Similar studies for GEO DataSets (Select 200095765) - GEO DataSets

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Items: 20

Select item 2000957651.

Genome-wide maps of R-loops in Arabidopsis

(Submitter supplied) Inspired by the important roles of the special chromatin structure R-loops, here we report a new method, ssDRIP-seq, for genome-wide identification of R-loops, and demonstrate its high efficiency, low bias, and strand-specificity when profiling the R-loops in Arabidopsis. Using this single-strand DNA ligation based library construction technique, we find that Arabidopsis R-loops are formed in both the sense and antisense orientations of genes, and prefer both AT and GC skews. more...

Organism:: Arabidopsis thaliana

Type:: Other

Platform:: GPL23157
5 Samples

Download data: BW, NARROWPEAK

Series

Accession:: GSE95765

ID:: 200095765

PubMed Similar studies SRA Run Selector

Select item 2001183382.

Long heat stress induced RNA dynamics in Arabidopsis

(Submitter supplied) Heat stress is a common stress for plants. Long heat stress can triger a series of biological responses. RNA-seq is a useful method to profile RNA dynamics in creatures. Here we profiles the RNA dynamics in heat stressed Arabidopsis. These data will help us understanding the stress response mechanism in plants.

Organism:: Arabidopsis thaliana

Type:: Expression profiling by high throughput sequencing

Platform:: GPL23157
8 Samples

Download data: TXT

Series

Accession:: GSE118338

ID:: 200118338

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 2001162323.

R-loop landscapes in Arabidopsis

(Submitter supplied) The R-loop is a common chromatin feature presented from prokaryotic to eukaryotic genomes and has been revealed to be involved in multiple cellular processes and associated with many human diseases. Here, we take the advantage of our recently developed ssDRIP method to profile genome-wide R-loop levels and provided a first-hand R-loop atlas during Arabidopsis development and in response to various environmental factors.

Organism:: Arabidopsis thaliana

Type:: Other

Platform:: GPL23157
53 Samples

Download data: BW

Series

Accession:: GSE116232

ID:: 200116232

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 2000283984.

Histone modifications of Arabidopsis thaliana (aerial tissue)

(Submitter supplied) Bioinformatics powered correlative analysis of epigenomic patterns is an effective method to help derive biological hypotheses that can be tested genetically or biochemically. To accommodate the variety and complexity of epigenomic and transcriptomic patterns, ANchored COrrelative Patterns (ANCORP) was developed as a platform to integrate and intuitively visualize a large number of genome-wide profiles. more...

Organism:: Arabidopsis thaliana

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

Platforms:: GPL10088 GPL10272
12 Samples

Download data: BED

Series

Accession:: GSE28398

ID:: 200028398

PubMed Similar studies SRA Run Selector

Select item 2001928225.

spKAS-seq reveals R-loop dynamics using low-input materials by detecting single-stranded DNA with strand specificity

(Submitter supplied) R-loops impact transcription and genome stability and are related to human diseases. Genome-wide R-loop mapping typically uses the S9.6 antibody or inactive RNase H, both requiring a large number of cells with varying results observed depending on the approach applied. Here, we present strand-specific KAS-seq (spKAS-seq) to map R-loops by taking advantage of the presence of a single-stranded DNA (ssDNA) in the triplex structure. more...

Organism:: Homo sapiens

Type:: Other

Platform:: GPL24676
46 Samples

Download data: BIGWIG

Series

Accession:: GSE192822

ID:: 200192822

PubMed Full text in PMC Similar studies

Select item 2001119446.

Characterization of functional relationships of R-loops with gene transcription and epigenetic modifications in rice

(Submitter supplied) We conducted genome-wide identification of R-loops followed by integrative analyses of R-loops with relation to gene expressionand epigenetic signatures in the rice genome. We found that the correlation between gene expression levels and profiled R-looppeak levels was dependent on the positions of R-loops within gene structures (hereafter named 'genic position'). Both antisenseonly (ASO)-R-loops and sense/antisense(S/AS)-R-loops sharply peaked around transcription start sites (TSSs), and these peaklevels corresponded positively with transcript levels of overlapping genes. more...

