Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

6 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RNA-directed DNA methylation in near-gene chromatin regulation

ABSTRACT: The purpose of this study was to measure DNA methylation and siRNA expression across the maize genome. The experimental data was derived from shotgun bisulfite sequencing, siRNA sequencing, and mRNA sequencing (Illumina, single end for all three)

INSTRUMENT(S): Illumina HiSeq 2000

ORGANISM(S): Zea mays

SUBMITTER: Kelly Dawe

PROVIDER: E-MTAB-4329 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

CHH islands: de novo DNA methylation in near-gene chromatin regulation in maize.

Gent Jonathan I JI Ellis Nathanael A NA Guo Lin L Harkess Alex E AE Yao Yingyin Y Zhang Xiaoyu X Dawe R Kelly RK

Genome research 20121226 4

Small RNA-mediated regulation of chromatin structure is an important means of suppressing unwanted genetic activity in diverse plants, fungi, and animals. In plants specifically, 24-nt siRNAs direct de novo methylation to repetitive DNA, both foreign and endogenous, in a process known as RNA-directed DNA methylation (RdDM). Many components of the de novo methylation machinery have been identified recently, including multiple RNA polymerases, but specific genetic features that trigger methylation ...[more]

PMID: 23269663

Similar Datasets

Identification and molecular charaterization of new tumor suppressor genes on prostate cancer

Project description:Transposon mutagenesis screens in mice has allowed us the identification of new tumor suppressor genes in cancer. To further explore the mechanistic role of these genes at the molecular level, we decided to study the transcriptome of human immortalized and cancer cells which underwent siRNA-mediated silencing of these tumor suppressors. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/

2016-02-17 | E-ERAD-432 | biostudies-arrayexpress

Chordoma Sequencing Project RNAseq

Project description:This is a continuation of the Chordoma Sequencing Project. All cancers arise due to somatically acquired abnormalities in DNA sequence. Systematic sequencing of cancer genomes allows acquisition of complete catalogues of all classes of somatic mutation present in cancer. These mutation catalogues will allow identification of the somatically mutated cancer genes that are operative and characterise patterns of somatic mutation that may reflect previous exogenous and endogenous mutagenic exposures. In this application, we aim to perform whole genome sequencing on 10 chordoma matched genome pairs. RNA Sequencing/Methylation and SNP6 and an additional sequencing of three cancer cell lines will be added to this work.

2014-06-25 | E-ERAD-128 | biostudies-arrayexpress

Triticum urartu strain:PI 428198 Genome sequencing and Transcriptome or Gene expression

Project description:For this project, we have sequenced, assembled and annotated a transcriptome of a diploid wheat Triticum urartu accession PI 428198. The sequencing libraries were prepared from shoot and root tissues harvested from 2-3 week old seedlings. All sequencing was carried out on the Illumina HiSeq platform using the 100 bp pair-end protocol (248.5 million reads). The assembly was constructed using a multiple k-mer approach with a de novo assembly algorithm implemented in CLC Genomics Workbench 5.5 and additional redundancy reduction with CD-HIT and blast2cap3 programs. Open reading frames and proteins were predicted using BLASTX searches and a findorf algorithm.

2013-06-11 | E-MTAB-5037 | biostudies-arrayexpress

Pseudogene RNAseq

Project description:RNA sequencing to validate findings of somatic pseudogenes acquired during cancer development

2016-05-17 | E-ERAD-223 | biostudies-arrayexpress

Hordeum vulgare strain:landrace Transcriptome or Gene expression

Project description:In the present study, we investigated the transcriptome features during hulless barley grain development. Using Illumina paired-end RNA-Sequencing, we generated two data sets of the developing grain transcriptomes from two hulless barley landraces.

2014-06-19 | E-MTAB-4307 | biostudies-arrayexpress

Arabidopsis thaliana CPL3 RNASeq

Project description:To determine transcriptome dynamics regulated by CPL3 during elicitation of immune responses, we performed RNA sequencing (RNA-seq) analysis of Col-0 WT and cpl3-3 mutant treated without or with flg22 for 30 min.

2014-12-05 | E-MTAB-4397 | biostudies-arrayexpress

In vivo RNA interference RNAi target sequencing of Trypanosoma brucei

Project description:A direct comparison of RNAi in vitro with RNAi in vivo is being performed using RNA interference (RNAi) target sequencing (RIT-Seq) of Trypanosoma brucei to identify all genes specifically required for growth in vivo (the infectome). Assembly of the bloodstream-form T. brucei RNAi library and the RNAi target sequencing (RIT-seq) approach in African trypanosomes were reported previously in Alsford, S. et al. High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome. Genome Res 21, 915-924, 264 doi:gr.115089.110 [pii] 265 10.1101/gr.115089.110 (2011) and Alsford,S et al. High-throughput decoding of antitrypanosomal drug efficacy and resistance. Nature 482, 232236 doi:10.1038/nature10771 (2012). This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/

2014-01-21 | E-ERAD-110 | biostudies-arrayexpress

Zea mays Transcriptome or Gene expression

Project description:We explored the gene expression profiles of developing maize kernel by RNA sequencing. Our purpose was to explore the sequence diversity across the inbred lines, especially in the gene regions, and to discover the gene regulatory networks employed in immature maize kernels.

2013-12-10 | E-MTAB-4239 | biostudies-arrayexpress

Gene expression profiles of the tuberous root development at seedling stages in turnips

Project description:In this study, we analyzed the expression profiles of both mRNAs and miRNAs in tuberous roots at an early stage before cortex splitting (ES), cortex splitting stage (CSS), and secondary root thickening stage (RTS) in turnip based on high-throughput sequencing technology.

2015-09-23 | E-MTAB-5073 | biostudies-arrayexpress

Transcriptome response of maize (B73) shoot-borne root stele to local high nitrate stimulation

Project description:In this study RNA-sequencing was used to monitor gene expression changes in stele tissue of maize (Zea mays L.) shoot-borne roots in response to local high nitrate stimulation to gain a better understanding of the mechanisms underlying nitrate signal and lateral root development.M

2015-10-08 | E-MTAB-4253 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data