Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Re-analysis by microarray using cDNA target of samples from psoriasis patients enrolled in an etanercept trial

ABSTRACT: cDNA and cRNA hybridization technologies have different, probe-specific sensitivities. We used samples from an etanercept trial (GSE11903) to explore in a real-life setting the uniqueness of each platform. We obtained total RNA for a subset of the samples in GSE11903 from Jim Krueger and generated expression profiles using labeled cDNA target. From 14 patients, available base-line lesional and non-lesional skin biopsy pairs as well as post-dose samples were analyzed. All the samples were run on Affymetrix HU133 Plus 2.0 microarrays.

ORGANISM(S): Homo sapiens

SUBMITTER: Jeannette Bigler

PROVIDER: E-GEOD-41663 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

Cross-study homogeneity of psoriasis gene expression in skin across a large expression range.

Bigler Jeannette J Rand Hugh A HA Kerkof Keith K Timour Martin M Russell Christopher B CB

PloS one 20130104 1

<h4>Background</h4>In psoriasis, only limited overlap between sets of genes identified as differentially expressed (psoriatic lesional vs. psoriatic non-lesional) was found using statistical and fold-change cut-offs. To provide a framework for utilizing prior psoriasis data sets we sought to understand the consistency of those sets.<h4>Methodology/principal findings</h4>Microarray expression profiling and qRT-PCR were used to characterize gene expression in PP and PN skin from psoriasis patients ...[more]

PMID: 23308107

Similar Datasets

Gene expression profiling in psoriatic lesional and non-lesional skin [brodalumab treatment]

Project description:To explore the psoriasis phenotype and pathways involved in psoriasis, we characterized gene expression in lesional and non-lesional skin from psoriasis patients. Furthermore, we explored the effects of various doses of brodalumab on lesional skin over time. From each of the 25 psoriasis patients, we obtained two pre-dose biopsies, one from a lesion and the other from non-lesional skin in the same general body geography, and two post-dose biopsies. Total RNA was extracted from 6mm punch biopsies that were split in half. A total of 99 samples were run on Affymetrix HU133 Plus 2.0 microarrays. There was no paired non-lesional sample for 'T_lesional_pre-dose' (skn55789).

2014-03-31 | E-GEOD-53552 | biostudies-arrayexpress

Gene expression profiling in psoriatic lesional and non-lesional skin [Set 1]

Project description:To explore the psoriasis phenotype, we characterize gene expression in lesional and non-lesional skin from psoriasis patients. We extracted total RNA from 5mm punch biopsies taken from 14 psoriatic patients. From each patient, we obtained two biopsies, one from a lesion and the other from non-lesional skin in the same general body geography. A total of 28 samples were run on Affymetrix HU133 Plus 2.0 microarrays.

2013-01-28 | E-GEOD-34248 | biostudies-arrayexpress

Gene expression profiling in psoriatic lesional and non-lesional skin [Set 2]

Project description:To explore the psoriasis phenotype and pathways involved in psoriasis, we characterized gene expression in lesional and non-lesional skin from psoriasis patients. From each of the 24 psoriasis patients, we obtained two biopsies, one from a lesion and the other from non-lesional skin in the same general body geography. Total RNA was extracted from 6mm punch biopsies that were split in half. A total of 48 samples were run on Affymetrix HU133 Plus 2.0 microarrays.

2013-01-28 | E-GEOD-41662 | biostudies-arrayexpress

Comparison of Gene Expression in Psoriatic Skin from Different Sources

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

2013-01-28 | E-GEOD-41664 | biostudies-arrayexpress

Effect of rBTNL2.Fc co-stimulation on murine CD4+ cells

Project description:Naïve T cell activation involves at least two signals from an antigen presenting cell (APC), one through the T cell receptor via interaction with APC peptide-MHC complexes and a second through interaction of CD28 with APC B7 ligands. Following activation, T cells up-regulate a host of other membrane-bound costimulatory molecules which can either promote or inhibit further T cell maturation and proliferation. In some cases, it is necessary to attenuate T cell activation to prevent deleterious inflammation, and inhibitory members of the B7/Butyrophilin family of ligands have evolved to balance the strong stimuli the activating B7 ligands confer. Human genetic association and in vitro studies have implicated one such ligand, BTNL2, in controlling inflammation at mucosal surfaces. Here we show that recombinant mouse BTNL2 modifies B7/CD28 signaling to promote expression of Foxp3, a transcription factor necessary for murine Treg development and function. BTNL2 blocks Akt-mediated inactivation of Foxo1, a transcription factor necessary for Foxp3 expression. Immunophenotyping and gene profiling reveal that BTNL2-induced Treg share many properties with natural Treg, and in vivo they suppress enteritis induced by mouse effector T cells. These findings describe a mechanism by which environmental antigen-driven formation of Treg may be orchestrated by APC expressing specific modulators of costimulatory signals. CD4+CD25- cells isolated from spleen were stimulated on plates coated with anti-mouse CD3 and human IgG (negative control), anti-mouse CD3, rB7-2, and IgG (positive control), and anti-mouse CD3, rB7-2, and rBTNL2 (experimental). Culturing was performed in duplicate for each condition.

