GEO DataSets

(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:

GPL9302 GPL13396

6 Samples

Download data: FASTA, TXT

(Submitter supplied) The secondary structure of an RNA molecule plays an integral role in its maturation, regulation, processing, and functionality. However, the global influence of this feature on plant gene expression is still for the most part unclear. Here, we use a high-throughput, sequencing-based, structure-mapping approach in conjunction with transcriptome-wide sequencing of polyA+-selected (RNA-seq), small (smRNA-seq), and ribosome-bound (ribo-seq) RNA populations to investigate the impact of RNA secondary structure on gene expression regulation in Arabidopsis. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13222

2 Samples

Download data: BED, TXT

(Submitter supplied) MicroRNAs (miRNAs) and small-interfering RNAs (siRNAs) negatively regulate their targets by 1) repressing translation, 2) endonucleolytic RNA cleavage, or 3) DNA methylation resulting in transcriptional silencing. P-body/decapping components are likely required for translational repression, but are not known to function in other posttranscriptional regulatory pathways or to affect smRNA levels. Here, we show that the P-body/decapping protein DCP5 is required for miRNA-mediated translational repression but not cleavage, and to regulate the transcription of specific miRNAs. more...

Organism:

Arabidopsis thaliana

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL9302

2 Samples

Download data: FASTA, TXT

(Submitter supplied) MicroRNAs (miRNAs) and small-interfering RNAs (siRNAs) negatively regulate their targets by 1) repressing translation, 2) endonucleolytic RNA cleavage, or 3) DNA methylation resulting in transcriptional silencing. P-body/decapping components are likely required for translational repression, but are not known to function in other posttranscriptional regulatory pathways or to affect smRNA levels. Here, we show that the P-body/decapping protein DCP5 is required for miRNA-mediated translational repression but not cleavage, and to regulate the transcription of specific miRNAs. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13396

4 Samples

Download data: FASTA, TXT

(Submitter supplied) The functional structure of all biologically active molecules is dependent on intra- and inter-molecular interactions. This is especially evident for RNA molecules whose functionality, maturation, and regulation requires formation of correct secondary structure through encoded base-pairing interactions. Unfortunately, intra- and inter-molecular base-pairing information is lacking for most RNAs. Here, we use high-throughput sequencing to interrogate all base-paired RNA in Arabidopsis thaliana, and identify ~200 new small (sm)RNA-producing substrates of RNA-DEPENDENT RNA POLYMERASE 6. more...

Organism:

Arabidopsis thaliana

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL9302

5 Samples

Download data: FASTA, TXT

(Submitter supplied) Post-transcriptional regulation in eukaryotes requires cis- and trans-acting features and factors including RNA secondary structure, and RNA-binding proteins (RBPs). However, a comprehensive view of the structural and RBP interaction landscape of RNAs in the nucleus has yet to be compiled for any organism. Here, we use our ribonuclease-mediated structure and RBP binding site mapping approach on Arabidopsis seedling nuclei in vivo to globally profile these features within the nuclear compartment. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL13222

10 Samples

Download data: BED, TXT

(Submitter supplied) Nitrate and other nitrogen metabolites can act as signals that regulate global gene expression in plants. Adaptive changes in plant morphology and physiology triggered by changes in nitrate availability are partly explained by these changes in gene expression. Despite several genome-wide efforts to identify nitrate-regulated genes, no comprehensive study of the Arabidopsis root transcriptome under contrasting nitrate conditions has been carried out. more...

Organism:

Arabidopsis thaliana

Type:

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

Platform:

GPL9062

8 Samples

Download data: TXT

(Submitter supplied) The composition of the transcriptome is regulated by both mRNA synthesis and degradation. One route for mRNA decay is through 5’ decapping, which can be initiated by decapping enzymes and small RNAs. Although decapped RNAs are an important intermediate for mRNA decay, their identity and abundance have never been studied on a large scale. Here we present an experimental method for transcriptome-wide profiling of decapped mRNAs. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL5762

24 Samples

Download data: GPR

(Submitter supplied) We profiled Arabidopsis transcriptom using RNA-seq. Each RNA library yielded 223-250 million 101-bp single-end reads (235M on average). Using Tophat and Cufflinks, 30,199~30,650 assembled transcripts were identified in each of 4 samples. Of them, 1340 ones were derived from intergenic regions including 278 long intergenic ncRNAs (LincRNAs). Comparing with the 6,480 lincRNAs we identified by analysis of 200 tiling array data sets, 2,708 lincRNAs were also detected by RNA-seq.