Organism:: Oryza sativa

Type:: Methylation profiling by high throughput sequencing; Other

Platforms:: GPL24468 GPL19290
10 Samples

Download data: BED, TXT

Series

Accession:: GSE111944

ID:: 200111944

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Select item 2000402097.

Regulatory impact of RNA secondary structure across the Arabidopsis thaliana transcriptome

(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

Series

Accession:: GSE40209

ID:: 200040209

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 2000285248.

DCP5, a highly conserved P-body-nucleating protein, regulates multiple small RNA-mediated silencing pathways in Arabidopsis

(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:: GPL13396 GPL9302
6 Samples

Download data: FASTA, TXT

Series

Accession:: GSE28524

ID:: 200028524

PubMed Full text in PMC Similar studies

Select item 2000285129.

DCP5, a highly conserved P-body-nucleating protein, regulates multiple small RNA-mediated silencing pathways in Arabidopsis (smRNA-seq)

(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

Series

Accession:: GSE28512

ID:: 200028512

PubMed Full text in PMC Similar studies

Select item 20002850910.

DCP5, a highly conserved P-body-nucleating protein, regulates multiple small RNA-mediated silencing pathways in Arabidopsis (RNA-seq)

Organism:: Arabidopsis thaliana

Type:: Expression profiling by high throughput sequencing

Platform:: GPL13396
4 Samples

Download data: FASTA, TXT

Series

Accession:: GSE28509

ID:: 200028509

PubMed Full text in PMC Similar studies

Select item 20012494311.

Genome-wide profiling of γH2AX in Arabidopsis

(Submitter supplied) The R-loop, composed of a DNA-RNA hybrid and the displaced single-stranded DNA, regulates diverse cellular processes. However, how cellular R-loops are sensed remain poorly understood. Here we report the discovery of the evolutionally conserved ALBA proteins (AtALBA1&2) functioning as the R-loops sensor of genic regions in higher plant Arabidopsis thaliana. AtALBA1 and 2 form a heterodimer protein complex and localize in the nucleus. more...

Organism:: Arabidopsis thaliana

Type:: Expression profiling by high throughput sequencing

Platform:: GPL23157
8 Samples

Download data: BW

Series

Accession:: GSE124943

ID:: 200124943

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 20012168312.

ALBA protein complex reads genic R-loops to maintain genome stability in Arabidopsis

Organism:: Arabidopsis thaliana

Type:: Other

Platform:: GPL23157
2 Samples

Download data: BW

Series

Accession:: GSE121683

ID:: 200121683

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 20005024213.

MNase-seq analysis of Col-0 and chr11-1 chr17-1

(Submitter supplied) Chromatin has a highly organized structure with the repeating nucleosome subunits. The position of nucleosomes on the chromatin is dynamically regulated by ATP-dependent chromatin remodeling factors (remodelers), therefore providing specific epigenetic information. However, the in vivo nucleosome distribution pattern in plants and how plant remodelers control the pattern formation are not yet clear. more...

Organism:: Arabidopsis thaliana

Type:: Other

Platform:: GPL17639
2 Samples

Download data: WIG

Series

Accession:: GSE50242

ID:: 200050242

PubMed Similar studies SRA Run Selector

Select item 20003939814.

smRNAs generated by single-stranded and double-stranded silencers

(Submitter supplied) To investigate possible smRNAs linked to TMM silencing by single-stranded and double-stranded silencers, we determined sequences of smRNAs by the Illumina high-throughput sequencing platform and compared silencing efficiency of different strategies. We found that single-stranded silencer alone could promote the production of smRNAs.

Organism:: Arabidopsis thaliana

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

Platform:: GPL11221
8 Samples

Download data: TXT

Series

Accession:: GSE39398

ID:: 200039398

PubMed Similar studies SRA Run Selector

Select item 20007018915.

