GEO DataSets

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

Organism:

Arabidopsis thaliana; Arabidopsis lyrata

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL13222 GPL19447 GPL20223

12 Samples

Download data: CSV

(Submitter supplied) Plant development is controlled by transcription factors (TFs) which form complex gene-regulatory networks. Genome-wide TF DNA-binding studies revealed that these TFs have several thousands of binding sites in the Arabidopsis genome, and may regulate the expression of many genes directly. Given the importance of natural variation in plant developmental programs, there is a need to understand the molecular basis of this variation at the level of developmental gene regulation. more...

Organism:

Arabidopsis thaliana; Arabidopsis lyrata

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL20223 GPL19447

3 Samples

Download data: CSV

(Submitter supplied) Plant development is controlled by transcription factors (TFs) which form complex gene-regulatory networks. Genome-wide TF DNA-binding studies revealed that these TFs have several thousands of binding sites in the Arabidopsis genome, and may regulate the expression of many genes directly. Given the importance of natural variation in plant developmental programs, there is a need to understand the molecular basis of this variation at the level of developmental gene regulation. more...

Organism:

Arabidopsis lyrata; Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL13222 GPL19447

9 Samples

Download data: CSV

(Submitter supplied) These analyses allowed the identification of more than 2000 genes regulated by the MADS TF, SEPALLATA3 (SEP3). Although the involvement of SEP3 in all flower organ development is well established, the single sep3 mutant shows no flower phenotype, due to redundancy with other SEPALLATA genes. The triple mutant, sep1sep2sep3, shows no floral organ development except sepals, while the sep1sep2 mutant showed characteristic WT flower with, from the outer to the inner whorl of the flower, 4 sepals, 4 petals, 6 stamens and one gynoecium. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21785

6 Samples

Download data: TXT

(Submitter supplied) In this study, we compare the DNA binding specifify and affinity of SEPALLATA3 and AGAMOUS complexes The MADS transcription factors, SEPALLATA3 (SEP3) and AGAMOUS (AG), are required for floral organ identity and determinacy of the floral meristem in Arabidopsis. Dimerization is obligatory for their DNA binding, however SEP3 and SEP3-AG also form tetrameric complexes. The goal of this study is to understand how homo and hetero-dimerization and tetramerization of MADS TFs affect genome-wide DNA-binding patterns. more...

Organism:

Arabidopsis thaliana

Type:

Other

Platform:

GPL17970

10 Samples

Download data: BEDGRAPH, NARROWPEAK

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

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platforms:

GPL9989 GPL9982

60 Samples

Download data: GPR, TXT

(Submitter supplied) This experiment describes gene expression after the activation of APETALA1-GR, to study and identify AP1 target genes. We used a 35S:AP1-GR ap1 cal line to induce a synchronized response activating the AP1-GR fusion protein in ap1 cal inflorescence-like meristems through dexamethasone treatment. Tissue samples were collected immediately after the treatment, as well as subsequent timepoints. The expression profiles of the individual samples were then analyzed by gene expression profiling using whole-genome oligonucleotide arrays (non-commercial; Meyerowitz Lab Arabidopsis Operon Array v4). more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL9989

20 Samples

Download data: GPR, TXT

(Submitter supplied) This experiment describes gene expression after the activation of APETALA1-GR, to study and identify AP1 target genes. We used a 35S:AP1-GR ap1 cal line to induce a synchronized response activating the AP1-GR fusion protein in ap1 cal inflorescence-like meristems through dexamethasone treatment. Tissue samples were collected immediately after the treatment, as well as subsequent timepoints. The expression profiles of the individual samples were then analyzed by gene expression profiling using whole-genome oligonucleotide arrays (non-commercial; Meyerowitz Lab Arabidopsis Operon Array v4). more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL9989

20 Samples

Download data: GPR, TXT

(Submitter supplied) The MADS-domain transcription factor APETALA1 (AP1) is a key regulator of Arabidopsis flower development. To understand the molecular mechanisms underlying AP1 function, we identified its target genes during floral initiation using a combination of gene expression profiling and genome-wide binding studies. Many of its targets encode transcriptional regulators, including known floral repressors. The latter genes are down-regulated by AP1, suggesting that it initiates floral development by abrogating the inhibitory effects of these genes. more...

Organism:

Arabidopsis thaliana

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL9062

4 Samples

Download data: SOA

(Submitter supplied) This experiment describes gene expression after the activation of APETALA1-GR, to study and identify AP1 target genes. We used a 35S:AP1-GR ap1 cal line to induce a synchronized response activating the AP1-GR fusion protein in ap1 cal inflorescence-like meristems through dexamethasone or dexamethasone+cycloheximide treatment. Tissue samples were collected at 3hrs after the treatment. The expression profiles of the individual samples were then analyzed by gene expression profiling using whole-genome oligonucleotide arrays (Agilent, custom-commercial).

