflorescence meristem (IM) in apetala1 cauliflower double mutants, which overproliferate IMs. more...
Organism:
Arabidopsis thaliana
Type:
Expression profiling by high throughput sequencing
Platform:
GPL11221
10 Samples
Download data: XLSX
Series
Accession:
GSE81401
ID:
200081401
8.

FASCIATED EAR4 encodes a bZIP transcription factor that controls shoot meristem size in maize

(Submitter supplied) fasciated ear4 (fea4) is a semi-dwarfed mutant with fasciated ears and tassels, and greatly enlarged vegetative and inflorescence meristems. Chromatin Immunoprecipitation-sequencing (ChIP-seq) and expression profiling by RNA-seq suggest that fea4 is required to regulate the auxin response and leaf differentiation programs in the periphery of the meristem, suggesting a new mechanism of meristem size regulation that is spatially and mechanistically distinct from the CLV-WUS model.
Organism:
Zea mays
Type:
Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms:
GPL15463 GPL19255
10 Samples
Download data: TXT
Series
Accession:
GSE61954
ID:
200061954
9.

Unraveling the KNOTTED1 regulatory network in maize meristems (ChIP-seq)

(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
Series
Accession:
GSE39161
ID:
200039161
10.

Unraveling the KNOTTED1 regulatory network in maize meristems

(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
Series
Accession:
GSE38487
ID:
200038487
11.

Comparison of infloresence transcriptome of bp er vs. bp er fil

(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
Series
Accession:
GSE86643
ID:
200086643
12.

Ground tissue circuitry regulates organ complexity in monocot roots [root meristem scRNA-seq]

(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:
GPL25410 GPL20156 GPL17628
9 Samples
Download data: CSV, TXT
Series
Accession:
GSE173087
ID:
200173087
13.

Ground tissue circuitry regulates organ complexity in monocot roots

(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
Series
Accession:
GSE172302
ID:
200172302
14.

Ground tissue circuitry regulates organ complexity in monocot roots [roottissues]

(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
Series
Accession:
GSE172280
ID:
200172280
15.

Ground tissue circuitry regulates organ complexity in monocot roots [slices]

(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
Series
Accession:
GSE172277
ID:
200172277
16.

Genetic Networks of Bract Suppression in Maize

(Submitter supplied) This project is to generate and analyze the transcriptomes of bract primordium of maize, and to identify the genes, pathways and networks that suppress bract outgrowth in maize inflorescence.
Organism:
Zea mays
Type:
Expression profiling by high throughput sequencing
Platform:
GPL17628
12 Samples
Download data: TXT
Series
Accession:
GSE179997
ID:
200179997

Supplemental Content

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