GPL17970[RGSE] - GEO DataSets

(Submitter supplied) Genome editing tools with high precision are key to develop improved crops but current technologies to place new DNA into specific locations in plant genomes are low frequency and error-prone. Transposable elements (TEs) evolved to insert their DNA seamlessly into genomes, albeit in a quasi-random pattern. We developed a genome engineering tool that controls the TE insertion site and subsequently the delivery of any cargo attached to this TE. more...

Organism:: Arabidopsis thaliana; Glycine max

Type:: Other

Platforms:: GPL21309 GPL17970
11 Samples

Download data: TSV

Series

Accession:: GSE227104

ID:: 200227104

PubMed Full text in PMC Similar studies

Select item 2002271033.

Targeted site integration in plants using a transposon system [Amplicon]

Organism:: Arabidopsis thaliana

Type:: Other

Platform:: GPL17970
8 Samples

Download data: TSV

Series

Accession:: GSE227103

ID:: 200227103

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Select item 2002542754.

Trichoderma atroviride small RNA1 targets the Arabidopsis PRIM2 gene to establish a mutualistic relationship

(Submitter supplied) This study investigates the multifaceted defense mechanisms of plants in response to beneficial fungi Trichoderma atroviride. The researchers focus on a small RNA, Ta_sRNA1, produced by T. atroviride during its interaction with Arabidopsis thaliana.

Organism:: Arabidopsis thaliana; Trichoderma atroviride

Type:: Non-coding RNA profiling by high throughput sequencing

Platforms:: GPL17970 GPL34134
10 Samples

Download data: TSV

Series

Accession:: GSE254275

ID:: 200254275

Select item 2002356745.

The ALOG domain defines a new family of plant-specific transcription factors acting during Arabidopsis flower development

(Submitter supplied) The ALOGs (Arabidopsis LIGHT-DEPENDENT SHORT HYPOCOTYLS 1 and Oryza G1) are Transcription Factors (TFs) from an evolutionarily conserved plant-specific family shown to play critical roles in meristem identity, inflorescence architecture and organ boundaries in diverse species from mosses to higher flowering plants. However, the DNA binding-specificity and molecular determinants of protein-DNA interactions of this family were uncharacterized. more...

Organism:: Arabidopsis thaliana

Type:: Other

Platform:: GPL17970
8 Samples

Download data: BED, BEDGRAPH

Series

Accession:: GSE235674

ID:: 200235674

Select item 2002495086.

Modifiers of genetic dominance at the Arabidopsis self-incompatibility locus retain proto-miRNA features and act through non-canonical gene silencing pathways

(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

Platforms:: GPL17970 GPL19580
48 Samples

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Series

Accession:: GSE249508

ID:: 200249508

Select item 2002495067.

Modifiers of genetic dominance at the Arabidopsis self-incompatibility locus retain proto-miRNA features and act through non-canonical gene silencing pathways - BSAS data

(Submitter supplied) Self-incompatibility (SI) in flowering plants is a common mechanism that prevents self-fertilization and promotes outcrossing. In Brassicaceae, the locus controlling SI is highly diverse and dozens of distinct alleles are organized in a complex dominance hierarchy: the gene controlling SI specificity in pollen always shows monoallelic expression in heterozygote individuals, and this is achieved through the action of sRNA precursors that resemble miRNAs, although the mechanism behind this remains elusive. more...

Organism:: Arabidopsis thaliana

Type:: Methylation profiling by high throughput sequencing

Platform:: GPL17970
39 Samples

Download data: TSV, TXT

Series

Accession:: GSE249506

ID:: 200249506

Select item 2002238768.

A tRNA modifying enzyme facilitates RNase P activity in Arabidopsis nuclei

(Submitter supplied) RNase P is the essential activity that performs the 5’ maturation of tRNA precursors. Beyond the ancestral form of RNase P containing a ribozyme, protein-only RNase P enzymes termed PRORP were identified in eukaryotes. In human mitochondria, PRORP forms a complex with two protein partners to become functional. In plants, although PRORP enzymes are active alone, we investigate their interaction network to understand their integration with gene expression pathways. more...

