GEO DataSets

(Submitter supplied) RNA-Seq from picln-1 mutant, prmt5-5 mutant and wt grown at 22°C for 9 days in a 12h light 12h dark photoperiod

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL9302

12 Samples

Download data: XLSX

(Submitter supplied) Iron (Fe) is an essential micronutrient whose uptake is tightly regulated to balance both deficiency and Fe excess induced oxidative stress. The non-essential heavy metal cadmium (Cd) both induces oxidative stress and an Fe deficiency like response. It is unclear how Cd induces this response, nor how it relates to Fe status sensing. Using next generation sequencing, H2O2 quantification in both wild type and the Fe over-accumulating mutant opt3-2, we explored how Cd interferes with Fe sensing. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL9302

36 Samples

Download data: TXT

(Submitter supplied) This experiment permit to obtain new regulatory genes downstream of STK-CES, CES-BEE1-BEE3 protein complexes, involved in various aspects of transmitting tract development

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL9302

6 Samples

Download data: CSV

(Submitter supplied) To explore the PRC2-associated RNA in Arabidopsis on a genome-wide scale, we designed a high-throughput sequencing followed by PRC2 RNA-IP. We used the transgenic plants to purify the Myc-tagged CLF protein, the homologs of EZH2 (the methyltransferase of PRC2 complex) in mammal.

Organism:

Arabidopsis thaliana

Type:

Other

Platform:

GPL9302

4 Samples

Download data: TXT

(Submitter supplied) XCT was originally identified due to the short circadian period observed in plants mutant for this gene. Proteins with homology to XCT are found across eukaryotes, but their molecular function is unknown. We have recently demonstrated that in Schizosaccharomyces pombe, the XCT ortholog Xap5 is a chromatin-associated protein that acts in a similar manner as the histone variant H2A.Z to suppress aberrant gene expression. more...

Organism:

Arabidopsis thaliana

Type:

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

Platforms:

GPL9302 GPL13222

18 Samples

Download data: GFF, TSV

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

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL9302

72 Samples

Download data

(Submitter supplied) Alternative polyadenylation (APA) has recently been recognized as a universal mechanism for gene regulation, but it remains unclear how APA is controlled. Here we report that the Arabidopsis thaliana Protein Arginine Methyltransferase 10 (AtPRMT10) regulates global APA with its protein partner HLP1, a conserved hnRNP A/B protein. HLP1 binds preferentially to A-rich and U-rich cis-elements around polyadenylation sites, thereby linking AtPRMT10 to the control of APA through protein-protein interactions. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL13222 GPL9302

11 Samples

Download data: BED, WIG

(Submitter supplied) In Arabidopsis seed development involves maternal small interfering RNAs (siRNAs) that induce RNA-directed DNA methylation (RdDM) through the NRPD1 pathway. To investigate their biological functions we characterized siRNAs in the endosperm and seed coat that were separated by laser capture microdissection (LCM) in reciprocal genetic crosses with an nrpd1 mutant. We also monitored the spatio-temporal activity of the NRPD1 pathway on seed development using AGO4:GFP::AGO4 (promoter:GFP::protein) reporter and promoter:GUS sensors of siRNA-mediated silencing. more...

Organism:

Arabidopsis thaliana

Type:

Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL9302 GPL13222 GPL21785

18 Samples

Download data: BEDGRAPH, TXT

(Submitter supplied) The plant circadian clock enables plants to adjust their physiology and modulate their developmental responses in anticipation of diurnal and seasonal changes in environmental conditions. Thus, it makes an important contribution to overall fitness. The complex regulatory network underlying the oscillatory mechanism of the clock is now well characterized, but we still know relatively little about how downstream processes are controlled. more...

