Rna directed dna methylation

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Genomics (561)
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Unknown (335)
Methylation profiling (72)
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Arabidopsis thaliana (281)
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Organisms

Arabidopsis thaliana (168)
Homo sapiens (41)
Mus musculus (16)
Oryza sativa (12)
Zea mays (7)
Solanum lycopersicum (5)
Oryza sativa Japonica Group (4)
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unidentified (1)
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Repository

biostudies-arrayexpress (524)
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geo (274)
pride (12)
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Disease

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2008 (25)
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CHEBI ID

CHEBI:15539 (1)
CHEBI:89575 (1)
CHEBI:57443 (1)
CHEBI:28498 (1)
CHEBI:42491 (1)
CHEBI:16069 (1)
CHEBI:49537 (1)
CHEBI:17633 (1)
CHEBI:16284 (1)
CHEBI:17808 (1)
CHEBI:28207 (1)
CHEBI:16001 (1)
CHEBI:16666 (1)
CHEBI:19569 (1)
CHEBI:90324 (1)
CHEBI:88356 (1)
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CHEBI:16891 (1)
CHEBI:47878 (1)
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CHEBI:24267 (1)
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CHEBI:50392 (1)
CHEBI:15641 (1)
CHEBI:1606 (1)
CHEBI:45931 (1)
CHEBI:15633 (1)

Metabolite Name

N-acetyl-L-aspartylglutamic acid (1)
HMG-CoA (1)
Retinoic acid (1)
Arginosuccinic acid (1)
Adenylosuccinate (1)
Nicotinamide Riboside (1)
N-acetyl spermidine (1)
N-acetyl spermine (1)
Succinyl-CoA (1)
Malonyl-CoA (1)
Acetoacetyl-CoA (1)
Propionyl-CoA (1)
Diiodothyronine (1)
5-methyl-THF (1)
7,8-dihydrofolate (1)
Folate (1)
S-adenosyl-L-homoCysteine (1)
Xanthosine-5-phosphate (XMP) (1)
S-adenosyl-L-methioninamine (1)
Thiamine-phosphate (TMP) (1)
Aminoimidazole carboxamide ribonucleotide (1)
S-methyl-5-thioadenosine (1)
Deoxyguanosine (1)
D-glucosamine-1-phosphate (1)
D-glucosamine-6-phosphate (1)
Acadesine (1)
Glycerophosphocholine (GPCho) (1)
Deoxyadenosine (1)
N-acetyl-glucosamine (1)
Acetylcarnitine DL (1)

First Public Date

2021 (37)
2023 (36)
2013 (34)
2020 (26)
2025 (25)
2019 (25)
2024 (24)
2017 (24)
2014 (24)
2022 (21)
2016 (21)
2018 (17)
2026 (15)
2015 (10)

Classification

fungi (1)

Study type

Transcription profiling by array (145)
RNA-seq of coding RNA (102)
Methylation profiling by high throughput sequencing (80)
ChIP-seq (53)
RNA-seq of non coding RNA (39)
Methylation profiling by array (32)
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DNA-seq (5)
ChIP-chip by array (4)
Other (4)
Unknown experiment type (3)
Animal - High-throughput sequencing (3)
Transcription profiling by SAGE (2)
High-throughput sequencing (2)
Cell line - High-throughput sequencing (2)
PRO-seq (1)
MeDIP-seq (1)
Translation profiling (1)
RNAi profiling by array (1)
Genotyping by array (1)
Proteomic profiling by array (1)
CUT&RUN (1)
RNA-seq of total RNA (1)

Release Date

2013 (96)
2014 (92)
2012 (90)
2015 (79)
2011 (68)
2010 (58)
2016 (57)
2021 (37)
2019 (36)
2009 (33)
2008 (31)
2020 (29)
2024 (24)
2022 (24)
2023 (22)
2018 (20)
2025 (17)
2017 (17)
2026 (7)
2005 (6)
2007 (5)
2006 (5)
2002 (3)
2004 (2)
2003 (1)

Lab affiliation

University of Edinburgh (2)
Department of Molecular, Cellular and Developmental Biology, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA (1)
Gregor Mendel Institute of the Austrian Academy of Sciences (1)
Howard Hughes Medical Institute, Department of Biology, Indiana University, Bloomington, Indiana, USA (1)
MRC Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, 5 Little France Drive, Edinburgh, EH16 4UU, UK. Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, EH9 3BF, UK. (1)
South China Botentical Garden, Chinese Academy of sciences (1)
State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Institute of Plant Biology, School of Life Sciences, Fudan University (1)
UCLA (1)
Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Centro de Biociências e Biotecnologia, Laboratório de Química e Função de Proteínas e Peptídeos, Prédio P5, Sala 228, Bairro Parque Califórnia, Campos dos Goytacazes, RS - CEP: 28013-602 (1)
University of edinburgh (1)
ucla (1)