Organism:: Arabidopsis thaliana

Type:: Non-coding RNA profiling by high throughput sequencing

Platform:: GPL17970
6 Samples

Download data: CSV

Series

Accession:: GSE223876

ID:: 200223876

PubMed Similar studies

Select item 2002302289.

Pseudouridine in small RNAs

(Submitter supplied) Pseudouridine is an isomer of uridine and is the most common RNA modification in both procaryotes and eucaryotes. It is found in ribosomal, transfer, and other structural RNA as well as in some mRNA and non-coding RNA. We have found abundant pseudouridine in small RNA and their precursors in Arabidopsis.

Organism:: Arabidopsis thaliana

Type:: Non-coding RNA profiling by high throughput sequencing

Platforms:: GPL19580 GPL17970
70 Samples

Download data: TXT

Series

Accession:: GSE230228

ID:: 200230228

PubMed Full text in PMC Similar studies

Select item 20021235610.

Uridylation is a genomic feature of encapsidated GFLV RNAs [Purified virions]

(Submitter supplied) Using 3' RACE-seq method, we measured uridylation frequencies of GFLV RNAs (K30 and B844 isolates) for total RNA of C. quinoa infected plants or for purified RNA from GFLV virions.

Organism:: Arabidopsis thaliana

Type:: Expression profiling by high throughput sequencing

Platform:: GPL17970
4 Samples

Download data: TXT

Series

Accession:: GSE212356

ID:: 200212356

Select item 20021235511.

Uridylation is a genomic feature of encapsidated GFLV RNAs [GFLV]

(Submitter supplied) To determine whether the single 3’ terminal uridine of the positive strand is encoded and whether this feature is shared by the negative strand, we attempted to map the 5’ and 3’ ends of the minus strand for both GFLV RNA1 and RNA2.

Organism:: Arabidopsis thaliana

Type:: Expression profiling by high throughput sequencing

Platform:: GPL17970
8 Samples

Download data: TXT

Series

Accession:: GSE212355

ID:: 200212355

Select item 20021229312.

Involvement of Arabidopsis TUTases in viral RNA uridylation

(Submitter supplied) Using 3' RACE-seq method, we analyzed the impact of URT1 and/or HESO1 inactivation on the uridylation of GFLV, TuMV and TCV RNAs in Arabidopsis.

Organism:: Arabidopsis thaliana

Type:: Expression profiling by high throughput sequencing

Platform:: GPL17970
68 Samples

Download data: TXT

Series

Accession:: GSE212293

ID:: 200212293

Select item 20021229213.

Diversity of phytoviral RNA U-tailing among ss(+) RNA phytoviruses

(Submitter supplied) Using 3' RACE-seq method, we analyzed global 3’ terminal RNA uridylation profiles for representatives of the main families of positive single-stranded RNA phytoviruses.

Organism:: Nicotiana benthamiana; Nicotiana obtusifolia; Chenopodium quinoa; Spinacia oleracea; Arabidopsis thaliana; Vitis vinifera

Type:: Expression profiling by high throughput sequencing

9 related Platforms
27 Samples

Download data: TXT

Series

Accession:: GSE212292

ID:: 200212292

PubMed Full text in PMC Similar studies

Select item 20021235814.

A global survey of phytoviral RNA 3' uridylation identifies extreme variations and virus-specific patterns

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

Organism:: Nicotiana benthamiana; Nicotiana obtusifolia; Chenopodium quinoa; Spinacia oleracea; Arabidopsis thaliana; Vitis vinifera

Type:: Expression profiling by high throughput sequencing

12 related Platforms
140 Samples

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Series

Accession:: GSE212358

ID:: 200212358

PubMed Full text in PMC Similar studies

Select item 20020784215.