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13222

4 Samples

Download data: TXT

(Submitter supplied) Long intergenic noncoding RNAs (lincRNAs) transcribed from intergenic regions play important roles in key biological processes.Analysis of published transcriptom datasets suggested some lincRNAs may be regulated by SERRATE,CBP20 and CBP80 in Arabidopsis. To further investigate the regulation, we use Arabidopsis lincRNA arrays v1 to detect lincRNA expression in se-2 and cbp20/80 double mutants.We found the expression levels of 940 lincRNAs (20%) out of the 4,634 lincRNAs with probes in array were significantly alerted in all mutants (P-value of eBays ANOVA < 0.05 & fold change of signal intensity > 2). more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL13750

9 Samples

Download data: TXT

(Submitter supplied) Long intergenic noncoding RNAs (lincRNA) transcribed from intergenic regions of eukaryotic genomes play important roles in key biological processes; yet, plant lincRNAs remain poorly characterized. Here we profiled lincRNA expression in inflorescences, leaves and roots using ATH lincRNA v1 array. we found 92% lincRNAs could be detected in at least 2 ATH lincRNA v1 arrays and majority of the lincRNAs were expressed at levels higher than those of pri-miRNAs but lower than those of mRNAs.Using a cut-off of 2-fold change, we identified 149 lincRNAs preferentially expressed in inflorescences, 232 in leaves and 164 in roots.

Organism:

Arabidopsis thaliana

Type:

Non-coding RNA profiling by array

Platform:

GPL13751

9 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) Small RNAs play important regulatory roles in most eukaryotes but only a small proportion of these molecules have been identified. We sequenced more than two million small RNAs from seedlings and the inflorescence of the model plant Arabidopsis thaliana. Known and new miRNAs were among the most abundant of the non-redundant set of more than 75,000 sequences, whereas more than half represented lower abundance small-interfering RNAs (siRNAs) that match repetitive sequences, intergenic regions, and genes. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by MPSS

Platform:

GPL2675

4 Samples

Download data

(Submitter supplied) m6A is a ubiquitous RNA modification in eukaryotes. Transcriptome-wide m6A patterns in Arabidopsis have been assayed recently. However, m6A differential patterns among organs have not been well characterized. The goal of the study is to comprehensively analyze m6A patterns of numerous types of RNAs, the relationship between transcript level and m6A methylation extent, and m6A differential patterns among organs in Arabidopsis.

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL13222

18 Samples

Download data: BEDGRAPH

(Submitter supplied) Post-transcriptional gene regulation plays a significant role in the response to Pi starvation. Here, we utilized advances in next-generation sequencing technology to examine changes in transcriptional control, RNA association with translating ribosomes in 14-day-old Arabidopsis seedlings subjected to 7 days of Pi starvation.

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL13222

7 Samples

Download data: TXT

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

Organism:

Medicago truncatula

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL11345

4 Samples

Download data: TXT

(Submitter supplied) Identification of microRNA targets in M. truncatula roots

Organism:

Medicago truncatula

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL11345

2 Samples

Download data: TXT

(Submitter supplied) Identification of microRNA expressed in M. truncatula roots

Organism:

Medicago truncatula

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL11345

2 Samples

Download data: TXT

(Submitter supplied) We report the application of ribosome profiling method to map ribosome locations on transcripts in de-etiolating Arabidopsis seedlings

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13222

8 Samples

Download data: TXT

(Submitter supplied) The functions of miRNAs and their target mRNAs in Arabidopsis development have been widely documented, however, roles of stress responsive miRNAs and their targets are not as well understood. Using small RNA deep sequencing and ATH1 microarrays to profile mRNAs, we identified IAR3 (IAA-Ala Resistant 3) as a novel target of miR167a.

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL198

18 Samples

Download data: CEL