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Links from GEO DataSets

Items: 20

1.

Circadian clock regulation of alternative splicing and alternative polyadenylation in Arabidopsis thaliana

(Submitter supplied) Purpose: Circadian clock in plants temporally coordinates biological processes throughout the day synchronizing gene expression with environmental changes. Here, we examined the genome-wide circadian and diurnal control of Arabidopsis transcriptome using high throughout RNA-seq approach. Methods: Transcriptional and posttranscritional profiles were identified and characterized for Arabidopsis seedlings grown under continuous light or long-day condition (16 h light/8 h dark) for one day (each condition has two biological replicates). more...
Organism:
Arabidopsis thaliana
Type:
Expression profiling by high throughput sequencing
Platform:
GPL21785
32 Samples
Download data: TXT
Series
Accession:
GSE137732
ID:
200137732
2.

SKIP Is a Component of the Spliceosome Linking Alternative Splicing and the Circadian Clock in Arabidopsis

(Submitter supplied) Circadian clocks generate endogenous rhythms in most organisms from cyanobacteria to humans and facilitate entrainment to environmental diurnal cycles, thus conferring a fitness advantage. Both transcriptional and posttranslational mechanisms are prominent in the basic network architecture of circadian systems. Posttranscriptional regulation, including mRNA processing, is emerging as a critical step for the clock function. more...
Organism:
Arabidopsis thaliana
Type:
Expression profiling by high throughput sequencing
Platform:
GPL11221
4 Samples
Download data: TXT
Series
Accession:
GSE32216
ID:
200032216
3.

A methyl transferase links the circadian clock to the regulation of alternative splicing

(Submitter supplied) Study on differential gene expression and splicing between wildtype and clock mutants. This study is part of a comparative analysis of the role of Protein Methyltransferase 5 in the regulation of transcriptional and post-transcriptional processes simultaneously in Arabidopsis and Drosophila. Circadian rhythms allow organisms to time biological processes to the most appropriate phases of the day/night cycle1. more...
Organism:
Arabidopsis thaliana; Drosophila melanogaster
Type:
Expression profiling by array; Expression profiling by genome tiling array
Platforms:
GPL198 GPL6882 GPL1979
18 Samples
Download data: CEL
Series
Accession:
GSE18808
ID:
200018808
4.

Adaptation of iCLIP to plants determines the binding landscape of the clock-regulated RNA-binding protein AtGRP7

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Arabidopsis thaliana
Type:
Expression profiling by high throughput sequencing; Other
Platforms:
GPL17639 GPL13222
45 Samples
Download data: BED
Series
Accession:
GSE99616
ID:
200099616
5.

Identification of differentially expressed genes by RNA-seq in AtGRP7 overexpression and knockdown lines

(Submitter supplied) A key function for RNA-binding proteins in orchestrating plant development and environmental responses is well established. However, the lack of a genome-wide view on their in vivo regulatory landscapes represents a gap in understanding the mode of action of plant RNA-binding proteins. Here, we conducted RNAseq to determine the genome-wide regulation repertoire of the circadian clock-regulated Arabidopsis thaliana glycine-rich RNA-binding protein AtGRP7.
Organism:
Arabidopsis thaliana
Type:
Expression profiling by high throughput sequencing
Platform:
GPL13222
18 Samples
Download data: TSV
Series
Accession:
GSE99615
ID:
200099615
6.

Identification of AtGRP7 targets by RIP-seq

(Submitter supplied) A key function for RNA-binding proteins in orchestrating plant development and environmental responses is well established. However, the lack of a genome-wide view on their in vivo binding targets and binding landscapes represents a gap in understanding the mode of action of plant RNA-binding proteins. Here, we conducted RNA Immunoprecipitation (RIP-seq) for genome-wide determining the binding repertoire of the circadian clock-regulated Arabidopsis thaliana glycine-rich RNA-binding protein AtGRP7.
Organism:
Arabidopsis thaliana
Type:
Other
Platform:
GPL13222
6 Samples
Download data: TSV
Series
Accession:
GSE99464
ID:
200099464
7.

Identification of AtGRP7 targets by iCLIP

(Submitter supplied) A key function for RNA-binding proteins in orchestrating plant development and environmental responses is well established. However, the lack of a genome-wide view on their in vivo binding targets and binding landscapes represents a gap in understanding the mode of action of plant RNA-binding proteins. Here, we adapt individual nucleotide resolution crosslinking immunoprecipitation (iCLIP) for genome-wide determining the binding repertoire of the circadian clock-regulated Arabidopsis thaliana glycine-rich RNA-binding protein AtGRP7. more...
Organism:
Arabidopsis thaliana
Type:
Other
Platform:
GPL17639
21 Samples
Download data: BED
Series
Accession:
GSE99427
ID:
200099427
8.

