Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

56 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Group A Streptococcus Gene Expression in Humans with Pharyngitis Using a Microarray

ABSTRACT: This study represents the first in vivo genome wide analysis of gene epxression of Group A Streptococcus (GAS) in humans with pharyngitis. The micorarray used is a custom microarray that relies on an electrochemical reaction as the measured signal rather than flourescence. Distinct clusters of gene expression were discovered and analyzed. A functional analysis examining differences and similarities between the clusters was performed. Samples were taken from pediatric patients who had received a throat swab as part of their clinical care for evaluating pharyngitis. Eleven samples that were culture postive for GAS were used along with 3 samples from subjects who were GAS culture negative. The microarray was a composite comprised of 12,000 probes, representing 2724 GAS open reading frames belonging to serotypes M1, M3, M4, M12, and M28. There were 1671 probe sets that were homologous for the M1 serotype and represented over 95% of the total predicted coding region. Probe sets were 30-40mers in length and were selected using a Combimatrix probe selection algorithm taking into account gene (>90% BLAST score) and serotype specificity, Tm, hairpins and GC content. In addition, 70 Combimatrix built in probes were used as negative controls for background subtraction.

ORGANISM(S): Homo sapiens

SUBMITTER: Luis Perez

PROVIDER: E-GEOD-22436 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Promiscuity of enhancer, coding and non-coding transcription functions in ultraconserved sequence elements

Project description:The manuscript by D. Licastro and colleagues “Promiscuity of enhancer, coding and non-coding transcription functions in ultraconserved sequence elements” presents an overview of experimental and computational approaches employed by the authors to perform a multi-facet characterization of ultraconserved elements (UCEs). The authors present an interesting analysis where they investigate the transcription of UCEs in mouse development at different stages by conductin an microarray experiment. Some of these results are further verified by RT-PCR. 12 Samples, 4 groups 3 samples per group.

2010-06-16 | E-GEOD-19371 | biostudies-arrayexpress

Transcriptional analysis of oxidative-stressed bean nodules elicited by Rhizobium etli expressing an heterologous globin (VHb)

Project description:A wide range of environmental stresses lead to an elevated production of reactive oxygen species (ROS) in plant cells thus resulting in oxidative stress. The biological nitrogen fixation in the legume - Rhizobium symbiosis is at high risk of damage from oxidative stress. Common bean (Phaseolus vulgaris) active nodules exposed to the herbicide Paraquat (1,1 '-Dimethyl-4, 4'-bipyridinium dichloride hydrate) that generates ROS accumulation, showed a reduced nitrogenase activity and ureide content. We analyzed the global gene response of stressed nodules using the Bean CombiMatrix Custom Array 90K, that includes probes from some 30,000 expressed sequence tags (EST). The experimental design, based on circular hybridizations, included four conditions as, with two independent biological replicates and three technical replicates for each conditions. A total of 2418 differentially expressed genes (DEG) were identified among the different combinations. Our results showed good correspondence among both the GO term and the MapMan enrichment analyses highlighting DEG from PQ-treated nodules assigned to the functional super-categories: trans-membrane transport, hormone signal transduction, stress response, and regulation. In this work we analyzed the effect of VHb-expressing R. etli CE3 in the symbiosis of common bean plants under oxidative stress experimentally generated by the addition of PQ for 48 hours. We analyzed the transcript profile, via microarray hybridization, using the Bean CombiMatrix Custom Array 90K, that includes probes from some 30,000 expressed sequence tags (EST).

2016-06-15 | E-GEOD-83324 | biostudies-arrayexpress

Transcript Profiling of the Common Bean - Rhizobium Symbiosis under Oxidative Stress

Project description:A wide range of environmental stresses lead to an elevated production of reactive oxygen species (ROS) in plant cells thus resulting in oxidative stress. The biological nitrogen fixation in the legume - Rhizobium symbiosis is at high risk of damage from oxidative stress. Common bean (Phaseolus vulgaris) active nodules exposed to the herbicide Paraquat (1,1 '-Dimethyl-4, 4'-bipyridinium dichloride hydrate) that generates ROS accumulation, showed a reduced nitrogenase activity and ureide content. We analyzed the global gene response of stressed nodules using the Bean CombiMatrix Custom Array 90K, that includes probes from some 30,000 expressed sequence tags (EST). A total of 4,280 ESTs were differentially expressed in oxidative stressed bean nodules; of these 2,218 were repressed. These genes were grouped in 44 different biological processes as defined by Gene Onthology. Analysis with the PathExpress bioinformatic tool, adapted for bean, identified five significantly repressed metabolic path This work presents the transcriptional profile of bean nodules, induced by strain Rhizobium tropici CIAT 899, under oxidative stress, generated experimentally by adding the herbicide Paraquat (1,1 '-Dimethyl-4, 4'-bipyridinium dichloride hydrate) for 48 hours. We analyzed the transcript profile, via microarray hybridization, using the Bean CombiMatrix Custom Array 90K, that includes probes from some 30,000 expressed sequence tags (EST). A total of 4,280 ESTs were differentially expressed in oxidative stressed bean nodules; of these 2,218 were repressed.

