Comment[ArrayExpressAccession]	E-GEOD-61956
MAGE-TAB Version	1.1								
Public Release Date	2015-07-01
Investigation Title	Multiple influences of UNBS1450 on histiocytic lymphoma cell line U937  A high throughput transcriptomic analysis								
Comment[Submitted Name]	Multiple influences of UNBS1450 on histiocytic lymphoma cell line U937  A high throughput transcriptomic analysis
Experiment Description	Analysis of the effect of UNBS1450 on U937 cells at different time points. This study attemps to elucidate early effect of the compound in this cell line at times preceding the accumulation of apoptotic markers We used 8 experimental conditions, comparing UNBS-treated cells to untreated ones after 0, 3, 6 and 9 hours of treatment. Four biological replicates were done, including dye-swaps.								
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	Diederich	Muller	Cerella	Gaigneaux	Radogna	Viry	Chateauvieux	Dicato	Diederich
Person First Name	Marc	Florian	Claudia	Anthoula	Flavia	Elodie	Sebastien	Mario	Marc
Person Email	marc.diederich@lbmcc.lu								
Person Affiliation	Laboratoire de Biologie Moléculaire et Cellulaire du Cancer								
Person Address	Laboratoire de Biologie Moléculaire et Cellulaire du Cancer, 9, rue Edward Steichen, Luxembourg, Luxembourg								
Person Roles	submitter								
Protocol Name	P-GSE61956-1	P-GSE61956-5	P-GSE61956-6	P-GSE61956-2	P-GSE61956-3	P-GSE61956-4	P-GSE61956-7		
Protocol Description	Data were processed in the R statistical environement using the Limma package. Background correction was performed using the normexp method and normalization was performed using Loess. Between-array normalization was performed using Aquantile method. ID_REF =  VALUE = processed log2 ratios (Cy5/Cy3)	Labeling was perfomed according to the manufacturer’s protocol, using 200ng of total RNA for the preparation of cDNA probes and Cy5- and Cy3-labeled cRNA probes (Low RNA Input Linear Amplification Kit, PLUS, Two-Color).	750ng of each cRNA were fragmented in the fragmentation buffer, in presence of blocking agent. Subsequently, samples were hybridized with hybridization buffer on microarrays slides in a Surhyb gasket for 17h at 65°C	Treatments with 20 nM UNBS1450 were started in the exponential growth phase, 24 h after seeding with 2x106 cells. The stop of cell treatment were performed after 0, 3, 6 and 9 h; a control sample was performed for each time point.	U937 cells (human histiocytic lymphoma, DSMZ) were cultured in RPMI 1640 medium containing 10% (v/v) of fetal calf serum, 1% (v/v) of antibiotic-antimycotic and 2mM of L-glutamine at 37°C, 5% CO2.	Total RNA was extracted from a batch of 2x106 to 5x106 cells by TRIzol and cleanup was performed with the RNeasy Mini Kit (Qiagen). Quantification of RNA was assessed by using Nanodrop. RNA integrity value was verified using an Agilent Bioanalyzer 2100.	Slides were scanned by an Axon 4100A microarray scanner. Images analysis and fluorescence quantification were performed using Axon GenePix Pro software version 6.1		
Protocol Type	normalization data transformation protocol	labelling protocol	hybridization protocol	sample treatment protocol	growth protocol	nucleic acid extraction protocol	array scanning protocol		
Experimental Factor Name	time	compound							
Experimental Factor Type	time	compound							
Comment[SecondaryAccession]	GSE61956								
Comment[GEOReleaseDate]	2015-07-01								
Comment[ArrayExpressSubmissionDate]	2014-10-01								
Comment[GEOLastUpdateDate]	2015-07-02								
Comment[AEExperimentType]	transcription profiling by array								
SDRF File	E-GEOD-61956.sdrf.txt