Investigation Title Transcription profiling of human HUVEC cell line infected with Neisseria meningitidis wild type and mutants vs uninfected sampled at 3 time points reveals meningococcal adhesion suppresses proapoptotic gene expression and promotes expression of genes supporting early embryonic and cytoprotective signaling of human endothelial cells. Comment[Submitted Name] Signaling of Neisseria meningitidis MC58 mutants to primary human umbilical vein endothelial cells (HUVEC) Experimental Design time_series_design disease_state_design co-expression_design transcription profiling by array Experimental Design Term Source REF mo mo mo EFO Comment[ArrayExpressReleaseDate] 2007-10-26 Comment[SecondaryAccession] GSE4646 Comment[AEMIAMESCORE] 5 Comment[SecondaryAccession] GDS2333 Comment[SecondaryAccession] GDS2332 Comment[ArrayExpressAccession] E-GEOD-4646 Comment[MAGETAB TimeStamp_Version] 2010-08-05 16:52:44 Last Changed Rev: 13058 Experimental Factor Name Time DiseaseState Experimental Factor Type time disease_state Experimental Factor Term Source REF Person Last Name Basler Person First Name Marek Person Mid Initials Person Email basler@biomed.cas.cz Person Phone Person Fax Person Address Laboratory of Molecular Biology of Bacterial Pathogens, Cell and Molecular Microbiology Division, Institute of Microbiology, Czech Academy of Sciences, Videnska 1083, Prague 4, CZ-142 20, Czech Republic Person Affiliation Institute of Microbiology, Czech Academy of Sciences Person Roles submitter Person Roles Term Source REF The MGED Ontology Quality Control Type Quality Control Term Source REF Replicate Type Replicate Term Source REF Normalization Type Normalization Term Source REF Date of Experiment Public Release Date 2007-10-26 PubMed ID 16958858 Publication DOI 16958858 Publication Author List Irena Linhartova, Marek Basler, Jeffrey Ichikawa, Vladimir Pelicic, Radim Osicka, Stephen Lory, Xavier Nassif, Peter Sebo Publication Title Meningococcal adhesion suppresses proapoptotic gene expression and promotes expression of genes supporting early embryonic and cytoprotective signaling of human endothelial cells. Publication Status journal_article Publication Status Term Source REF The MGED Ontology Experiment Description Time courses of gene expression profiles of primary human umbilical vein endothelial cells (HUVEC) during infection with piliated and adherent wild-type (WT), frpC/frpA-deficient mutant, or the non-adherent (?pilD) Neisseria meningitidis MC58 bacteria defective in production of the type IV pilus, were analyzed respectively. Total RNA isolated from uninfected HUVEC (reference) and HUVEC after 1, 4 or 6 hours of infection with N. meningitidis mutants was labeled according to standard Affymetrix protocol and hybridized to HG-U133A GeneChips. Data were analyzed by Robust Multi-array Analysis algorithm. For every condition at least two biological replicates were analyzed, totally representing 23 Affymetrix GeneChips. Protocol Name P-GEOD-4646-18 P-GEOD-4646-16 P-GEOD-4646-17 P-GEOD-4646-12 P-GEOD-4646-15 P-GEOD-4646-10 P-GEOD-4646-19 P-GEOD-4646-13 P-GEOD-4646-11 P-GEOD-4646-14 P-GEOD-4646-3 P-GEOD-4646-1 P-GEOD-4646-2 P-GEOD-4646-4 P-GEOD-4646-5 P-GEOD-4646-7 P-GEOD-4646-6 P-GEOD-4646-8 P-AFFY-6 Protocol Type grow grow grow grow grow grow grow grow grow grow specified_biomaterial_action specified_biomaterial_action specified_biomaterial_action specified_biomaterial_action nucleic_acid_extraction