XAP5 CIRCADIAN TIMEKEEPER regulates RNA splicing and the circadian clock by genetically separable pathways

(Submitter supplied) Regulators of post-transcriptional events, such as pre-mRNA splicing factors, are involved in controlling the pace of the circadian clock. However, in most cases the underlying mechanisms remain unclear. Previously, we have identified XAP5 CIRCADIAN TIMEKEEPER (XCT) as an Arabidopsis thaliana circadian clock regulator with uncharacterized molecular functions. To investigate a possible role for XCT in RNA splicing, we performed PacBio Isoform Sequencing (Iso-Seq) on wild-type Col-0, reduction-of-function allele xct-1, null allele xct-2, the complemented line xct-2 XCT and prl1-2 (a mutate with known defects in intron retention). more...
Organism:
Arabidopsis thaliana
Type:
Expression profiling by high throughput sequencing; Other
Platform:
GPL32947
18 Samples
Download data: TXT
Series
Accession:
GSE220902
ID:
200220902
9.

Genome-wide analysis of wild type and gemin2 mutant plants exposed to cold

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Arabidopsis thaliana
Type:
Expression profiling by high throughput sequencing
Platforms:
GPL11221 GPL19080
24 Samples
Download data
Series
Accession:
GSE63407
ID:
200063407
10.

Genome-wide analysis of wild type and gemin2 mutant plants [cold exposure]

(Submitter supplied) The goal of this study was to compare the transcriptional profile (RNA-seq) of wild type and gemin2 Arabidopsis mutants plants exposed to 10ºC for 0, 1 and 24 hours.
Organism:
Arabidopsis thaliana
Type:
Expression profiling by high throughput sequencing
Platform:
GPL19080
18 Samples
Download data: XLSX
Series
Accession:
GSE63406
ID:
200063406
11.

Genome-wide analysis of gemin2 mutant transcriptome

(Submitter supplied) The goal of this study was to compare the transcriptional profile (RNA-seq) of gemin2 Arabidopsis mutant with wild type plants grown under continous light conditions
Organism:
Arabidopsis thaliana
Type:
Expression profiling by high throughput sequencing
Platform:
GPL11221
6 Samples
Download data: XLS
Series
Accession:
GSE63405
ID:
200063405
12.

Genome-wide analysis of the lsm4 and lsm5 mutant transcriptomes

(Submitter supplied) The goal of this study was to compare the transcriptional profile (RNA-seq) of lsm4 and lsm5 Arabidopsis mutants with their respective wild type plants grown under continous light conditions
Organism:
Arabidopsis thaliana
Type:
Expression profiling by high throughput sequencing
Platform:
GPL19080
24 Samples
Download data: XLSX
Series
Accession:
GSE60387
ID:
200060387
13.

Coupling between alternative polyadenylation and alternative splicing is limited to terminal introns

(Submitter supplied) Alternative polyadenylation has been implicated as an important regulator of gene expression. In some cases, alternative polyadenylation is known to couple with alternative splicing to influence last intron removal. However, it is unknown whether alternative polyadenylation events influence alternative splicing decisions at upstream exons. Knockdown of the polyadenylation factors CFIm25 or CstF64 was used as an approach in identifying alternative polyadenylation and alternative splicing events on a genome-wide scale. more...
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platform:
GPL10999
4 Samples
Download data: TXT
14.

Diurnal cycle effect on whole leaf, mesophyll and vasculature: time course

(Submitter supplied) Many organisms acquired circadian clock system to adapt daily and seasonal environmental changes. Mammals have the master clock in the brains’ suprachiasmatic nucleus (SCN) that synchronizes other circadian clocks in the peripheral tissues or organs. Plants also have circadian clock in their bodies, but the presence of the tissue-specific functions of circadian clock is remained elusive. The aim of this experiment is to compare tissue-specific gene expression profile using gene expression Microarray.
Organism:
Arabidopsis thaliana
Type:
Expression profiling by array
Platform:
GPL17416
72 Samples
Download data: CEL
Series
Accession:
GSE50438
ID:
200050438
15.