2013-01-31 | E-GEOD-42385 | biostudies-arrayexpress

Gene array of human mammary epithelial cell HMEC transfected with miR-106a-3p mimic against transfected control mimic

Project description:Since a single miRNA can potentially target hundreds of genes. In parallel, to study the effect of the over-expression of miR-106a-3p on global gene expression patterns, we isolated total RNA from HMEC cells transfected with miR-106a-3p mimic and performed microarray analysis (HG-U133 Plus 2.0).

2018-03-28 | E-MTAB-6594 | biostudies-arrayexpress

Expression data from mouse lung treated with MACA, BSA or HBSS

Project description:We hypothesize that there is a set of differentially-expressed gene biomarkers that distinguishes the immune response associated with the induction of allergic sensitization from non-allergic immune responsiveness following a single exposure. The goal of this preliminary study was to identify potential biomarkers that differentiate the response to allergens vs non-allergens following an acute exposure in naïve individuals. We evaluated the gene transcriptional responses of mouse lungs following a single exposure to agents of high or low allergenicity or vehicle control. Female BALB/c mice received a single intratracheal aspiration exposure to Metarhizium anisopliae crude antigen (MACA) or bovine serum albumin (BSA) in Hank's Balanced Salt Solution (HBSS) or HBSS alone. RNA was isolated from lung tissue of 3-4 biological replicates from each treatment group at 3h and 12h post-treatment.

2010-03-07 | E-GEOD-18707 | biostudies-arrayexpress

Translation profiling of Drosophila after dietary restriction

Project description:Analysis of the translational changes induced upon DR in male Drosophila. Experiment Overall Design: 1-2 day old flies were transferred onto 4% or 0.25% YE food for 6 days. ~100 male flies were then ground and RNA was separated by size on a sucrose gradient and fractionated using a Teledyne density gradient fractionator and a polysome profile was produced by monitoring the abs at 252nm. RNA was then prepared from the low (1-4 ribosomes bound) and high (5 or more ribosomes bound) translation fractions. A translational index was then calculated for each mRNA. The changes in translational index upon DR were then evaluated. This was done in triplicate on individual biological replicates.

2009-10-09 | E-GEOD-16738 | biostudies-arrayexpress

Effect of Diabetes on Retinal Müller Cells

Project description:Rat Retinal Müller cells from diabetic rats (diabetes duration 6 months) compared to Rat Retinal Müller cells from healthy rats. Diabetes was induced by streptozotozine. Diabetic rats were treated with small doses of insulin to prevent catabolism. Keywords: ordered

2004-11-17 | E-GEOD-1979 | biostudies-arrayexpress

microRNA expression during ovine adult mammary gland development

Project description:The mammary gland undergoes extensive remodeling between the begin- ning of pregnancy and lactation; this involves cellular processes including cell proliferation, differentiation, and apoptosis, all of which are under the control of numerous regulators. To unravel the role played by miRNA, we describe here 47 new ovine miRNA cloned from mammary gland in early pregnancy displaying strong similari- ties with those already identified in the cow, human, or mouse. A microarray study of miRNA variations in the adult ovine mammary gland during pregnancy and lactation showed that 100 miRNA are regulated according to three principal patterns of expression: a de- crease in early pregnancy, a peak at midpregnancy, or an increase throughout late pregnancy and lactation. One miRNA displaying each pattern (miR-21, miR-205, and miR-200b) was analyzed by qRT- PCR. Variations in expression were confirmed for all three miRNA. Using in situ hybridization, we detected both miR-21 and miR-200 in luminal mammary epithelial cells when expressed, whereas miR-205 was expressed in basal cells during the first half of pregnancy and then in luminal cells during the second half. We therefore conclude that miR-21 is strongly expressed in the luminal cells of the normal mammary gland during early pregnancy when extensive cell prolif- eration occurs. In addition, we show that miR-205 and miR-200 are coexpressed in luminal cells, but only during the second half of pregnancy. These two miRNA may cooperate to maintain epithelial status by repressing an EMT-like program, to achieve and preserve the secretory phenotype of mammary epithelial cells. 5 samples for sheep and 5 samples for mouse

2013-01-04 | E-GEOD-32654 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

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