#####################################################			
[IDF]			
#			
# MAGE-TAB Submission 'Junction array profiling of Gray (LBNL) breast cancer cell lines'			
#			
# All lines beginning with the '#' character are treated as comments and ignored.			


# This section contains the top-level information for your experiment.			
Investigation Title	Junction array profiling of Gray (LBNL) breast cancer cell lines		
Experiment Description			
Experimental Design	cell_type_comparison_design	in_vitro_design	co-expression_design

# Please create as many Experimental Factors here as you need to			
# describe the variables investigated by your experiment.			
Experimental Factor Name	CELLTYPE		
Experimental Factor Type	cell_type

"# Quality Control Type examples: dye_swap_quality_control, biological_replicate, technical_replicate"	
Quality Control Type	

"# Dates should be entered in the form YYYY-MM-DD. If you are using MS Excel,"	
# it is recommended that you set your spreadsheet to 'text' format throughout	
# to help avoid any unwanted changes made by Excel.	
Public Release Date	

"# Please list contact details in columns, below:"	
Person Last Name	Heiser
Person First Name	Laura
Person Mid Initials	M
Person Email	lmheiser@lbl.gov
Person Phone	
Person Address	"1 Cyclotron Rd., Berkeley, CA 94720"					
Person Affiliation	LBNL					
Person Roles	submitter					

"# Please list all publications associated with this submission, in columns:"						
PubMed ID						
Publication Author List						
Publication Title						
Publication Status						

# The next section describes the protocols used in your						
"# experiment. Please select your own Protocol Names (e.g. 'GROWTH',"						
# 'TREATMENT') for use within this spreadsheet						
Protocol Name	GROWTH	TREATMENT	EXTRACTION	LABELING	NORMALIZATION	TRANSFORMATION
Protocol Type	grow	specified_biomaterial_action	nucleic_acid_extraction	labeling	bioassay_data_transformation	bioassay_data_transformation
Protocol Description	<your growth protocol text here>	<your treatment protocol text here>	<your nucleic acid extraction protocol text here>	<your labeling protocol text here>	<your normalization protocol text here>	<your transformation protocol text here>

#####################################################																								
[SDRF]																								
# The SDRF section contains all the information linking your samples																								
# to your data files. Please feel free to add as many new																								
# Characteristics[] or FactorValue[] columns as necessary to																								
# completely describe your experiment. See this web page for help with																								
# supported data file formats:																								
#   http://tab2mage.sourceforge.net/docs/datafiles.html																								
#																								

