GEO DataSets

(Submitter supplied) Nuclear-localized RNA binding proteins are involved in various aspects of RNA metabolism, which in turn modulates gene expression. However, the functions of nuclear-localized RNA binding proteins in plants are poorly understood. Here we report the functions of two proteins containing RNA recognition motifs, At RZ-1B and At RZ-1C, in Arabidopsis. At RZ-1B and At RZ-1C were localized to nuclear speckles and interacted with a spectrum of serine/arginine-rich (SR) proteins through their C-termini. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL9302

4 Samples

Download data: BW

(Submitter supplied) This study examines how histone modification confers salt stress in Arabidopsis. The floral initiator SKB1 is found to mediate the plant’s response to salt stress by altering the methylation status of histone H4R3 and of the small nuclear ribonucleoprotein (snRNP) LSM4, and thereby affecting the expression of stress-responsive genes.

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL11375

6 Samples

Download data

(Submitter supplied) Analysis of atsf1-2 mutant seedlings for pre-mRNA splicing defect. The atsf1-2 mutant is a homozygous T-DNA insertion line isolated from a SALK line, SALK_062177. Results identify transcripts with altered alternative splicing pattern in the atsf1-2 mutant. We used microarrays to examine the transcriptome profile in the atsf1-2 mutant and identified genes of which transcript levels were changed significantly.

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL198

6 Samples

Download data: CEL, CHP

(Submitter supplied) In this study, we analyzed the Arabidopsis homologue of PRMT5, AtPRMT5’s function in RNA processing. RNA-seq analyses revealed that AtPRMT5 is involved in a subset of pre-mRNA splicing. Several RNA processing factors involved in regulating flowering time were validated that the corresponding intron retention surely exists in atprmt5 mutants. AtSm proteins can also be methylated by AtPRMT5 in vitro and in vivo, which may be the reasons for the pre-mRNA splicing defects in atprmt5. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL10272

2 Samples

Download data: BEDGRAPH

(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) Introduction: The Plant Organelle RNA Recognition (PORR) domain proteins are nucleus-encoded RNA-binding proteins that have acquired specific roles in organelle RNA metabolism as splicing factors of chloroplast group II introns. LEFKOTHEA (At5g62990) is a nuclear gene encoding a PORR domain protein that carries a transit peptide (TP) and monopartite or bipartite nuclear localization signals (NLS). These motifs result in dual-targeting of LEFKOTHEA to the nucleus and chloroplasts implying a role in the splicing of chloroplast group II introns and nuclear pre-mRNA introns. more...

Organism:

Arabidopsis thaliana

Type:

Other

Platform:

GPL17639

2 Samples

Download data: XLSX

(Submitter supplied) Introduction: The Plant Organelle RNA Recognition (PORR) domain proteins are nucleus-encoded RNA-binding proteins that have acquired specific roles in organelle RNA metabolism as splicing factors of chloroplast group II introns. LEFKOTHEA (At5g62990) is a nuclear gene encoding a PORR domain protein that carries a transit peptide (TP) and monopartite or bipartite nuclear localization signals (NLS). These motifs result in dual-targeting of LEFKOTHEA to the nucleus and chloroplasts implying a role in the splicing of chloroplast group II introns and nuclear pre-mRNA introns. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13222

2 Samples

Download data: XLSX

(Submitter supplied) The early flowering Arabidopsis cäö mutant is defective in the BRR2a helicase involved in splicing. In order to get some explanation about the phenotype, we compared the expression profiles of wt and mutant with RNA-seq. In addtion, the same RNA-seq data was used to measure the extent of intron retention in the cäö mutant

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17311

6 Samples

Download data: TSV

(Submitter supplied) We characterized the biological and molecular functions of AtC3H17, a unique Arabidopsis gene encoding a non-tandem CCCH zinc finger protein, in plant development. To investigate the downstream regulatory mechanisms of AtC3H17, whole genome microarray expression profiling was carried out. The experiment was designed to identify differentially expressed genes between WT and AtC3H17-overexpressing transgenic plants (AtC3H17 OXs) grown for 14 days under SD growth conditions. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL9020

4 Samples

Download data: TXT

(Submitter supplied) We performed a tranascriptomic analysis of Ler, ebs and shl-2 plants in order to reveal targets whose transcription is regulated by EBS and SHL.

