#####################################################
[IDF]
#
#
"# Please save this page to disk, and edit it using any spreadsheet program (e.g.,"
"# Microsoft Excel, OpenOffice.org Calc). This file can be imported into either of"
# these applications as a tab-delimited text file. It is highly recommended that
"# you set the cell format to plain text throughout the spreadsheet, to avoid"
# 'helpful' changes made by the spreadsheet application. Once you have completed
# this spreadsheet please upload it using the submissions webpage alongside your
# data files:
#    http://www.ebi.ac.uk/cgi-bin/microarray/magetab.cgi
#
# Please see http://tab2mage.sourceforge.net/docs/magetab_subs.html for
# information on filling in the IDF and SDRF sections below.
#
# All lines beginning with the '#' character are treated as comments and ignored.				


# This section contains the top-level information for your experiment.				
Investigation Title	PUT EXPERIMENT TITLE HERE			
Experiment Description	PUT EXPERIMENT DESCRIPTION HERE			
Experimental Design	cell_type_comparison_design	organism_part_comparison_design	in_vitro_design	co-expression_design
Comment[AEExperimentType]	transcription profiling by array			

"# Please create as many Experimental Factors here as you need to, cell type and organism_part are given as examples only, replace this with whatever is the main variable(s) in your experiment"				
# describe the variables investigated by your experiment.				
Experimental Factor Name	CELLTYPE	ORGANISM_PART		
Experimental Factor Type	cell_type	organism_part		

"# 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	
Person First Name	
Person Mid Initials	
Person Email	
Person Phone	
Person Address	
Person Affiliation	
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, or re-use ArrayExpress"								
# protocols by using the assigned ArrayExpress protocol accession								
# numbers in your SDRF. If you have already submitted protocols to								
"# ArrayExpress, you can retrieve these using this web page:"								
#    http://www.ebi.ac.uk/aerep/								
Protocol Name	GROWTH	TREATMENT	EXTRACTION	LABELING	HYBRIDIZATION	SCANNING	NORMALIZATION	TRANSFORMATION
Protocol Type	grow	specified_biomaterial_action	nucleic_acid_extraction	labeling	hybridization	image_acquisition	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 hybridization protocol text here>	<your scanning protocol text here>	<your normalization protocol text here>	<your transformation protocol text here>

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[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																													
#																													
"# The first line below has been filled in with example terms, where possible:"																													
Source Name	Material Type	Characteristics[Organism]	Characteristics[Age]	Unit[TimeUnit]	Characteristics[CellLine]	Characteristics[BioSourceType]	Characteristics[Sex]	Characteristics[BioSourceProvider]	Characteristics[CellType]	Protocol REF	Protocol REF	Protocol REF	Extract Name	Protocol REF	Labeled Extract Name	Label	Protocol REF	Hybridization Name	Array Design REF	Comment[Array serial number]	Protocol REF	Scan Name	Array Data File	Protocol REF	Derived Array Data File	Protocol REF	Derived Array Data Matrix File	Factor Value[CELLTYPE]	Factor Value[ORGANISMPART]
# Unique IDs for biosources (experimental starting materials)	# MaterialType term from MGED ontology	# Sample latin species name	"# Sample Age value, e.g. 20 years"	# Time units for Characteristic	# 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	# Unique IDs for extracts (RNA or DNA)	# RNA/DNA labeling	# Unique IDs for labeled extracts	"# Labeling dye, e.g. Cy3, biotin, 33P"	# Hyb protocol	# Unique IDs for hybs	"# ArrayExpress array accession, e.g. A-MEXP-27"	# Array serial number/chip lot	# Image acquisition	# Unique IDs for scans	"# Unprocessed data file e.g. CEL, GPR"	# Data normalization	# Normalized data	# Protocol producing final data matrix file	# Final data matrix file(s)	# Value for CELLTYPE Experimental Factor	# Value for ORGANISM Experimental Factor
Cell culture 1	cell	Homo sapiens		hours						GROWTH	TREATMENT	EXTRACTION	RNA Extract 1	LABELING	Labeled Extract 1.Cy3	Cy3	HYBRIDIZATION	Hybridization 1			SCANNING	Scan 1		NORMALIZATION		TRANSFORMATION