Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

39 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcription profiling by array of human and Arabidopsis cells to develop a pipeline for data processing of Agilent oligonucleotide expression arrays

ABSTRACT: From analysis of error and reproducibility to a pipeline for data processing of Agilent oligonucleotide expression arrays.

ORGANISM(S): Arabidopsis thaliana

DISEASE(S): acute myelomonocytic leukaemia

SUBMITTER: Mahdad Noursadeghi

PROVIDER: E-TABM-942 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

Error, reproducibility and sensitivity: a pipeline for data processing of Agilent oligonucleotide expression arrays.

Chain Benjamin B Bowen Helen H Hammond John J Posch Wilfried W Rasaiyaah Jane J Tsang Jhen J Noursadeghi Mahdad M

BMC bioinformatics 20100624

<h4>Background</h4>Expression microarrays are increasingly used to obtain large scale transcriptomic information on a wide range of biological samples. Nevertheless, there is still much debate on the best ways to process data, to design experiments and analyse the output. Furthermore, many of the more sophisticated mathematical approaches to data analysis in the literature remain inaccessible to much of the biological research community. In this study we examine ways of extracting and analysing ...[more]

PMID: 20576120

Similar Datasets

Transcription profiling of human monocyte-derived macrophages infected with HIV-1 or stimulated with interferon-beta, interferon-gamma or lipopolysaccharide

Project description:Transcriptional profiling of HIV-1 infected and that of IFNbeta, IFNgamma or LPS stimulated human monocyte derived macrophages.

2009-09-01 | E-MEXP-2032 | biostudies-arrayexpress

Transcription profiling of human monocyte-derived macrophages infected with HIV-1 or uninfected and stimulated with E. coli lipopolysaccharide

Project description:Whole genome expression profiling of HIV-1 infected and uninfected monocyte-derived macrophages

2009-01-01 | E-MEXP-1904 | biostudies-arrayexpress

Inhibition of macrophage IL10 responses by HIV 1

Project description:Inhibition of macrophage IL10 responses by HIV 1

2015-01-31 | E-TABM-1163 | biostudies-arrayexpress

Delta lgt paper

Project description:We have used a lipoprotein-deficient mutant Streptococcus pneumoniae strain, delta lgt, to investigate the role of lipoproteins during inflammatory responses to live S. pneumoniae.

2015-01-31 | E-MTAB-1541 | biostudies-arrayexpress

Paracrine activation of hCMEC/D3 cells by LPS-stimulated macrophages

Project description:Transcriptional profiling of hCMEC/D3 endothelial cells after six hour incubation with conditioned media from unstimulated or LPS-stimulated monocyte derived macrophages

2015-12-31 | E-MTAB-3692 | biostudies-arrayexpress

Transcription profiling by array of pro-inflammatory phenotype of recently isolated human alveolar macrophages

Project description:Human alveolar macrophages and monocyte derived macrophages were compared using genome-wide transcriptional profiling.

2012-09-19 | E-TABM-1206 | biostudies-arrayexpress

Transcriptional profiling of in vivo immune responses to mycobacteria using the tuberculin skin test

Project description:Transcriptional profiling of biopsies from tuberculin skin test sites was performed to investigate the interaction of complex cellular and molecular networks at the interface between innate and adaptive immunity which coordinate anti-mycobacterial responses in vivo.

2012-05-13 | E-TABM-1157 | biostudies-arrayexpress

Neutrophil-derived pro-inflammatory cytokine response and degranulation in function of time and dose of LPS treatment.

Project description:The purpose of the present study was to elucidate in more details the molecular mechanisms of neutrophil-mediated inflammation. We therefore investigated the time-dependent stimulatory potential of LPS from Escherichia coli on cytokine response in neutrophil-like HL-60 cells. <br><br>To get a general overview on the total mRNA changes in DMSO-differentiated HL-60 cells, we performed whole-transcript analysis of LPS-stimulated dHL-60 cells after 2h and 6h of LPS treatment. The samples were collected from three independent experiments from three different passages in cell culture. Non-stimulated dHL-60 cells served as control. We identified the differentially expressed cytokine genes implicated in the human inflammatory response and prominent for their role in neutrophil-mediated inflammatory processes.

2014-12-17 | E-MTAB-1393 | biostudies-arrayexpress

The effect of bacterial capsule on macrophage transcriptional responses to Streptococcus Pneumoniae.

Project description:Streptococcus Pneumoniae capsule is a major virulence factor. The capsule is known to inhibit complement fixation and phagocytes, but its impact on innate immune responses is not known. To address this question, we compared transcriptional responses by human monocyte derived macrophages in responses to wild type S. pneumoniae with isogenic mutant bacteria lacking their capsule. We conducted these experiments with and without macrophage pretreatment with cytochalasin D to evaluate the impact of phagocytosis, and we also made comparisons to mutant S.pneumoniae lacking bacterial lipoprotein which is known to be necessary for maximal innate immune responses.

2018-04-02 | E-MTAB-5894 | biostudies-arrayexpress

Chicken erythrocytes stimulated with LPS, PGN and Poly(I:C)

Project description:Erythrocytes represent the most abundant cell type of the bloodstream in all vertebrates. The principal feature that differenciates erythrocytes of non-mammals is that unlike mammals they mantain the nucleus in their terminal differentiation. While the main function associated to erythrocytes is the oxygen and carbon dioxide transport, some other functions, no less important, have been attributed to these cells. The focus of this study was to investigate the response of cultured chicken erythrocytes to bacterial lipopolysaccharide (LPS), bacterial peptidoglycan (PGN) and to the analog viral dsRNA Poly(I:C) using a comercial microarray platform from Agilent. Chicken erythrocytes were isolated from blood by twice Ficoll 1.007 density gradient centrifugations. For primary cell culture, erythrocytes were resuspended in DMEM (PAA Laboratories) supplemented with 10% heat-inactivated fetal bovine serum (FBS, PAA Laboratories) and the antibiotic Primocin (100 μg/ml, Invivogen) at a density of 7.5x106 cells/ml in six well cell culture plates (NUNC) and cultured at 37ºC and 5% CO2. Erythrocytes were stimulated with LPS from E. coli (serotype 0111:B4, Sigma) and Poly(I:C) (Invivogen) at 50 μg/ml, and with peptidoglycan from E.coli (0111:B4, Invivogen) at 5 μg/ml. All culture plates were incubated for 12h. Total RNA was extracted from the cultures using 1 ml of Tri Reagent (Sigma) following the manufacturer’s instructions with minor modifications. Quantity and integrity was analyzed by Nanodrop1000 (ThermoScientific) and Bioanalyzer 2100 (Agilent Technologies) respectively. Three biological replicates were used.

2011-11-22 | E-GEOD-33813 | 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