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

A cross platform genome wide comparison of the relationship of promoter DNA methylation to gene expression

ABSTRACT: This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

ORGANISM(S): Homo sapiens

SUBMITTER: Jeffrey Plume

PROVIDER: E-GEOD-34779 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

DNA methylation data from human lymphoblasts [NimbleGen]

Project description:DNA methylation profiling of IAS subjects Lymphoblasts RNA isolated from Iowa Adoption Study participants to compare the relationship between DNA methylation and gene expression on a genome-wide scale

2012-12-28 | E-GEOD-34778 | biostudies-arrayexpress

Expression data from human lymphoblasts [Affymetrix]

Project description:Transcriptional profiling of IAS subjects Lymphoblasts RNA isolated from Iowa Adoption Study participants to compare the relationship between DNA methylation and gene expression on a genome-wide scale

2012-12-28 | E-GEOD-34776 | biostudies-arrayexpress

DNA methylation variation in Arabidopsis has a genetic basis and appears to be involved in local adaptation

Project description:Here we investigate DNA methylation variation in Swedish Arabidopsis thaliana accessions, demonstrating that methylation of transposable elements is temperature sensitive and associated with genetic polymorphism in both cis and trans, whereas gene body methylation is highly correlated with climate of origin and associated with genetic polymorphism in trans that shows evidence of local adaptation. While genome-wide surveys of naturally occurring DNA methylation have been published previously, the degree of genetic control revealed here is unprecedented. Furthermore, the observation that DNA methylation is associated with climate, and is apparently adaptively important, is completely novel. Bisulfite sequencing of 152 Swedish Arabidobsis accessions grown at 10 C and 121 grown at 16 C

2015-03-28 | E-GEOD-54292 | biostudies-arrayexpress

Identification of genes activated under CoCl2 treatment in an Sp1 dependent manner and under hypoxia without serum condition in an ovarian cancer cell line

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2015-04-01 | E-GEOD-55565 | biostudies-arrayexpress

Genome and transcriptome sequencing of lung cancers reveal diverse mutational and splicing events [array component]

Project description:Lung cancer is a highly heterogeneous disease in terms of both underlying genetic lesions and response to therapeutic treatments. We performed deep whole genome sequencing and transcriptome sequencing on 19 lung cancer cell lines and 3 lung tumor/normal pairs (provisional dbGaP accession number; phs000299.v2.p1). Overall, our data show that cell line models exhibit similar mutation spectra to human tumor samples. Taken together, these data present a comprehensive genomic landscape of a large number of lung cancer samples and further demonstrate that cancer specific alternative splicing is a widespread phenomenon that has potential utility as therapeutic biomarkers. Nineteen non-small cell lung cancer cell lines were assayed for genotype, copy number and LOH using Illumina Omni2.5-4 arrays, GenomeStudio V2011.1, and a modified version of the PICNIC (PMID 19837654) algorithm.

2012-09-26 | E-GEOD-40908 | biostudies-arrayexpress

Identification of genes activated under CoCl2 treatment in an Sp1 dependent manner in an ovarian cancer cell line

Project description:To identify genes activated under CoCl2 treatment of a cancer cell line in an Sp1 dependent manner, we performed cDNA microarray analysis with an ovarian cancer cell line, in which Sp1 is silenced via RNA interference. Cells were transfected with scramble or Sp1 siRNA and cultured for 40 h. Cells were further cultured for 4 h under 0.5 mM CoCl2 exposure. Total RNA was isolated for cDNA microarray analysis.

2015-04-01 | E-GEOD-55563 | biostudies-arrayexpress

Epigenome analysis of human epidermal and dermal samples with aging and sun exposure

Project description:Genome wide DNA methylation profiling of epidermal and dermal samples obtained from sun-exposed and sun-protected body sites from younger (<35 years old) and older (>60 years old) individuals. The Illumina Infinium 450k Human DNA methylation Beadchip was used to obtain DNA methylation profiles across approximately 450,000 CpGs in dermal and epidermal samples. Samples included 10 younger sun protected dermal samples, 10 younger sun exposed dermal samples, 10 older sun protected dermal samples, 10 older sun exposed dermal samples, 9 younger sun protected epidermal samples, 9 younger sun exposed epidermal samples, 10 older sun protected epidermal sample, 10 older sun exposed epidermal samples. Bisulphite converted DNA from the 78 samples were hybridized to the Illumina Infinium 450k Human Methylation Beadchip.

2015-03-23 | E-GEOD-51954 | biostudies-arrayexpress

Identification of genes activated in cancer cells cultured under hypoxia and serum-free condition

Project description:To identify genes activated under hypoxia (1%O2) and serum-free treatment of a cancer cell line, we performed cDNA microarray analysis with an ovarian cancer cell line, OVSAYO. Cells were cultured under normoxia /hypoxia (1%O2) and serum-plus/serum-minus conditions for 16 hours. Total RNA was isolated for cDNA microarray analysis.

2015-04-01 | E-GEOD-55564 | biostudies-arrayexpress

TYROSINE MODIFICATION ANALYSIS OF FUSION GLYCOPROTEIN FROM HUMAN RESPIRATORY SYNCYTIAL VIRUS A2

Project description:Map the location of the dityrosine bond in the purified crosslinked sample(DT-preF) by LC-ESI-MS/MS.The uncrosslinked protein (preFC) was used for comparison.

2024-03-05 | PXD048897 | Pride

Expression analysis of Clostridium difficile wild type and fur (ferric uptake regulator) mutant in high iron.

Project description:Investigation of whole genome gene expression level changes in a Clostridium difficile fur (ferric uptake regulator) mutant, compared to the wild type strain 630 erm. The fur mutant analyzed in this study is further described in Ho and Ellermeier (2015) J. Bacteriology A microarray study using total RNA recovered from three separate wild type cultures of Clostridium difficile 630 erm strain and three separate cultures of a fur mutant strain (ltrA::ermR) were grown in Tryptone-Yeast Extract medium containing 0.25 mM ferric chloride . Each chip measures the expression level of 3,786 of the 3,787 open reading frames of the C. difficile 630 genome with 18 probes (60 oligomers each) for each gene.

2015-05-27 | E-GEOD-69218 | 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