Investigation Title	Transcription profiling of human primary brain microvascular endothelial cell to investigate the effect of treatment with Plasmodium falciparum infected erythrocytes	
Comment[Submitted Name]	Effect of Plasmodium falciparum infected erythrocytes on primary human brain microvascular endothelial cell	
Experimental Design	unknown_experiment_design_type	transcription profiling by array	
Experimental Design Term Source REF		EFO	
Comment[SecondaryAccession]	GSE9861	
Comment[ArrayExpressReleaseDate]	2009-01-13	
Comment[AEMIAMESCORE]	4	
Comment[ArrayExpressAccession]	E-GEOD-9861	
Comment[MAGETAB TimeStamp_Version]	2010-08-09 16:22:57 Last Changed Rev: 13058	
Experimental Factor Name	
Experimental Factor Type	
Experimental Factor Term Source REF	
Person Last Name	Tripathi	
Person First Name	Abhai	
Person Mid Initials	K.	
Person Email	atripath@jhsph.edu	
Person Phone	
Person Fax	
Person Address	Sullivan, Molecular Microbiology, Johns Hopkins University School of Public Health, 615 N Wolfe St, Baltimore, 21231, India	
Person Affiliation	Johns Hopkins University School of Public Health	
Person Roles	submitter	
Person Roles Term Source REF	The MGED Ontology	
Quality Control Type	
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Date of Experiment	
Public Release Date	2009-01-13	
PubMed ID	
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Publication Title	
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Publication Status Term Source REF	
Experiment Description	Cerebral malaria is a multifactorial condition that begins with high numbers of infected erythrocytes binding to human brain endothelium without invasion into the brain. Here we investigated the global transcriptional gene response of primary human brain endothelial cells after incubation with high numbers of infected erythrocytes; High or low parasite binding phenotypes did not alter gene response. Predominate amongst signaling pathways were the NF-kB proinflammatory response. The inflammatory pathways were validated by direct measurement of proteins. This study delineates the strong inflammatory component of human brain endothelium contributing to cerebral malaria. Experiment Overall Design: Total of 8 samples (4 control and 4 treated) were analyzed. 4 control samples included two normal RBC control and two medium controls. 4 treated samples includes 2 exposed to low binding Pf-IRBC and 2 exposed to high binding Pf-IRBC (Pf-IRBC-P). Medium and RBC controls were finally used as four replicates of control and all four Pf-IRBC or Pf-IRBC-P exposed endothelial cells were used as 4 separate treated controls.	
Protocol Name	P-G9861-2	P-G9861-1	P-G9861-4	P-G9861-3	P-AFFY-6	
Protocol Type	specified_biomaterial_action	grow	nucleic_acid_extraction	labeling	feature_extraction	
Protocol Description	Before each experiment percoll enriched Pf-IRBCs (trophozoites) were stained with Giemsa and examined by light microscopy for quality controlFor all the studies the Pf-IRBC to HBMEC ratio was kept at 50:1 to cover the whole surface of monolayer and to mimic the conditions of brain sequestration. For controls the matched identical uninfected RBCs from the same donor used for parasite culture was maintained under the same conditions. For microarray studies HBMECs were grown to confluence in 6-well plate and then co-cultured with Pf-IRBCs and uninfected RBCs at 37 °C for another 6 hours. After incubation the culture-supernatants were aspirated carefully and stored at -70C for follow-up studies. Endothelial monolayers were then washed twice with ice-cold PBS and then immediately resuspended into 1 ml of Trizol reagent.	Cells were cultured in RPMI 1640 medium, supplemented with fetal calf serum (10%), Nu serum IV (10%), vitamins (1%), nonessential amino acids (1%), sodium pyruvate (1 mM) and L-glutamine (2 mM). The cells were maintained in T25 flasks (Corning Costar Corporation, Cambridge, MA) in a humid atmosphere at 37°C with 5% CO2. For microarray experiments and cytokine determinations (ELISA, Protein Array and BD Flex bead assay), the cells were used at < passage 6. For microarray experiments HBMEC was grown in collagen coated 6 well plates until cells achieved about 80-90 % confluence, then medium was changed to RPMI 1640 with 5% FBS one day before co-incubation with P. falciparum	Total RNA was extracted from cells homogenized in TRIZOL according to manufacturer's instructions.	5 ug total RNA was processed according to the Affymetrix Technical manual Rev5 protocol to generate biotinylated cRNA.	Title: Affymetrix CEL analysis. Description: 	
Protocol Parameters	
Protocol Hardware	
Protocol Software					MicroArraySuite 5.0	
Protocol Contact	
Protocol Term Source REF	
SDRF File	E-GEOD-9861.sdrf.txt	
Term Source Name	ncbitax		The MGED Ontology	ArrayExpress	EFO	The MGED Ontology	
Term Source File	http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html		http://mged.sourceforge.net/ontologies/MGEDontology.php	http://www.ebi.ac.uk/arrayexpress	http://www.ebi.ac.uk/efo/	http://mged.sourceforge.net/ontologies/MGEDontology.php	
Term Source Version