Source Name	Material Type	Characteristics[Organism]	Characteristics[Age]	Characteristics[CellLine]	Characteristics[BioSourceType]	Characteristics[Sex]	Characteristics[BioSourceProvider]	Characteristics[CellType]	Protocol REF	Protocol REF	Protocol REF	Protocol REF	Labeled Extract Name	Label	Hybridization Name	Comment[Array serial number]	Array Data File	Comment[EXP]	Protocol REF	Derived Array Data File	Protocol REF	Derived Array Data Matrix File	Comment[CDF]	Factor Value[CELLTYPE]
# Unique IDs for biosources (experimental starting materials)	# MaterialType term from MGED ontology	# Sample latin species name	"# Sample Age value, e.g. 20 years"	# Sample CellLine value	# Sample BioSourceType value	# Sample Sex value	# Sample BioSourceProvider value	# Sample CellType value	"# Growth protocol, where applicable"	# Sample treatment protocol	# RNA/DNA extraction	# RNA/DNA labeling	# Unique IDs for labeled extracts	"# Labeling dye, e.g. Cy3, biotin, 33P"	# Unique IDs for hybs	# Array serial number/chip lot	"# Unprocessed data file, e.g. CEL, GPR"	# EXP file where available	# Data normalization	# Normalized data	# Protocol producing final data matrix file	# Final data matrix file(s)	# CDF library file (do not upload CDF unless custom array used)	# Value for CELLTYPE Experimental Factor
184A1N4		Homo sapiens		184A1N4	fresh_sample	female	Georgetown	epithelial									0230_184A1N4_Junct1.CEL							
184B5		Homo sapiens		184B5	fresh_sample	female	Georgetown	epithelial									0231_184B5_Junct1.CEL							
600MPE		Homo sapiens		600MPE	fresh_sample	female	Gray Lab	epithelial									0232_600MPE_Junct1.CEL							
BT20		Homo sapiens		BT20	fresh_sample	female	Georgetown	epithelial									0234_BT20_Junct1.CEL
BT474		Homo sapiens		BT474	fresh_sample	female	Gray Lab	epithelial									0235_BT474_Junct1.CEL
BT549		Homo sapiens		BT549	fresh_sample	female	Georgetown	epithelial									0293_BT549_Junct1.CEL
CAMA1		Homo sapiens		CAMA1	fresh_sample	female	Gray Lab	epithelial									0237_CAMA1_Junct1.CEL
HCC1143		Homo sapiens		HCC1143	fresh_sample	female	Adi gazdar	epithelial									0243_HCC1143_Junct1.CEL
HCC1187		Homo sapiens		HCC1187	fresh_sample	female	Adi gazdar	epithelial									0244_HCC1187_Junct1.CEL
HCC1500		Homo sapiens		HCC1500	fresh_sample	female	Adi gazdar	epithelial									0248_HCC1500_Junct1.CEL
HCC1954		Homo sapiens		HCC1954	fresh_sample	female	Adi gazdar	epithelial									0254_HCC1954_Junct1.CEL
HCC3153		Homo sapiens		HCC3153	fresh_sample	female	Adi gazdar	epithelial									0257_HCC3153_Junct1.CEL
HCC38		Homo sapiens		HCC38	fresh_sample	female	Adi gazdar	epithelial									0240_HCC38_Junct1.CEL
MCF10A		Homo sapiens		MCF10A	fresh_sample	female	Georgetown	epithelial									0294_MCF10A_Junct1.CEL
MCF10F		Homo sapiens		MCF10F	fresh_sample	female	Gray Lab	epithelial									0261_MCF10F_Junct1.CEL
MCF12A		Homo sapiens		MCF12A	fresh_sample	female	Chris Benz	epithelial									0260_MCF12A_Junct1.CEL
MCF7		Homo sapiens		MCF7	fresh_sample	female	Georgetown	epithelial									0262_MCF7_Junct1.CEL
MDAMB157		Homo sapiens		MDAMB157	fresh_sample	female	Georgetown	epithelial									0264_MDAMB157_Junct1.CEL
MDAMB231		Homo sapiens		MDAMB231	fresh_sample	female	Georgetown	epithelial									0266_MDAMB231_Junct1.CEL
MDAMB361		Homo sapiens		MDAMB361	fresh_sample	female	Georgetown	epithelial									0267_MDAMB361_Junct1.CEL
MDAMB415		Homo sapiens		MDAMB415	fresh_sample	female	Georgetown	epithelial									0268_MDAMB415_Junct1.CEL
MDAMB453		Homo sapiens		MDAMB453	fresh_sample	female	Georgetown	epithelial									0271_MDAMB453_Junct1.CEL
SKBR3		Homo sapiens		SKBR3	fresh_sample	female	Georgetown	epithelial									0273_SKBR3_Junct1.CEL
SUM159PT		Homo sapiens		SUM159PT	fresh_sample	female	Steve Ethier	epithelial									0282_SUM159PT_Junct1.CEL
SUM185PE		Homo sapiens		SUM185PE	fresh_sample	female	Steve Ethier	epithelial									0283_SUM185PE_Junct1.CEL
SUM52PE		Homo sapiens		SUM52PE	fresh_sample	female	Steve Ethier	epithelial									0279_SUM52PE_Junct1.CEL
T47D		Homo sapiens		T47D	fresh_sample	female	Georgetown	epithelial									0286_T47D_Junct1.CEL
ZR751		Homo sapiens		ZR751	fresh_sample	female	Georgetown	epithelial									0289_ZR751_Junct1.CEL
ZR75B		Homo sapiens		ZR75B	fresh_sample	female	Georgetown	epithelial									0291_ZR75B_Junct1.CEL