GEO DataSets

(Submitter supplied) The Arabidopsis thaliana ATH1 encodes a BEL1-like TALE homeodomain (BLH) transcription factor that controls the development of shoot organ boundaries. As part of a screen for genes that mediate the function of ATH1 in shoot development, we performed ChIP-seq to identify genome-wide ATH1 binding sites in developing seedlings.

Organism:

Arabidopsis thaliana

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL9062

6 Samples

Download data: NARROWPEAK, TXT

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

Organism:

Arabidopsis thaliana

Type:

Genome binding/occupancy profiling by high throughput sequencing; Methylation profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing; Expression profiling by high throughput sequencing

4 related Platforms

19 Samples

Download data: TXT, WIG

(Submitter supplied) 5-methyl cytosine in plant genomes occurs in all sequence contexts, especially in heterochromatin, transposons and other repeats. During replication, nascent cytosines in symmetric contexts (CG) are guided for methylation by hemi-methyl C on the parental DNA strands of both daughter chromatids. However nascent cytosines in the asymmetric CHH context or in symmetric CHG (where H=A, T or C) use modified histones and 24-nt small interfering RNAs to restore methylation to each daughter chromatid. more...

Organism:

Arabidopsis thaliana

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL9062

8 Samples

Download data: TXT

(Submitter supplied) Characterization of transparent testa mutants from large T-DNA collections

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL9062

18 Samples

Download data: TXT

(Submitter supplied) We investigated genome-wide variation in AS in Arabidopsis thaliana accessions Col and Ler using RNA-seq. We identified many cis-regulatory elements associated with AS events, among which polypyrimidine tracts (e.g., UCUCUC and CUCUCU) were significantly overrepresented, especially in the exons upstream of each AS event. We found that variation in cis-regulatory element sequences contributed to divergence in AS levels, but not to differential gene transcription between the two Arabidopsis accessions.

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL9062

4 Samples

Download data: TXT

(Submitter supplied) MSH1 depletion caused whole genome wide gene expression changes in Arabidopsis, to conduct comparative genomic analysis, here we generate gene expression profile for wild type and  msh1 memory line 

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL9062

6 Samples

Download data: TXT

(Submitter supplied) MSH1 depletion caused whole genome wide Methylome changes in Arabidopsis, to conduct comparative genomic analysis, here we generate methylome for  MSH1-RNAi line and transgene segregated out msh1 memory line 

Organism:

Arabidopsis thaliana

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL9062

6 Samples

Download data: COV

(Submitter supplied) To uncover the possible regulatory mechanism in regulatory alternative splicing in plants evolution, we used RNA-seq to compare the transcriptomes in Arabidopsis ecotypes Col and C24. We found different class of AS types have different regulatory mechanisms in Arabidopsis and divergence of alternative splicing in different class is varied in evolution. Sequence variation analysis had found evolution divergent AS events significantly altered their sequences compared to conserved events and the variation is AS class specific.

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL9062

12 Samples

Download data: TXT

(Submitter supplied) MicroRNAs (miRNAs) are 21-24 nucleotide (nt) small non-coding RNAs that regulate a wide variety of biological processes at the posttranscriptional level. MiRNA expression often exhibits spatial and temporal specificity. However, genome-wide miRNA expression patterns in different Arabidopsis organs during plant development have not yet been fully investigated. In this study, we sequenced 59 small RNA libraries generated from different tissue types at different developmental stages of Arabidopsis. more...

Organism:

Arabidopsis thaliana

Type:

Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL9062 GPL11221

59 Samples

Download data: TXT

(Submitter supplied) The goal of this study is to globally identify miRNA/siRNA cleavage sites on mRNAs in Arabidopsis wild type and ago1-27 mutant.

Organism:

Arabidopsis thaliana

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL9062

2 Samples

Download data: TXT

(Submitter supplied) The Arabidopsis thaliana REPRESSOR OF GA gene (RGA) encodes a DELLA protein that associates with multiple transcription factors to control plant growth in response to the hormone gibberellin (GA) (1). As part of a screen for genes that mediate the function of RGA in stem growth and shoot meristem function, we performed ChIP-seq to identify genome-wide loci associated with RGA in inflorescence apices. more...

Organism:

Arabidopsis thaliana

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL9062

6 Samples

Download data: NARROWPEAK, 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

Platforms:

GPL9062 GPL17639

11 Samples

Download data

(Submitter supplied) Analysis of H3.3 position and abundance in the presence and absence of a functionnal ATRX protein: we wanted to analyse how the absence of the Arabidopsis putative ATRX chaperone would impact the abundance and the distribution of H3.3 variant at a genome-wide level.

Organism:

Arabidopsis thaliana

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL9062

5 Samples

Download data: WIG, XLS

(Submitter supplied) Transcriptome comparison was used to determine the genes that are affected by the mutations in cae2-1, CA1-1 and the cae2-1 CA1-1 enhancer.

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL9062

8 Samples

Download data: XLSX

(Submitter supplied) Mechanism, inheritance patterns and biological significance remain unclear. Here, we generated genome-wide integrated maps of H3K27me3 modification and transcriptome for Col, C24 and their F1 hybrid, and their clf mutants. We found that H3K27me3 modification profiles were divergent between Col and C24, and were inherited mainly additively in hybrid. By comparing H3K27me3 modification ratio between parents to allelic H3K27me3 modification ratio in hybrid, we identified cis- and trans-regulatory divergence for H3K27me3 modification variation between Col and C24, and found that cis-regulatory divergence was the predominant contributor to H3K27me3 variation. more...

Organism:

Arabidopsis thaliana

Type:

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

Platform:

GPL9062

18 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; Non-coding RNA profiling by high throughput sequencing; Other

Platforms:

GPL17639 GPL9062

5 Samples

Download data: GFF

(Submitter supplied) We report the small RNA analysis of Arabidopsis plants deficient for the expression DDB2 involved in global genome repair using small RNA sequencing. In addition we performed RNA immunoprecipitation (RIP) of DDB2.

Organism:

Arabidopsis thaliana

Type:

Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL17639 GPL9062

3 Samples

Download data: GFF

(Submitter supplied) We report the methylome analysis of Arabidopsis plants deficient for the expression of 2 factors involved in global genome repair using whole genome bisulfite sequencing technology

Organism:

Arabidopsis thaliana

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL9062

2 Samples

Download data: GFF

(Submitter supplied) The goal of this study is to establish the global gene expression profiles of Arabidopsis wild type and ago1-27 mutant plants, and identify novel potential miRNA targets.

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL9062

2 Samples

Download data: TXT

(Submitter supplied) Hybrid plants and animals grow larger and more vigorously than the parents, a common phenomenon known as hybrid vigor or heterosis. Heterosis often correlates with the genetic distance between hybridizing parents, but the mechanism for this is largely unknown. We found that genetic distance was correlated with natural variation of stress responses under the control of the circadian clock. CIRCADIAN-CLOCK-ASSOCIATED1 (CCA1) and LATE-ELONGATED-HYPOCOTYL (LHY) or CCA1 alone mediate expression amplitudes and periods of these stress-responsive genes in stress and non-stress conditions. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL9062

12 Samples

Download data: TXT