Organism:

Arabidopsis thaliana

Type:

Genome variation profiling by SNP array

Platform:

GPL9984

16 Samples

Download data: TXT

(Submitter supplied) This experiment describes gene expression after the activation of APETALA1-GR, to study and identify AP1 target genes. We used a 35S:AP1-GR ap1 cal line to induce a synchronized response activating the AP1-GR fusion protein in ap1 cal inflorescence-like meristems through dexamethasone treatment. Tissue samples were collected immediately after the treatment, as well as subsequent timepoints. The expression profiles of the individual samples were then analyzed by gene expression profiling using whole-genome oligonucleotide arrays (Agilent, custom-commercial). more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL9982

20 Samples

Download data: TXT

(Submitter supplied) Comparion of gene expression profiles of wild-type and apetala1 inflorescences The gene expression profile of inflorescences of the floral homeotic mutant apetala1 was compared to wild-type inflorescences (Ler) using a whole-genome oligonucleotide array (Agilent, custom-commercial). Experiment was performed in triplicate.

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL9982

3 Samples

Download data: TXT

(Submitter supplied) The floral transition in Arabidopsis is tightly controlled by complex genetic regulatory networks in response to endogenous and environmental flowering signals. SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1 (SOC1) and SHORT VEGETATIVE PHASE (SVP), two key MADS-domain transcription factors, perceive these signals and function as antagonistic flowering regulators. To understand how they mediate the floral transition, we mapped in vivo binding sites of SOC1 and SVP using chromatin immunoprecipitation followed by hybridization to whole-genome tiling arrays (ChIP-chip). more...

Organism:

Arabidopsis thaliana

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL10977

12 Samples

Download data: BAR, BPMAP, CEL

(Submitter supplied) In this study, we applied sequential DNA affinity purification sequencing (seq-DAP-seq) to identiy genome-wide binding of a heterocomplex formed by two transcription factors of the MADS familly SEP3 and AG(AP1-I) (AG with its I domain switched with that of AP1). We compared the genome wide binding of SEP3-AG(AP1-I) to that of our previously published SEP3-AG data

Organism:

Arabidopsis thaliana

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL17970

3 Samples

Download data: BED, BEDGRAPH

(Submitter supplied) Multicellular organisms develop new structures by initiating specific gene regulatory programs through coordinated changes at the transcriptional and chromatin levels. Master transcription factors orchestrate such global changes but the underlying molecular mechanisms remain unclear. Here we focus on LEAFY (LFY), a key regulator of flower development in angiosperms. The resolution of the crystallographic structure of its N-terminal domain shows that it forms an unanticipated Sterile Alpha Motif (SAM) domain. more...

Organism:

Arabidopsis thaliana

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL9302

6 Samples

Download data: BED

(Submitter supplied) Floral organ identities in plants are specified by the combinatorial action of homeotic master regulatory transcription factors (TFs). How these factors achieve their regulatory specificities is however still largely unclear. Genome-wide in vivo DNA binding data show that homeotic MADS-domain proteins recognize partly distinct genomic regions, suggesting that DNA binding specificity contributes to functional differences of homeotic protein complexes. more...

Organism:

synthetic construct

Type:

Other

Platforms:

GPL9423 GPL15228

28 Samples

Download data: CSV

(Submitter supplied) The transition to flowering in plants is controlled by a regulatory network that responds to both developmental and environmental signals. The MADS-box genes FLOWERING LOCUS C (FLC) and SHORT VEGETATIVE PHASE (SVP) are major flowering repressors that enhance responses to environmental cues such as winter temperatures, high ambient temperatures and photoperiod. FLC and SVP physically interact in vivo and mutation of each gene causes early flowering while the double mutant is more extreme. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL18660

48 Samples

Download data: CEL

(Submitter supplied) The MADS-box transcription factors FLOWERING LOCUS C (FLC) and SHORT VEGETATIVE PHASE (SVP) are major transcriptional repressors controlling flowering time. They enhance responses to environmental cues such as winter temperatures, high ambient temperatures and photoperiod, acting at least in part by blocking transcription of the floral pathway integrators. As other MADS-box transcription factors, FLC and SVP can interact in vivo forming multimeric complexes. more...

Organism:

Arabidopsis thaliana

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL17639

18 Samples

Download data: CSV

(Submitter supplied) Background The homeodomain leucine zipper (HD-Zip) transcription factor family is one of the largest plant specific superfamilies, and includes genes with roles in modulation of plant growth and response to environmental stresses. Many HD-Zip genes are characterized in Arabidopsis (Arabidopsis thaliana), and members of the family are being investigated for abiotic stress responses in rice (Oryza sativa), maize (Zea mays), poplar (Populus trichocarpa) and cucumber (Cucmis sativus). more...

Organism:

Glycine max

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15008

21 Samples

Download data: TXT