HOS1 versus hos1 mRNA sequencing

(Submitter supplied) Sequencing of mRNA extracted from 14 day old Columbia and hos1-3 seedlings grown at 22°C 12:12 light dark Cold acclimation has been shown to be attenuated by the degradation of the INDUCER OF CBF EXPRESSION1 protein by the E3 ubiquitin ligase HIGH EXPRESSION OF OSMOTICALLY RESPONSIVE GENES1 (HOS1). However, recent work has suggested that HOS1 may have a wider range of roles in plants than previously appreciated. more...
Organism:
Arabidopsis thaliana
Type:
Expression profiling by high throughput sequencing
Platform:
GPL17639
6 Samples
Download data: DIFF, FPKM_TRACKING
Series
Accession:
GSE84606
ID:
200084606
16.

Achilles-mediated and sex-specific regulation of circadian mRNA rhythms in Drosophila

(Submitter supplied) The circadian clock is an evolutionarily conserved mechanism that drives rhythmic expression of downstream genes. The core circadian clock drives the expression of clock-controlled genes either directly or indirectly, which in turn play critical roles in carrying out many rhythmic physiological processes. Nevertheless, the molecular mechanisms by which clock output genes orchestrate rhythmic signals from the brain to peripheral tissues are largely unknown. more...
Organism:
Drosophila melanogaster
Type:
Expression profiling by high throughput sequencing
Platform:
GPL21306
96 Samples
Download data: TXT
Series
Accession:
GSE120100
ID:
200120100
17.

Contribution of time of day and the circadian clock to the heat stress responsive transcriptome in Arabidopsis

(Submitter supplied) In Arabidopsis, a large subset of heat responsive genes exhibits diurnal or circadian oscillations. However, to what extent the dimension of time and/or the circadian clock contribute to heat stress responses remains largely unknown. To determine the direct contribution of time of day and/or the clock to differential heat stress responses, we probed wild-type and mutants of the circadian clock genes CCA1, LHY, PRR7, and PRR9 following exposure to heat (37°C) and moderate cold (10°C) in the early morning (ZT1) and afternoon (ZT6). more...
Organism:
Arabidopsis thaliana
Type:
Expression profiling by high throughput sequencing
Platform:
GPL19580
35 Samples
Download data: XLS
Series
Accession:
GSE116004
ID:
200116004
18.

Exploring the transcriptional landscape of plant circadian rhythms using genome tiling arrays

(Submitter supplied) A casual look at the behavior and function of animals and plants clearly shows that many physiological processes are periodic and tied to cyclical changes in a day. As suggested by the persistence of some rhythms in the absence of external cues, organisms are able to anticipate changes in the daily environment with an internal oscillator know as the circadian clock. Transcription is an important mechanism in maintaining these oscillations. more...
Organism:
Arabidopsis thaliana
Type:
Expression profiling by genome tiling array; Non-coding RNA profiling by genome tiling array
Platforms:
GPL1979 GPL1980
24 Samples
Download data: CEL
Series
Accession:
GSE13814
ID:
200013814
19.

The m6A reader CPSF30-L regulates alternative polyadenylation affecting nitrate signaling in Arabidopsis

(Submitter supplied) As the most ubiquitous internal modification of eukaryotic mRNA, m6A (N6-methyladenosine) modification plays a vital role in almost every aspect of mRNA metabolism. However, the evidence of m6A in regulating the alternative polyadenylation (APA) is limited. APA is controlled by a large protein-RNA complex with many components including CPSF30. Arabidopsis CPSF30 has two isoforms, the longer one named CPSF30-L containing an additional YTH (YT512-B Homology)-domain in the C terminus, which is unique in plant. more...
Organism:
Arabidopsis thaliana
Type:
Expression profiling by high throughput sequencing; Other
Platforms:
GPL19580 GPL26208
24 Samples
Download data: BW
Series
Accession:
GSE145109
ID:
200145109
20.

Deep Transcriptional Profiling of Rice Using Illumina's Sequencing By Synthesis Technology

(Submitter supplied) Identification of all expressed transcripts in a sequenced genome is essential both for genome analysis and for realization of the goals of systems biology. We used the transcriptional profiling technologies like ‘massively parallel signature sequencing (MPSS)’ and ‘Sequencing by Synthesis’ (SBS) to develop a comprehensive expression atlas of rice (Oryza sativa cv Nipponbare). Illumina’s SBS technology can generate large amounts of sequence data in a short time at low cost compared to traditional Sanger sequencing based methods. more...
Organism:
Oryza sativa
Type:
Expression profiling by high throughput sequencing
Platform:
GPL9147
43 Samples
Download data: TXT
Series
Accession:
GSE25596
ID:
200025596
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