##################################################### [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 high throughput sequencing "# 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 SEQUENCING DATA_GENERATION NORMALIZATION TRANSFORMATION Protocol Type grow specified_biomaterial_action nucleic_acid_extraction sequencing scanning bioassay_data_transformation bioassay_data_transformation Protocol Description "# You MUST sepcify the sequencing platform used, e.g. Illumina Genome Analyzer II, on the line below" Protocol Hardware ##################################################### [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 Comment[LIBRARY_LAYOUT] Comment[LIBRARY_SOURCE] Comment[LIBRARY_STRATEGY] Comment[LIBRARY_SELECTION] Protocol REF Assay Name Technology Type Protocol REF 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) # either SINGLE or PAIRED "# one of GENOMIC, NON GENOMIC, SYNTHETIC, VIRAL RNA, OTHER" "# one of WGS, WCS, CLONE, POOLCLONE, AMPLICON, BARCODE, CLONEEND, FINISHING, ChIP-Seq, MNase-Seq, EST, FL-cDNA, CTS, OTHER" "# one of RANDOM, PCR, RANDOM PCR, RT-PCR, HMPR, MF, CF-S, CF-M, CF-H, CF-T, MSLL, cDNA, ChIP, MNase, other, unspecified" # Sequencing protocol # Unique IDs for assays # Type of assay # Data generation protocol # Unprocessed data file e.g. SRF # 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 SINGLE GENOMIC WGS RANDOM SEQUENCING assay 1 high_throughput_sequencing DATA_GENERATION NORMALIZATION TRANSFORMATION