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Matrix Template
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| # Use this template for 3' or whole Gene expression studies when summarization probe set data will be provided in Matrix table format | |||||||||||
| Series | |||||||||||
| # This section describes the overall experiment | |||||||||||
| title | |||||||||||
| Summary | |||||||||||
| Overall Design description | |||||||||||
| Experiment Class (assay Type) | methylation_profiling | ||||||||||
| Experiment Design type | ExperimentDesignType | ||||||||||
| Technology type | microarray | ||||||||||
| quality control type | QualityControlDescriptionType | ||||||||||
| contributer (person or SEEK ID) | |||||||||||
| project | Project | ||||||||||
| Samples | |||||||||||
| # The Sample names in the first column are arbitrary but they must match the column headers of the Matrix table (see next worksheet). | |||||||||||
| #To find the Affymetrix platform accession numbers (GPLxxxx), go to http://www.ncbi.nlm.nih.gov/projects/geo/query/browse.cgi?mode=findplatform | |||||||||||
| Sample name | title | CEL file | source name | organism | characteristics: Strain or line | characteristic:tag | moelcule | label | description | platform | |
| SAMPLE 1 | organism | MaterialType | LabelCompound | ||||||||
| SAMPLE 2 | organism | MaterialType | LabelCompound | ||||||||
| SAMPLE 3 | organism | MaterialType | LabelCompound | ||||||||
| SAMPLE 4 | organism | MaterialType | LabelCompound | ||||||||
| SAMPLE 5 | organism | MaterialType | LabelCompound | ||||||||
| SAMPLE 6 | organism | MaterialType | LabelCompound | ||||||||
| SAMPLE 7 | organism | MaterialType | LabelCompound | ||||||||
| SAMPLE 8 | organism | MaterialType | LabelCompound | ||||||||
| SAMPLE 9 | organism | MaterialType | LabelCompound | ||||||||
| SAMPLE X | organism | MaterialType | LabelCompound | ||||||||
| Protocols | |||||||||||
| # This section includes protocols and fields which are common to all Samples. | |||||||||||
| # Protocols which are applicable to specific Samples or specific channels should be included in additional columns of the SAMPLES section instead | |||||||||||
| growth protocol | |||||||||||
| treatment protocol | |||||||||||
| extract protocol | |||||||||||
| label protocol | |||||||||||
| hyb protocol | |||||||||||
| scan protocol | |||||||||||
| data processing | |||||||||||
| value definition |
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| # Template for an Affymetrix matrix table submission. | ||||||||||
| # The ID_REF column should include the full list of probeset ids of the Affymetrix array (see Matrix Example tabs at bottom) | ||||||||||
| # The sample names in the Matrix table (e.g. 'SAMPLE 1') must match the Sample name in the SAMPLES section of the Metadata file. | ||||||||||
| # The Matrix table should include summarized/scaled/normalized probeset data generated by GC-RMA, dCHIP, MAS 5.0, or whatever algorithm/software was used for primary analysis. | ||||||||||
| # P-values or other measurements can be added as additional columns for each sample | ||||||||||
| ID_REF | SAMPLE 1 | SAMPLE 2 | SAMPLE 3 | SAMPLE 4 | SAMPLE 5 | SAMPLE 6 | SAMPLE 7 | SAMPLE 8 | SAMPLE 9 | SAMPLE X |
