GEO DataSets

(Submitter supplied) Throughout evolution, the duplication and functional divergence of transcription factors (TFs) has driven cellular and organismal complexity. Mechanisms by which paralogous TFs functionally diverge are thus of broad interest yet remain poorly understood. One well-established mechanism underlying TF divergence is the occupation and regulation of distinct sets of genes. Here we test for new mechanisms using CORONA (CNA) and PHABULOSA (PHB), two representative members of the CLASS III HOMEODOMAIN LEUCINE ZIPPER (HD-ZIPIII) family of plant TFs. more...

Organism:

Arabidopsis thaliana

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24270

31 Samples

Download data: BIGWIG

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

Organism:

Arabidopsis thaliana

Type:

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

Platforms:

GPL30821 GPL24270

79 Samples

Download data: BIGWIG, TAB

(Submitter supplied) This study aimed to identify changes in Arabidopsis thaliana microRNAs during the early stages of infection by the fungal pathogen Fusarium graminearum. This study is relevant to Agriculture, as F. graminearum is a major pathogen of cereal crops; microRNAs provide a rapid and early response by the plant to trigger changes in expression of genes involved in limiting the infection and immunity.

Organism:

Arabidopsis thaliana

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL24270

20 Samples

Download data: TXT

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

Organism:

Arabidopsis thaliana

Type:

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

Platform:

GPL24270

7 Samples

Download data: TXT

(Submitter supplied) Unlike plants in the field, which experience significant temporal fluctuations in environmental conditions, plants in the laboratory are typically grown in controlled, stable environments. Therefore, signaling pathways evolved for survival in continuously fluctuating environments often remain functionally latent in laboratory settings. Here, we show that TGA1 and TGA4 act as hub transcription factors through which the expression of genes involved in high-affinity nitrate uptake are regulated in response to shoot-derived phloem mobile polypeptides, CEP DOWNSTREAM 1 (CEPD1), CEPD2 and CEPD-like 2 (CEPDL2) as nitrogen (N) deficiency signals, and Glutaredoxin S1 (GrxS1) to GrxS8 as N sufficiency signals. more...

Organism:

Arabidopsis thaliana

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24270

2 Samples

Download data: BED

(Submitter supplied) Unlike plants in the field, which experience significant temporal fluctuations in environmental conditions, plants in the laboratory are typically grown in controlled, stable environments. Therefore, signaling pathways evolved for survival in continuously fluctuating environments often remain functionally latent in laboratory settings. Here, we show that TGA1 and TGA4 act as hub transcription factors through which the expression of genes involved in high-affinity nitrate uptake are regulated in response to shoot-derived phloem mobile polypeptides, CEP DOWNSTREAM 1 (CEPD1), CEPD2 and CEPD-like 2 (CEPDL2) as nitrogen (N) deficiency signals, and Glutaredoxin S1 (GrxS1) to GrxS8 as N sufficiency signals. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24270

5 Samples

Download data: DIFF, TXT

(Submitter supplied) Strigolactone (SL) signalling plays many roles in plants, however, the downstream responsive genes remain unclear. SUPPRESSOR OF MORE AXILLARY GROWTH2-LIKE 7 (SMXL7) is degraded upon SL signalling. Here, we generated Arabidopsis carrying a transgene SMXL7pro:SMXL7d53-GR, where a SL-insensitive version of SMXL7 is tagged with the ligand binding domain of the glucocorticoid receptor (GR). SMXL7d53-GR will be translocated to the nucleus upon dexamethasone (dex), and we profiled the gene expression in mock or dex treated plants and revealed the downstream responsive genes of SL signalling.

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24270

8 Samples

Download data: CSV

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

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL30821 GPL24270

36 Samples

Download data: GTF, TSV

(Submitter supplied) In Arabidopsis thaliana, ARGONAUTE1 (AGO1) plays a central role in microRNA (miRNA) and small interfering RNA (siRNA)-mediated silencing. Nuclear AGO1 is loaded with miRNAs and exported to the cytosol where it associates to the rough ER to conduct miRNA-mediated translational repression, mRNA cleavage and biogenesis of phased siRNAs. These latter, as well as other cytosolic siRNAs, are loaded into cytosolic AGO1, but in which compartment this happens is not known. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24270