labeling labeling hybridization feature_extraction Protocol Description Confluent monolayers of HUVECs in 9 cm Petri dishes were infected with Neisseria meningitidis MC58 delta pilD (MOI=10) and cultivated in RPMI medium, 5% CO2, humidified atmosphere, 37°C, 6 hours Confluent monolayers of HUVECs in 9 cm Petri dishes were infected with Neisseria meningitidis MC58 delta pilD (MOI=10) and cultivated in RPMI medium, 5% CO2, humidified atmosphere, 37°C, 1 hour Confluent monolayers of HUVECs in 9 cm Petri dishes were infected with Neisseria meningitidis MC58 delta pilD (MOI=10) and cultivated in RPMI medium, 5% CO2, humidified atmosphere, 37°C, 4 hours Confluent monolayers of HUVECs in 9 cm Petri dishes were cultivated in RPMI medium, 5% CO2, humidified atmosphere, 37°C, 6 hours Confluent monolayers of HUVECs in 9 cm Petri dishes were infected with Neisseria meningitidis MC58 WT (MOI=10) and cultivated in RPMI medium, 5% CO2, humidified atmosphere, 37°C, 6 hours Confluent monolayers of HUVECs in 9 cm Petri dishes were cultivated in RPMI medium, 5% CO2, humidified atmosphere, 37°C, 1 hour Confluent monolayers of HUVECs in 9 cm Petri dishes were infected with Neisseria meningitidis MC58 delta frpC/frpA (MOI=10) and cultivated in RPMI medium, 5% CO2, humidified atmosphere, 37°C, 4 hours Confluent monolayers of HUVECs in 9 cm Petri dishes were infected with Neisseria meningitidis MC58 WT (MOI=10) and cultivated in RPMI medium, 5% CO2, humidified atmosphere, 37°C, 1 hour Confluent monolayers of HUVECs in 9 cm Petri dishes were cultivated in RPMI medium, 5% CO2, humidified atmosphere, 37°C, 4 hours Confluent monolayers of HUVECs in 9 cm Petri dishes were infected with Neisseria meningitidis MC58 WT (MOI=10) and cultivated in RPMI medium, 5% CO2, humidified atmosphere, 37°C, 4 hours Monolayers of HUVECs in 9 cm Petri dishes infected with Neisseria meningitidis MC58 delta pilD were washed and collected into Trizol by cell-scraper Monolayers of HUVECs in 9 cm Petri dishes were washed and collected into Trizol by cell-scraper Monolayers of HUVECs in 9 cm Petri dishes infected with Neisseria meningitidis MC58 WT were washed and collected into Trizol by cell-scraper Monolayers of HUVECs in 9 cm Petri dishes infected with Neisseria meningitidis MC58 delta frpC/frpA were washed and collected into Trizol by cell-scraper Trizol extraction of total RNA was performed according to the manufacturer's instructions. Total RNA was purified on RNeasy minicolumns (Qiagen) and by NaOAc/ethanol precipitation. Biotinylated cRNA were prepared according to the standard Affymetrix protocol. Biotinylated cRNA were prepared according to the standard Affymetrix protocol Following fragmentation, cRNA was hybridized for 16 hr at 45C on Affymetrix Human Genome HG-U133A GeneChip. GeneChips were washed and stained in the Affymetrix Fluidics Station. Title: Affymetrix CEL analysis. Description: Protocol Parameters Protocol Hardware Protocol Software MicroArraySuite 5.0 Protocol Contact Protocol Term Source REF SDRF File E-GEOD-4646.sdrf.txt Term Source Name mo The MGED Ontology ArrayExpress mo EFO The MGED Ontology Term Source File http://mged.sourceforge.net/ontologies/MGEDontology.php http://mged.sourceforge.net/ontologies/MGEDontology.php http://www.ebi.ac.uk/arrayexpress http://mged.sourceforge.net/ontologies/MGEDontology.php http://www.ebi.ac.uk/efo/ http://mged.sourceforge.net/ontologies/MGEDontology.php Term Source Version