Comment[ArrayExpressAccession]	E-GEOD-42067
MAGE-TAB Version	1.1							
Public Release Date	2012-12-15
Investigation Title	Three human cell types respond to multi-walled carbon nanotubes and titanium dioxide nanobelts with cell-specific transcriptomic and proteomic expression [SAE cells]							
Comment[Submitted Name]	Three human cell types respond to multi-walled carbon nanotubes and titanium dioxide nanobelts with cell-specific transcriptomic and proteomic expression [SAE cells]
Experiment Description	To identify key biological pathways that define toxicity or biocompatibility after nanoparticle exposure, three human cell types were exposed in vitro to two high aspect ratio nanoparticles for 1 hr or 24 hr and collected for global transcriptomics. Transcriptional responses were measured by global microarray analysis of cells in culture. Groups (N=3 biological replicates) of SAE cells exposed to 0, 10 or 100 ug/ml MWCNT or TiO2-NB nanoparticles for 1 or 24 hr.							
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	Tilton	Tilton	Orr					
Person First Name	Susan	Susan	Galya					
Person Mid Initials	C.	C						
Person Email	susan.tilton@pnnl.gov							
Person Affiliation	Pacific Northwest National Laboratory							
Person Phone	509-371-7981							
Person Address	Computational Biology and Bioinformatics, Pacific Northwest National Laboratory, 902 Battelle Blvd, Richland, WA, USA							
Person Roles	submitter							
Protocol Name	P-GSE42067-1	P-GSE42067-6	P-GSE42067-3	P-GSE42067-8	P-GSE42067-7	P-GSE42067-2	P-GSE42067-4	P-GSE42067-5
Protocol Description	ID_REF =  VALUE = RMA-normalized log2 signal intensity	Biotin-labeled cRNA (15 M-5g) was fragmented to a size range between 50-200 bases for array hybridization. After hybridization, the arrays were washed and stained with streptavidin-phycoerythrin.	Small airway epithelial (SAE) cells were obtained from Lonza Walkersville Inc. Cells were maintained in Lonza Clonetics SABM media (cat # cc-3119) supplemented with Lonza Clonetics SAGM single quots (cat# cc-4124). For experimental conditions, adherent SAEC cells were washed with HBSS (cat# cc-5022) and trypsin (cat# cc-5012) was then used to dislodge the cells. A trypsin neutralizing solution (cat# cc-5002) was then added and the cells were centrifuged at 250 x g for 5 min. The supernatant was discarded and the cells were resuspended and counted as stated above. All cultures were maintained in 37M-0C water-jacketed CO2 incubators (ThermoForma).	Raw intensity data were quantile normalized by Robust Multi-Array Analysis (RMA) summarization and probes were subject to quality control to measure the efficiency of transcription, integrity of hybridization, and consistency of qualitative calls.	The arrays were scanned at a resolution of 2.5 microns using an Affymetrix GeneChip Scanner 3000.	For transcriptomics analysis, cells were suspended at 1 x 106 cells per ml and plated in 25 cm2 flasks at 5 x 106 cells/flask. The multi-walled carbon nanotubes (MWCNT) or titanium nanobelts (TiO2-NB) were added directly to the wells at specified concentrations (0, 10 or 100 M-5g/ml) in media. The cells were cultured for either 1 or 24 h. At the end of the culture period the adherent cells were washed once in PBS and the RNA was isolated as described below.	Total RNA was collected using the RNeasy Kit (Qiagen, Valencia, CA).	Complementary DNA was synthesized from 3 M-5g of total RNA in the presence of an oligo-dT primer containing a T7 RNA polymerase promoter, and an in vitro transcription reaction was performed in the presence of a mixture of biotin-labeled ribonucleotides to produce biotinylated cRNA from the cDNA template, according to manufacturerM-bM-^@M-^Ys protocols (Affymetrix One-Cycle Target Labeling Kit).
Protocol Type	bioassay_data_transformation	hybridization	grow	feature_extraction	image_aquisition	specified_biomaterial_action	nucleic_acid_extraction	labeling
Experimental Factor Name	TREATMENT	TIME	DOSE					
Experimental Factor Type	treatment	time	dose					
Comment[SecondaryAccession]	GSE42067							
Comment[GEOReleaseDate]	2012-12-15							
Comment[ArrayExpressSubmissionDate]	2012-11-06							
Comment[GEOLastUpdateDate]	2012-12-20							
Comment[AEExperimentType]	transcription profiling by array							
SDRF File	E-GEOD-42067.sdrf.txt