9 Samples

Download data: TSV

(Submitter supplied) In Arabidopsis thaliana, ARGONAUTE1 (AGO1) plays a central role in microRNA (miRNA) and small interfering RNA (siRNA)-mediated silencing. Nuclear AGO1 is loaded with miRNAs and exported to the cytosol where it associates to the rough ER to conduct miRNA-mediated translational repression, mRNA cleavage and biogenesis of phased siRNAs. These latter, as well as other cytosolic siRNAs, are loaded into cytosolic AGO1, but in which compartment this happens is not known. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24270

9 Samples

Download data: CSV, GTF

(Submitter supplied) Despite the importance of Nitric oxide (NO) in both plant and animal development, the regulatory and mechanism of NO function remain elusive. Here, we show that NO promotes Arabidopsis shoot stem cell differentiation via the RNA directed DNA Methylation (RdDM) pathway. Knocking out of the components of the RdDM pathway causes meristematic defects, and at least in part could block the stem cell and niche-specific genes responding to the NO signaling. more...

Organism:

Arabidopsis thaliana

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24270

6 Samples

Download data: BW

(Submitter supplied) Despite the importance of Nitric oxide (NO) in both plant and animal development, the regulatory and mechanism of NO function remain elusive. To test if response to NO in the ap1/cal mutant is comparable to the Col-o wild type, we then analysed the genome wide transcriptome profiling of NO responsive genes both in the wild type and ap1/cal seedling using RNA-seq. We observed that about 88% of differential expressed genes in wild type were overlapped with ap1/cal mutant.

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24270

12 Samples

Download data: CSV

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

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing; Methylation profiling by high throughput sequencing

Platforms:

GPL13222 GPL24270

16 Samples

Download data: BW, TXT

(Submitter supplied) Polycomb Repressive Complexes (PRCs) control gene expression through the incorporation of H2Aub and H3K27me3. In recent years, there is increasing evidence of the complexity of PRCs’ interaction networks and the interplay of these interactors with PRCs in epigenome reshaping, which is fundamental to understand gene regulatory mechanisms. Here, we identified UBIQUITIN SPECIFIC PROTEASE 5 (UBP5) as a chromatin player able to counteract the deposition of the two PRCs epigenetic hallmarks in Arabidopsis thaliana. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24270

8 Samples

Download data: TXT

(Submitter supplied) Seeds in the experimental group were exposed to 48 h of traffic noise recorded in a highly congested area of the city, while the control group was kept under background white noise. While traffic noise exposure made no effects on seed germination, noise treatment significantly increased the growth of seedlings by 39%. By employing RNA-sequencing profiling, we further investigated the noise-induced molecular changes in the A. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24270

6 Samples

Download data: TXT

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

Organism:

Arabidopsis thaliana

Type:

Methylation profiling by high throughput sequencing; Other; Expression profiling by high throughput sequencing

Platforms:

GPL21785 GPL24270 GPL26208

361 Samples

Download data

(Submitter supplied) In sexually propagating organisms, genetic and epigenetic mutations are evolutionarily relevant only if they occur in the germline and provide inherited information to the next generation. In contrast to most animals, plants are thought to lack an early segregating germline, implying that somatic cells can contribute genetic information to the progeny if they differentiate into meiocytes. Here we demonstrate that two ARGONAUTE proteins, AGO5 and AGO9, are expressed in the reproductive lineage throughout development and mark an early-segregating germline. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24270

210 Samples

Download data: CSV

(Submitter supplied) In sexually propagating organisms, genetic and epigenetic mutations are evolutionarily relevant only if they occur in the germline and provide inherited information to the next generation. In contrast to most animals, plants are thought to lack an early segregating germline, implying that somatic cells can contribute genetic information to the progeny if they differentiate into meiocytes. Here we demonstrate that two ARGONAUTE proteins, AGO5 and AGO9, are expressed in the reproductive lineage throughout development and mark an early-segregating germline. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL24270 GPL26208

67 Samples

Download data: CSV

(Submitter supplied) In sexually propagating organisms, genetic and epigenetic mutations are evolutionarily relevant only if they occur in the germline and provide inherited information to the next generation. In contrast to most animals, plants are thought to lack an early segregating germline, implying that somatic cells can contribute genetic information to the progeny if they differentiate into meiocytes. Here we demonstrate that two ARGONAUTE proteins, AGO5 and AGO9, are expressed in the reproductive lineage throughout development and mark an early-segregating germline. more...

Organism:

Arabidopsis thaliana

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL24270

24 Samples

Download data: CSV

(Submitter supplied) The goals of this study are to compare the gene expression in Wild-type (Col-0) and msil2/4 double mutant inflorescence stems.

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24270

4 Samples

Download data: XLSX