Nodulin homeobox (NDX) is required for heterochromatin homeostasis in Arabidopsis [RNA-seq]

(Submitter supplied) Nodulin homeobox (NDX) is a nuclear protein described as the regulator of specific euchromatic genes that controls multiple aspects of Arabidopsis development. At the molecular level, NDX was shown to i) interact with the Polycomb repressive complex 1 (PRC1) to promote deposition of repressive histone marks at abscisic acid-responsive gene loci, and (ii) stabilize an R-loop structure within the Flowering Locus C (FLC) to control its expression. more...

Organism:: Arabidopsis thaliana

Type:: Expression profiling by high throughput sequencing

Platform:: GPL17970
4 Samples

Download data: BW, TSV

Series

Accession:: GSE207842

ID:: 200207842

PubMed Full text in PMC Similar studies

Select item 20020184116.

Nodulin homeobox (NDX) is required for heterochromatin homeostasis in Arabidopsis

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

Organism:: Arabidopsis thaliana

Type:: Genome binding/occupancy profiling by high throughput sequencing; Other; Non-coding RNA profiling by high throughput sequencing; Expression profiling by high throughput sequencing

4 related Platforms
30 Samples

Download data: BW, HIC

Series

Accession:: GSE201841

ID:: 200201841

PubMed Full text in PMC Similar studies

Select item 20013425817.

Transcriptome and binding data indicate that citral inhibits single strand DNA-binding proteins

(Submitter supplied) BCKGROUND: Citral is a phytochemical monoterpene aldehyde that has been reported to be phytotoxic to a number of plant species. When treated in a solution, citral was phytotoxic to barnyard grass, wild oat, redroot pigweed, ribwort, lettuce, and barley, but not active on soybean, rice, maize, wheat, field bindweed, or common purslane. To investigate the mechanism of citral phytotoxicity in plant, we performed transcriptome analysis experiments using the model plant Arabidopsis. more...

Organism:: Arabidopsis thaliana

Type:: Expression profiling by high throughput sequencing

Platforms:: GPL17970 GPL17639
72 Samples

Download data: CSV

Series

Accession:: GSE134258

ID:: 200134258

PubMed Similar studies SRA Run Selector

Select item 20018129218.

The histone H3K27 demethylase REF6/JMJ12 Promotes thermomorphogenesis in Arabidopsis

(Submitter supplied) Dynamic trimethylation of histone H3 at Lys27 (H3K27me3) affects gene expression and controls plant development and environmental responses. In Arabidopsis thaliana, RELATIVE OF EARLY FLOWERING 6/JUMONJI DOMAIN-CONTAINING PROTEIN 12 (REF6/JMJ12) demethylates H3K27me3 by recognizing a specific DNA motif; however, little is known about how REF6 activates target gene expression after recognition, especially in environmental responses. more...

Organism:: Arabidopsis thaliana

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

Platform:: GPL17970
24 Samples

Download data: BIGWIG

Series

Accession:: GSE181292

ID:: 200181292

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 20016557519.

An siRNA-guided AGO protein recruits Polymerase V to initiate RNA-directed DNA methylation

(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

5 related Platforms
111 Samples

Download data: TSV

Series

Accession:: GSE165575

ID:: 200165575

PubMed Full text in PMC Similar studies

Select item 20016557320.

An siRNA-guided AGO protein recruits Polymerase V to initiate RNA-directed DNA methylation (BSA-seq dataset)

(Submitter supplied) Foreign DNA is silenced in plants by small RNA-directed DNA methylation (RdDM). RNA Polymerase V (Pol V) is the key protein required to recruit DNA methyltransferases to a RdDM target region. However, the mechanism required for the initial recruitment of Pol V to a targeted locus remains a mystery. In this study, we used first generation (T1) transgene transformations to elucidate a novel mechanism by which Pol V is recruited to both new transgenic and endogenous loci. more...

Organism:: Arabidopsis thaliana

Type:: Methylation profiling by high throughput sequencing

Platform:: GPL17970
66 Samples

Download data: TSV

Series

Accession:: GSE165573

ID:: 200165573

PubMed Full text in PMC Similar studies SRA Run Selector

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