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An IDN2-containing complex involved in RNA-directed DNA methylation in Arabidopsis [BS-seq]

Illumina-based whole genome bisulfite sequencing libraries for 4 RNA-directed DNA methylation mutants Examining DNA methylation levels in leaf tissue of RNA-directed DNA methylation mutants

ORGANISM(S): Arabidopsis thaliana

2012-05-26 | E-GEOD-36143 | biostudies-arrayexpress

An IDN2-containing complex involved in RNA-directed DNA methylation in Arabidopsis

This SuperSeries is composed of the following subset Series: GSE36129: An IDN2-containing complex involved in RNA-directed DNA methylation in Arabidopsis [leaves RNA-seq] GSE36143: An IDN2-containing complex involved in RNA-directed DNA methylation in Arabidopsis [BS-seq] GSE37206: An IDN2-containin...

ORGANISM(S): Arabidopsis thaliana

2012-05-25 | E-GEOD-36148 | biostudies-arrayexpress

Polymerase-IV occupancy at RNA-directed DNA methylation sites requires SHH1

DNA methylation is an epigenetic modification that plays critical roles in gene silencing, development, and the maintenance of genome integrity. In Arabidopsis, DNA methylation is established by DOMAINS REARRANGED METHYLTRANSFERASE 2 (DRM2) and is targeted by 24 nt small interfering RNAs (siRNAs) th...

ORGANISM(S): Arabidopsis thaliana

2013-05-13 | E-GEOD-45368 | biostudies-arrayexpress

An IDN2-containing complex involved in RNA-directed DNA methylation in Arabidopsis [leaves RNA-seq]

Illumina TruSeq mRNA libraries for 4 RNA-directed DNA methylation mutants Examining mRNA levels in leaf tissue of RNA-directed DNA methylation mutants

ORGANISM(S): Arabidopsis thaliana

2012-05-26 | E-GEOD-36129 | biostudies-arrayexpress

Interplay Between Active Chromatin Marks and RNA-directed DNA Methylation in Arabidopsis thaliana

DNA methylation is an epigenetic mark that is associated with transcriptional repression of transposable elements and protein coding genes. Conversely, transcriptionally active regulatory regions are strongly correlated with histone 3 lysine 4 di- and trimethylation (H3K4m2/3). We previously showed ...

ORGANISM(S): Arabidopsis thaliana

2013-11-01 | E-GEOD-49090 | biostudies-arrayexpress

An IDN2-containing complex involved in RNA-directed DNA methylation in Arabidopsis (flowers RNA-seq)

Illumina mRNA libraries for 7 RNA-directed DNA methylation mutants. Examining mRNA levels in floral tissue of RNA-directed DNA methylation mutants.

ORGANISM(S): Arabidopsis thaliana

2012-05-26 | E-GEOD-37206 | biostudies-arrayexpress

DTF1 is a core component of RNA-directed DNA methylation and may assist in the recruitment of Pol IV

DNA methylation is an important epigenetic mark in many eukaryotic organisms. De novo DNA methylation in plants can be achieved by the RNA-directed DNA methylation (RdDM) pathway, where the plant-specific DNA-dependent RNA polymerase Pol IV transcribes target sequences to initiate 24-nt siRNA produ...

ORGANISM(S): Arabidopsis thaliana

2013-06-03 | E-GEOD-44209 | biostudies-arrayexpress

IBM1, a JmjC domain histone demethylase, is involved in the regulation of RNA-directed DNA methylation through epigenetic control of RDR2 and DCL3 expression in Arabidopsis.

The small RNA mediated DNA methylation (RdDM) is highly elaborated in Arabidopsis as an important epigenetic pathway controls expression of genes and multiple developmental processes. RDR2 and DCL3 are necessary factors to the 24-nt siRNA biogenesis and the RdDM pathway. Here, we find that IBM1 (inc...

ORGANISM(S): Arabidopsis thaliana

2012-08-03 | E-GEOD-32284 | biostudies-arrayexpress

Small RNA mediated DNA (cytosine-5) methyltransferase 1 inhibition leads to aberrant DNA methylation

Mammalian cells contain copious amounts of RNA including both coding and non-coding RNA (ncRNA). Generally the ncRNAs function to regulate gene expression at the transcriptional and post-transcriptional level. Among ncRNA, the long ncRNA and small ncRNA can affect histone modification, DNA methylati...

ORGANISM(S): Homo sapiens

2015-04-21 | E-GEOD-68027 | biostudies-arrayexpress

DDM1 and RdDM are the major regulators of transposon DNA methylation in Arabidopsis

Eukaryotic DNA methylation is found in silent transposable elements and active genes. Nucleosome remodelers of the DDM1/Lsh family are thought to be specifically required to maintain transposon methylation, but the reason for this is unknown. Here, we find that a chromatin gradient that extends from...

ORGANISM(S): Arabidopsis thaliana

2013-04-17 | E-GEOD-41302 | biostudies-arrayexpress

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1491 Results

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