Organism:

Arabidopsis thaliana

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL9302

2 Samples

Download data: XLSX

(Submitter supplied) Illumina 100bp single end sequencing was used to profile the transcriptomes of wild type (Columbia) and opt3-2 mutant Arabdiopsis leaves and roots under hydroponic conditions ( 4 weeks old, bolting stage). Sequencing resulted in 381 million uniquely mapping reads accross 36 libraries. Each sample was barcoded and divided into three sequencing lanes, while each genotype/tissue combination is represented by 3 biological replicates consisting of 3-4 individual plants (2 genotypes x 2 tissues x 3 biological replicates x 3 technical replicates = 36 libraries). more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL9302

36 Samples

Download data: TXT

(Submitter supplied) DAWDLE (DDL) is a conserved forkhead-associated (FHA) domain-containing protein that plays essential roles in development and immunity. It was found to act in the biogenesis of microRNAs (miRNAs) and endogenous small interfering RNAs (siRNAs), which regulate gene expression at transcriptional and/or post-transcriptional levels. However, its global effect on miRNA accumulation still is not known. To determine the global effect of DDL on the accumulation of miRNAs and siRNAs, we compared the small RNA profile in ddl-1 with that in WS (Wild-type, WT). more...

Organism:

Arabidopsis thaliana

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL9302

4 Samples

Download data: TXT

(Submitter supplied) CDC5 is a conserved DNA-binding protein that is required for development and immunity. It promotes the accumulation of microRNAs (miRNAs) and endogenous small interfering RNAs (siRNAs), which repress gene expression. In this project, we aim to determine its global effect of on the accumulation of miRNAs and siRNAs. We compared the small RNA profile in cdc5-1 with that in Col (Wild-type, WT). Small RNA libraries prepared from inflorescences of cdc5-1 and Col was subjected to Illumina deep sequencing analyses. more...

Organism:

Arabidopsis thaliana

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL9302

4 Samples

Download data: TXT

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

Organism:

Arabidopsis thaliana

Type:

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

Platforms:

GPL14926 GPL9302

12 Samples

Download data: CEL

(Submitter supplied) To learn more about the role of FRUITFULL (FUL), in pistil/silique development, we performed a ChIP-seq experiment to identify direct targets of FUL in the pistil/silique.

Organism:

Arabidopsis thaliana

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL9302

4 Samples

Download data: CSV

(Submitter supplied) Arabidopsis thaliana Col-0 as a wild type and camta1/2/3/sid2-1 as a mutant were compared in their gene expression at the end of day. By comparing the transcriptomes, we showed the presence of SA-independent and CAMTA-dependent pathway at ambient temperature.

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL9302

6 Samples

Download data: CSV

(Submitter supplied) RNAseq transcriptome of leaves and roots of Arabidopsis thaliana Columbia-0 grown under control (ES media) and Fe-deficiency (-Fe +100 µM FRZ) conditions.

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL9302

12 Samples

Download data: TXT

(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) LHY and CCA1 encode single MYB transcription factors, involved in circadian clock. However, direct target genes of LHY and CCA1 in a genomic scale were largely unknown. To reveal bound genes by CCA1, chimeric protein CCA1-FLAG was expressed under CCA1 promoter in cca1 lhy (CCA1pro:CCA1-FLAG/ cca1 lhy). ChIP was performed using anti-FLAG antibody (F3165; SIGMA), which was bound to Dynabeads Protein G (100-03D; Life Technologies), and ChIP DNA were analyzed by IonPGM or Illumina GAII.

Organism:

Arabidopsis thaliana

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL9302 GPL19056

2 Samples

Download data: BED

(Submitter supplied) We were interested in changes in small RNA abundance changes in response to developmental transitions in Arabidopsis thaliana shoots, with special focus on vegetative phase change. We specifically wanted to separate the temporal changes in gene expression that result from vegetative phase change and those from flowering. Because of the close timing between the juvenile-to-adult and adult-to-reproductive developmental transitions in Arabidopsis grown under long day conditions, we used the late-flowering genotype FRI;FLC developed by the lab of Richard Amasino by introgressing the FRI allele from Sf-2 into the Col-0 genetic background, which is fri;FLC. more...

Organism:

Arabidopsis thaliana

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL9302

28 Samples

Download data: TXT

(Submitter supplied) The two Arabidopsis ecotypes that are adapted to Italy and Sweden, respectively, showed different degree of freezing tolerance. By comparing the low temperature transcriptomes of the IT and SW ecotypes, we showed CBF pathway plays a significant role in natural variation of freezing tolerance.

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL9302

18 Samples

Download data: CSV