Comment[ArrayExpressAccession]	E-GEOD-51857
MAGE-TAB Version	1.1										
Public Release Date	2013-10-30
Investigation Title	CREB3L1 is a metastasis suppressor that represses expression of genes regulating metastasis, invasion and angiogenesis										
Comment[Submitted Name]	CREB3L1 is a metastasis suppressor that represses expression of genes regulating metastasis, invasion and angiogenesis
Experiment Description	This SuperSeries is composed of the SubSeries listed below. Refer to individual Series										
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	Anderson	Anderson	Mellor								
Person First Name	Deborah	Deborah	Paul								
Person Email	deborah.anderson@saskcancer.ca										
Person Affiliation	University of Saskatchewan										
Person Phone	13069667038										
Person Address	University of Saskatchewan, 107 Wiggins Road, Saskatoon, Saskatchewan, Canada										
Person Roles	submitter										
Protocol Name	P-GSE51857-1	P-GSE51857-2	P-GSE51857-5	P-GSE51857-9	P-GSE51857-6	P-GSE51857-10	P-GSE51857-3	P-GSE51857-4	P-GSE51857-8	P-GSE51857-7	P-GSE51857-11
Protocol Description	The data was analyzed with Partek Genomics Suite v6.6 using RMA (data in log2) ID_REF =  VALUE = log2 RMA	Arrays were processed using Nimblegen's standard protocol for Nimblescan 2.4 ChIP data extraction software at Nimblegen. The ratio_peaks.gff is the ratio of signal for each transcript on the chip between the ChIP sample and the input, which is used to determine if a positive signal is unique to the ChIP sample. The 'ratio_peaks_mapToFeatures_All_Peaks.txt' file contains data with the identity of the feature on it e.g. name and accession number. ID_REF =  VALUE = scaled, log2 (ChIP/Input) ratio	Biotin labelling was prepared using the 3' IVT Express Kit according to manufacturers instructions.	1 M-5g ChIP DNA was directly labeled by Klenow (New England Biolabs) random priming with Cy5 or Cy3 nonamers per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).	cRNA was hybridized and stained using the Genechip hybridization, stain and wash kit according to manufacturers instructions.	The labeled ChIP DNA was precipitated with 0.1 volume 5M NaCl and 1 volume isopropanol, and hybridized in 45 ul of buffer containing 20% formamide, 1.2 M betaine, 0.1 ug/ul herring sperm DNA and 10 ug of human COT1 DNA (Invitrogen). Arrays were hybridized in Maui hybridization stations for 16-18 h at 42C, and then washed in 42C 0.2% SDS/0.2x SSC, room temperature 0.2x SSC, and 0.05x SSC. Hybridization buffers and washes were completed using manufacturer's protocols (http://www.nimblegen.com/products/lit/lit.html)	Cells were grown in 5% CO2 at 37C	RNA was extracted using the Qiagen RNA extraction kit according to manufacturers instructions.	Chromatin Immunoprecipitation (ChIP) assay was performed using an EpiQuickM-bM-^DM-" Chromatin Immunoprecipitation Kit (EpigentekM-bM-^DM-") and a HA-X (F-7) antibody (Santa Cruz). All procedures were carried out according to the manufacturerM-bM-^@M-^Ys specifications. The ChIP DNA was then amplified using a GenomePLex Whole Genome Amplification Kit -4 (WGA-4) (Sigma), according to the manufacturerM-bM-^@M-^Ys specifications. The amplified DNA was then purified using a QIAquickM-. PCR purification kit (Qiagen).	Gene chips were scanned using Genechip Scanner 3000 7G	Arrays were scanned on an Axon 4000B scanner per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).
Protocol Type	normalization data transformation protocol	normalization data transformation protocol	labelling protocol	labelling protocol	hybridization protocol	hybridization protocol	growth protocol	nucleic acid extraction protocol	nucleic acid extraction protocol	array scanning protocol	array scanning protocol
Experimental Factor Name	CHIP ANTIBODY	CELL LINE	TANSFECTED WITH	CELL TYPE	ORGANISM						
Experimental Factor Type	chip antibody	cell line	tansfected with	cell type	organism						
Comment[SecondaryAccession]	GSE51857										
Comment[GEOReleaseDate]	2013-10-30										
Comment[ArrayExpressSubmissionDate]	2013-10-29										
Comment[GEOLastUpdateDate]	2013-10-31										
Comment[AEExperimentType]	transcription profiling by array										
Comment[AEExperimentType]	ChIP-chip by tiling array										
SDRF File	E-GEOD-51857.sdrf.txt