GEO DataSets

(Submitter supplied) DCL1 and HYL1 are the core components of miRNA biogenesis machinery. hyl1-null mutants accumulate low levels of miRNAs and cause pleiotropic morphological phenotypes. Here, we reported that we identified 5 new alleles of DCL1 which are able to suppress the hyl1 morphological phenotypes and restore the miRNA accumulation level in hyl1 plants. These new alleles are located in the helicase and RNaseIIIa domains of DCL1, highlighting the critical functions of these domains. more...

Organism:

Arabidopsis thaliana

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL14599

8 Samples

Download data

(Submitter supplied) MicroRNAs (miRNAs) play key regulatory roles in numerous developmental and physiological processes in animals and plants. The elaborate mechanism of miRNA biogenesis involves transcription and multiple processing steps. Here, we report the identification of a pair of evolutionarily conserved NOT2_3_5 domain containing proteins, NOT2a and NOT2b (previously known as At-NOT2 and VIP2, respectively), as components involved in Arabidopsis miRNA biogenesis. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL9062

2 Samples

Download data: WIG

(Submitter supplied) Light and microRNAs (miRNAs) are key external and internal signals for plant development respectively. However the relationship between light signaling and miRNA biogenesis pathways remains unknown. Here we found that miRNA processer DCL1/HYL1 interacts with a basic helix–loop–helix (bHLH) transcription factor, phytochrome-interacting factor 4 (PIF4), which mediates the destabilization of DCL1 during dark-red light transition. more...

Organism:

Arabidopsis thaliana

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL13222

6 Samples

Download data: TXT

(Submitter supplied) miRNAs are regulators of gene expression in plants and animals. Their biogenesis is precisely controlled to secure normal development of organisms. Here we report that TOUGH (TGH) is a novel component of DCL1-HYL1-SE complex that processes of primary transcripts of miRNAs (pri-miRNAs) into miRNAs in Arabidopsis. Lack of TGH impairs multiple DCL activities in vitro and reduces the accumulation of miRNAs and siRNAs in vivo. more...

Organism:

Arabidopsis thaliana

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL11221

4 Samples

Download data: TXT

(Submitter supplied) We applied the tiling arrays to study the Arabidopsis whole-genome transcriptome in Arabidopsis ago1-25 and hyl1-2 mutants.

Organism:

Arabidopsis thaliana

Type:

Expression profiling by genome tiling array

Platforms:

GPL10977 GPL10978

18 Samples

Download data: CEL, TXT

(Submitter supplied) DICER-LIKE1 (DCL1) is required for miRNA biogenesis and embryonic pattern formation. Presumably the patterning defects observed in dcl1-5 null embryos are due to the loss of miRNAs and the consequent up-regulation of their respective targets. To test which miRNA targets were up-regulated in dcl1 embryos relative to wild-type embryos, we performed genome-wide transcript profiling of wild-type and dcl1-5 early globular embryos using directional mRNA-Seq.

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL9302

2 Samples

Download data: TXT

(Submitter supplied) microRNAs (miRNAs) play important roles in the regulation of gene expression. In Arabidopsis, mature miRNAs are processed from primary miRNA transcripts (pri-miRNAs) by nuclear HYL1/SE/DCL1 complexes that form Dicing bodies (D-bodies). Here we report that a RNA-binding protein MOS2 bound to pri-miRNAs and was required for their efficient processing. MOS2 did not interact with HYL1, SE, and DCL1 and was not localized in D-bodies. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11221

4 Samples

Download data: TXT

(Submitter supplied) Microarray expression profiles of wild-type, ago1-10, ago1-11, and dcl1-9 Arabidopsis thaliana ec. Landsberg erecta seedling at 9, 21, and 35 days after germination. Keywords: mutant response

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL71

37 Samples

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(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

Platform:

GPL21785

10 Samples

Download data: TXT

(Submitter supplied) In order to assess the possible effects of m6A on miRNA biogenesis we performed small RNA (sRNA) sequencing to compare their levels in WT Col-0 plants to those in mutant lines with severely reduced m6A levels. The reduced mta line contains MTA cDNA under the ABI3 promoter in MTA null mutant background (ABI3:MTA) and ABI3 being an embryo specific promoter rescues the embryo lethal phenotype of MTA knockout while keeping the levels of MTA in mature plants severely low34. more...

Organism:

Arabidopsis thaliana

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL21785

6 Samples

Download data: TXT

(Submitter supplied) We performed m6A-RNA immunoprecipitation followed by sequencing (m6A-IP Seq) using libraries produced with unfragmented ployA+ RNA from 4 week old WT Col-0 and mta plants.

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21785

4 Samples

Download data: TXT

(Submitter supplied) In order to gain insight into m6A in control and salt stress, we performed an miCLIP-sequencing experiment in control and salt treated plants

Organism:

Arabidopsis thaliana

Type:

Other

Platform:

GPL13222

8 Samples

Download data: NARROWPEAK

(Submitter supplied) In order to gain insight into stability of transcripts in the presence and absence of m6A in control and salt stress, we performed an mRNA sequencing experiment in control and salt treated plants

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13222

4 Samples

Download data: BED12

(Submitter supplied) In order to gain insight into abundance of transcripts in the presence and absence of m6A in control and salt stress, we performed an mRNA sequencing experiment in control and salt treated plants

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13222

4 Samples

Download data: TXT

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

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL13222

50 Samples

Download data: NARROWPEAK, TXT

(Submitter supplied) In order to investigate the influence of m6A on RNA secondary-structure and RNA-protein interactions, we performed protein-interaction profile sequencing (PIP-seq)

Organism:

Arabidopsis thaliana

Type:

Other

Platform:

GPL13222

16 Samples

Download data: BED, TXT

(Submitter supplied) In order to gain insight into relative stability of transcripts in plants that lacked m6A, we performed global mapping of uncapped and cleaved transcripts

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13222

2 Samples

Download data: TXT

(Submitter supplied) In order to gain insight into abundance of transcripts in the presence and absence of m6A, we performed an mRNA sequencing expirement in both mta and Col-0 plants.

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13222

8 Samples

Download data: NARROWPEAK

(Submitter supplied) In order to gain insight into abundance of transcripts in the presence and absence of m6A, we performed an mRNA sequencing expirement in both mta and Col-0 plants.

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13222

8 Samples

Download data: TXT

(Submitter supplied) Using small RNA-Seq(sRNA-Seq) to get miRNA profiling of WT, snrk2.2/3/6, and hyl1-2 mutant

Organism:

Arabidopsis thaliana

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL17639

6 Samples

Download data: TXT