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL198

9 Samples

Download data: CEL

(Submitter supplied) RNA sequencing was used to identify alternative splicing events and differentially expressed genes (DEG) in 35S:HIN1 stable transgenic line compared to Col-0 wild type. Two treatments were analyzed for each genotype: unstressed control and a 96 hours moderate severity low water potential (-0.7 MPa) treatment. RNA sequencing analysis found that overexpression of HIN1 in unstressed plants was sufficient to duplicate the effects of stress on nearly 40% of the genes where intron retention was normally suppressed by stress in wild type. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17639

12 Samples

Download data: CSV, TXT

(Submitter supplied) Serine phosphorylation of conserved Y1S2P3T4S5P6S7 repeats of RNA polymerase II carboxy-terminal domain (RNAPII CTD) plays a central role in the regulation of transcription and co-transcriptional RNA processing. Maintenance of CTD phosphoserine-7 mark in Arabidopsis requires the CDKF;1 kinase, which mediates in vivo activation of downstream-acting CDKD CTD kinase family. Knockout mutations of CDKF;1 lead to over 50% reduction of RNAPII CTD Ser-7 phosphorylation as early as 7 days after germination in seedlings. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL198

6 Samples

Download data: CEL, CHP

(Submitter supplied) The 70-mer oligo was designed from the 3'-end of 26,090 annotated genes. Every 70-mer oligo is spotted once on each slide. Protocol: This oligonucleotide array is produced from the Operon Version 1.0 Array-Ready Oligo set (AROS). The 70-mer oligo was designed from the 3'-end of 26,090 annotated genes. Every 70-mer oligo is spotted once on each slide.

Organism:

Arabidopsis thaliana

3 Series

18 Samples

Download data

(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:

GPL23157 GPL24025

8 Samples

Download data: BW

(Submitter supplied) Ambient temperature dependent flowering time is an important feature that is required for plants to reproduce in various environmental conditions. The rising global temperature poses a significant challenge to the growth and reproduction of plants. In Arabidopsis thaliana, FLM-β, a major splicing isoform of the flowering repressor gene FLOWERING LOCUS M, is down-regulated in response to increasing temperature and represents a critical mechanism for plants to respond to temperature changes. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24025

4 Samples

Download data: TXT

(Submitter supplied) Ambient temperature dependent flowering time is an important feature that is required for plants to reproduce in various environmental conditions. The rising global temperature poses a significant challenge to the growth and reproduction of plants. In Arabidopsis thaliana, FLM-β, a major splicing isoform of the flowering repressor gene FLOWERING LOCUS M, is down-regulated in response to increasing temperature and represents a critical mechanism for plants to respond to temperature changes. more...

Organism:

Arabidopsis thaliana

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL23157

4 Samples

Download data: BW

(Submitter supplied) We report the application of illumina high throughput RNA sequencing for rrc1-3 mutants in both light and dark conditions(three replicates under each condition) in Arabidopsis. By obtaining over 100 million reads (150bp paired_end) for each rRNA depleted lib, we compared the transcriptome profile between rrc1-3 mutant and Col-0 wild type light and dark conditions. We find that genome wide spliciing activities are general defective in rrc1-3 mutant comparing to Col-0 wild type, which indicates the importance of post-transcriptional processing on gene expression regulation. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL21785 GPL21179

12 Samples

Download data: XLSX

(Submitter supplied) Comparison of plants that overexpress PK12 and non-transformed plants. Plants were grown for 10 days under long day conditions (GSM3816-GSM3819) or plants were grown for 21 days under long day conditions (GSM3820-GSM3823) . Hybridization was performed on arrays from Arabidopsis Keck Resource Lab Array (Yale University) containing 12K (GSM3816-GSM3819) or 9K (GSM3820-GSM3823)Arabidopsis ESTs. The 4 samples corresponding to each array represent 2 repetitions of 2 independent biological experiments. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platforms:

GPL242 GPL243

8 Samples

Download data

(Submitter supplied) To investigate the function of RNA-binding protein HRLP in flowering time control, we created hrlp-2 mutant and collected 9-day-old seedlings to perform RNA-seq.

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26208

6 Samples

Download data: TXT