2012-06-30 | E-GEOD-37638 | biostudies-arrayexpress

The Detection and Subtyping of Seasonal Influenza A H1N1 Isolates Using a Microarray

Project description:An influenza A microarray was used to type influenza A H1N1 specimens collected in Washington State and the results compared with identification by both culture and real time RT PCR. The microarray was more sensitive than conventional influenza testing. Cluster analysis of the microarray data discriminated specimens into distinct clades. Specimens from two pediatric decedents formed a unique clade upon H1 analysis. Keywords: Comparative genome study; Influenza A strains; Subtype H1N1 23 influenza A H1N1 specimens collected in Washington State were subtyped by microarray and data was compared with identification by both culture and real time RT PCR.

2008-10-31 | E-GEOD-12226 | biostudies-arrayexpress

Identification of responsive probes for mRNA transcripts of the pig (S. scrofa) genome

Project description:Pig mRNAs Ensembl transcripts (Ver. 56) and UniGene (Ver. 38) sequences were used to produce a dedicated microarray platform to analyze mRNAs gene expression. Based on sequence similarity we rejected UniGene features that overlapped more than 40% with an Ensembl transcript. After this filter we obtained 40,267 UniGene clusters and 19,603 Ensembl transcripts (protein coding + pseudogenes + retrotransposed elements). Starting from these sequences, the microarray probes were computed using 6 different algorithms (YODA, Picky, ArrayOligoSelector, OligoPicker, OligoFaktory, CommOligo). Two probes in the most 3M-bM-^@M-^Y end was tested for their specificity and performance. For any transcript with a replicated tested probe, we used the most responsive and specific in an hybridization trial with a pool of mRNAs from 20 tissues to construct the definitive gene expression microarray for the pig. Definitive 90K Combimatrix gene expression microarrays were composed by 17,048 replicated probes and 963 not replicated specific for the Ensembl transcripts, 11,363 replicated probes specific for the UniGene clusters of length comprised between 778 nt and 1,348 nt, and 28,790 single probes specific for the remaining UniGene clusters (GEO: GPL13259). Microarray was probed with a pool of RNAs from 20 different tissues (superior vena cava, adipose tissue, lung, spleen, stomach, liver, intestine, kidney, descending aorta, left atrium, left ventricle, skeletal muscle, pulmonary aorta, skin, tongue, ascending aorta, arterial white cells blood, venal white cells blood, coronary valve, lymph node). Moreover each tissue sample was performed by a pool of 3 different adult pigs because they was not inbred.

2014-03-31 | E-GEOD-28636 | biostudies-arrayexpress

Transcription profiling by array of Enterococcus faecium grown in open circuit (control) and closed circuit (current collection) to observe the difference in extracellular electron transfer (EET) mechanisms.

Project description:Enterococcus faecium was grown in open circuit (control) and closed circuit (current collecting) to observe the difference in extracellular electron transfer (EET) mechanisms. mRNA was extracted, amplified and used on Combimatrix custom arrays to obtain a

2010-07-08 | E-MTAB-268 | biostudies-arrayexpress

YBT-1520-Combimatrix

Project description:We investigated the virulence and pathogenic related gene expression by performing the transcriptomics analysis of B. thuringiensis serovar kurstaki strain YBT-1520 over a time course, using CombiMatrix (microarray) technique.

2015-12-31 | E-MTAB-2162 | biostudies-arrayexpress

Bifidobacterium bifidum PRL2010 actively changes the expression profiles of mouse

Project description:We studied the global transcription profiling of mouse upon colonization with Bifidobacterium bifidum PRL2010 by using DNA microarrays. Two groups of mice consisting each of two animals were orally inoculated with either 109 CFU of PRL2010 cells (test strain) or water (control). Animals were 3 months old female BALB/c mice. Bacterial colonization was established by five consecutive daily administrations using a micropipette tip placed immediately behind the incisors.

2013-11-19 | E-GEOD-48495 | biostudies-arrayexpress

Transcription profiling by array of Pseudomonas aeruginosa was grown in open circuit (control) and closed circuit (current collecting) to observe the difference in extracellular electron transfer (EET) mechanisms.

Project description:Pseudomonas aeruginosa was grown in open circuit (control) and closed circuit (current collecting) to observe the difference in extracellular electron transfer (EET) mechanisms. mRNA was extracted, amplified and used on Combimatrix custom arrays to obtain

2010-07-08 | E-MTAB-269 | biostudies-arrayexpress

Transcription profiling by array of Shewanella oneidensis was grown in open circuit (control) and closed circuit (current collecting) to observe the difference in extracellular electron transfer (EET) mechanisms.

Project description:Shewanella oneidensis was grown in open circuit (control) and closed circuit (current collecting) to observe the difference in extracellular electron transfer (EET) mechanisms. mRNA was extracted, amplified and used on Combimatrix custom arrays to obtain an expression profile. Analysis was performed using R.

2010-07-08 | E-MTAB-266 | 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