Comment[ArrayExpressAccession]	E-GEOD-41983
MAGE-TAB Version	1.1							
Public Release Date	2012-11-03
Investigation Title	Monocyte-like THP-1 Cells: Trichosporon asahii Infected vs Control							
Comment[Submitted Name]	Monocyte-like THP-1 Cells: Trichosporon asahii Infected vs Control
Experiment Description	Transcriptional profiling of Monocyte-like THP-1 Cells   with Trichosporon asahii Infected THP-1 Cells comparing  untreated THP-1 cells Two-condition experiment,Trichosporon asahii Infected THP-1 Cells  vs  THP-1 Cells.  Biological replicates: 3  infected THP-1 Cells, independently grown and harvested.One replicate per array.							
Term Source Name	ArrayExpress	EFO
Term Source File	http://www.ebi.ac.uk/arrayexpress/	http://www.ebi.ac.uk/efo/efo.owl						
Person Last Name	Cong	Cong	Yang					
Person First Name	Lin	Lin	Rong					
Person Mid Initials			Y					
Person Email	conglin369@163.com							
Person Affiliation	General Hospital of Beijing Military Command							
Person Address	General Hospital of Beijing Military Command, 5 Nanmencang, Dongcheng District, Beijing , China							
Person Roles	submitter							
Protocol Name	P-GSE41983-1	P-GSE41983-6	P-GSE41983-3	P-GSE41983-8	P-GSE41983-7	P-GSE41983-2	P-GSE41983-4	P-GSE41983-5
Protocol Description	ID_REF =  VALUE = normalized log2 ratio (Cy5/Cy3) representing test/reference PRE_VALUE = (Cy5/Cy3) ratio representing test/reference	Arrays were hybridized was preformed in a CapitalBio BioMixerTM II Hybridization Station overnight at a rotation speed of 8 rpm and a temperature of 42M-bM-^DM-^C and washed with two consecutive solutions (0.2% SDS, 2M-CM-^W SSC at 42M-bM-^DM-^C for 5 min, and 0.2M-CM-^W SSC for 5 min at room temperature).	The cells were grown in a 5% humidified CO2 incubator at 37M-0C in RPMI 1640 medium supplemented with 10% heat-inactivated fetal bovine serum,2 mM L-Glutamine, penicillin (100 units/ml) and streptomycin (100 M-NM-<g/ml).Cells were resuspended at a concentration of 1 M-CM-^W 106 cells/ml. Cell differentiation was induced by treatment with 10ng/ml phorbol myristate acetate (PMA) at 37M-0C for 6 h. Cells were then washed twice with HanksM-bM-^@M-^Y balanced salt solution without Ca2+ and Mg2+ and incubated without PMA at 37M-0C for a further 22 h	LOWESS normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal. Agilent software was used.	confocal LuxScanTM scanner and the images obtained were then analyzed using LuxScanTM 3.0 software (Both from CapitalBio)	1 M-CM-^W 10^7 PMA-stimulated THP-1 cells were infected with T. asahii (5 M-CM-^W 107 cells) at the multiplicity of infection (MOI) of 5 (5 fungi/1 cell) for 3 h at 37M-0C.	Total RNA extracted using Trizol following manufacturer's instructions	2 M-NM-<g amplified RNA was mixed with 4 M-NM-<g random nanomer, denatured at 65M-bM-^DM-^C for 5min, and cooled on ice. Then, 5 M-NM-<L of 4M-CM-^Wfirst-strand buffer, 2 M-NM-<L of 0.1M DTT, and 1.5 M-NM-<L CbcScript M-bM-^EM-! reverse transcriptase were added. The mixtures were incubated at 25M-bM-^DM-^C for 10 min, then at 37M-bM-^DM-^C for 90 min. The cDNA products were purified using a PCR NucleoSpin Extract II Kit (MN) and vacuum evaporated to 14 M-NM-<L. The cDNA was mixed with 4 M-NM-<g random nanomer, heated to 95M-bM-^DM-^C for 3 min, and snap cooled on ice for 5 min. Then, 5 M-NM-<L Klenow buffer, dNTP, and Cy5-dCTP or Cy3-dCTP (GE Healthcare) were added to final concentrations of 240 M-NM-<M dATP, 240 M-NM-<M dGTP, 240 M-NM-<M dTTP, 120 M-NM-<M dCTP, and 40 M-NM-<M Cy-dCTP. 1.2 M-NM-<L Klenow enzyme was then added, and the reaction was performed at 37M-bM-^DM-^C for 90 min. Labeled cDNA was purified with a PCR NucleoSpin Extract II Kit (MN) and resuspended in elution buffer. Labeled controls and test samples were quantitatively adjusted based on the efficiency of Cy5-dCTP or Cy3-dCTP incorporation and dissolved in 80 M-NM-<l hybridization solution containing 3M-CM-^WSSC, 0.2% SDS, 5M-CM-^WDenhardtM-bM-^@M-^Ys solution and 25% formamide. DNA in hybridization solution was denatured at 95M-bM-^DM-^C for 3 min prior to loading onto a microarray
Protocol Type	bioassay_data_transformation	hybridization	grow	feature_extraction	image_aquisition	specified_biomaterial_action	nucleic_acid_extraction	labeling
Experimental Factor Name	TREATMENT							
Experimental Factor Type	treatment							
Comment[SecondaryAccession]	GSE41983							
Comment[GEOReleaseDate]	2012-11-03							
Comment[ArrayExpressSubmissionDate]	2012-11-01							
Comment[GEOLastUpdateDate]	2012-11-04							
Comment[AEExperimentType]	transcription profiling by array							
SDRF File	E-GEOD-41983.sdrf.txt