Human and mouse DRIP-seq and DRIPc-seq

(Submitter supplied) This study profiles RNA:DNA hybrid formation in human and mouse cell lines.

Organism:: Homo sapiens; Mus musculus

Type:: Other; Expression profiling by high throughput sequencing; Methylation profiling by high throughput sequencing

Platforms:: GPL13112 GPL17021 GPL11154
13 Samples

Download data: BED, BEDGRAPH, WIG

Series

Accession:: GSE70189

ID:: 200070189

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 20000827916.

Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation

(Submitter supplied) Maintenance of CG methylation (mCG) patterns is essential for chromatin-mediated epigenetic regulation of transcription in plants and mammals. Using successive generations of an Arabidopsis thaliana mutant deficient in maintaining mCG, we found that mCG loss triggered genome-wide activation of alternative epigenetic mechanisms. However, these mechanisms involving RNA-directed DNA methylation, inhibiting expression of DNA demethylases, and retargeting of histone H3K9 methylation act in a stochastic and uncoordinated fashion. more...

Organism:: Arabidopsis thaliana

Type:: Methylation profiling by array

Platform:: GPL198
6 Samples

Download data: CEL, CHP, TXT

Series

Accession:: GSE8279

ID:: 200008279

Select item 20009888617.

Defining the location of promoter-associated R-loops at near-nucleotide resolution using bisDRIP-seq

(Submitter supplied) R-loops are features of chromatin consisting of a strand of DNA hybridized to RNA, as well as the expelled complementary DNA strand. R-loops are enriched at promoters where they have recently been shown to have important roles in modifying gene expression. However, the location of promoter-associated R-loops and the genomic domains they perturb to modify gene expression remain unclear. To resolve this issue, we developed a bisulfite-based approach, bisDRIP-seq, to map R-loops across the genome at near-nucleotide resolution in MCF-7 cells. more...

Organism:: Homo sapiens

Type:: Other

Platform:: GPL16791
20 Samples

Download data: BEDGRAPH, TXT

Series

Accession:: GSE98886

ID:: 200098886

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 20007657118.

LHP1, CLF binding sites and their role in H3K27me3 spreading in Arabidopsis thaliana

(Submitter supplied) LHP1 regulates H3K27me3 spreading

Organism:: Arabidopsis thaliana

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

Platform:: GPL17639
13 Samples

Download data: WIG

Series

Accession:: GSE76571

ID:: 200076571

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 20002506119.

h3k4me2_col_chr4-Analysis of epigenomic changes in hybrids Arabidopsis thaliana Col-0, C24 and Cvi accessions

(Submitter supplied) a2e_heterosis - h3k4me2_col_chr4 - Arabidopsis thaliana accessions (Col-0, C24 and Cvi) and their hybrid were used to investigate the dynamics of the epigenome after intraspecific hybridization between - H3K4me2 profiling in Col

Organism:: Arabidopsis thaliana

Type:: Genome variation profiling by genome tiling array; Genome binding/occupancy profiling by genome tiling array

Platform:: GPL10772
8 Samples

Download data: GPR

Series

Accession:: GSE25061

ID:: 200025061

Select item 20002506020.

h3k4me2_colxc24_chr4-Analysis of epigenomic changes in hybrids Arabidopsis thaliana Col-0, C24 and Cvi accessions

(Submitter supplied) a2e_heterosis - h3k4me2_colxc24_chr4 - Arabidopsis thaliana accessions (Col-0, C24 and Cvi) and their hybrid were used to investigate the dynamics of the epigenome after intraspecific hybridization between - H3K4me2 profiling in ColxC24 hybrids

Organism:: Arabidopsis thaliana

Type:: Genome variation profiling by genome tiling array; Genome binding/occupancy profiling by genome tiling array

Platform:: GPL10772
8 Samples

Download data: GPR

Series

Accession:: GSE25060

ID:: 200025060

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