Minimum information that has to be provided about a published microarray experiment:

1. expression level measurement results, in particular:
1. the TIFF image file from the hybridised microarray scanning;
2. image analysis output (of the particular image analysis software that has been used) for each spot, for each channel;
3. a derived value summarising each spot in the authors interpretation (such as background subtracted intensity of the spot typically used for Stanford or Incyte technologies);
2. the following annotations:
1. array
• array name (e.g., "Stanford Human 10K set),
• platform type: spotted vs. synthesized (spotted - oligos, PCR products, plasmids, colonies),
• if commercial array,
• provider
• unique ID from the provider
• array dimensions
• spot dimensions
• number of columns and rows, or number of spots
• brief description
• substrate
2. each element (spot) on the array
• sequence info (if known)
• sequence accession number in EMBL (GenBank, DDBJ) if known
• sequence itself (if databases do not contain it)
• number of oligos and the reference sequence (or accession number) for Affymetrix chips, plus the oligo sequences, if given
• clone info (obligatory, if sequence is not verified)
• clone ID (plus clone provider and date) if sequence is not verified by the chip designer
• quality information from the clone provider
• checking of the DNA quality (none, resequenced, quality check by gel separation, amount of DNA)
• if the element can be used for normalisation or control (e.g., element should have expected value)
3. sample source and treatment: Note that some of these categories are relevant only in particular contexts. For instance, tissue is relevant only to multi-cellular organisms. The categories mentioned below should be considered as a tree-like structure, and depending on the particular path along the tree, only some of the specified categories become relevant.
• cell source and type (if derived from primary sources (s))
• organism (NCBI taxonomy)
• sex
• age
• development stage
• organism part (tissue)
• animal/plant strain or line (if applicable)
• genetic variation (gene knockout, transgenic variation)
• individual (if applicable)
• unique identifier for references in other hybridisations or overall experiment description
• individual genetic characteristics (disease alleles, polymorphisms, etc.)
• disease state (or normal)
• target cell type
• separation technique (none, trimming, microdissection, FACS, ...)
• estimated % target
• cell line and source (if applicable)
• treatments
• in vivo (organism or individual treatments)
• in vitro treatments (cell culture conditions)
• treatment type (e.g., small molecule, heat shock, cold shock, food deprivation, .)
• compound
• verbal description (laboratory protocol)
4. controls
• control type (prelabeled and added at hybridization [calibration of scan intensity to quantity]; added at sample labeling [quantitate sample labeling]; added at sample amplification [IVT or PCR control], ...)
• ID for the controls
• associated normalisation type array elements
5. hybridisation extract preparation
• reference to the respective extract preparation protocol, if exits in the database
• cell rupture method
• chemical extraction procedure
• physical extraction procedure
• whether total RNA, mRNA, or genomic is extracted
• type of preselection
• amount of nucleic acids extracted
• target amplification (RNA polymerases, PCR)
• which label is used (e.g., Cy3, Cy5, 33P)
• the labelling ratio
• laboratory protocol (free text)
6. hybridisation procedure
• reference to the respective hybridisation protocol, if already exits in the database
• the solution (e.g., concentration of solutes)
• blocking agent
• wash procedure
• time, concentration, volume, temperature
• description of the hybridisation instruments
• laboratory protocol (free text)
7. scanning
• reference to the respective scanning protocol, if already exits in the database
• scanning hardware
• scanning software
• parsed header of the TIFF file, including laser power, spatial resolution, pixel space
• laboratory protocol (free text)
8. image analysis and quantitation
• reference to the image analysis software or algorithm (including author, version)
• relevant parameters
• any normalisation that has been applied before the final output (was there a scalar adjustment of the measurements)
• also, we would like to encourage the image analysis software developers to try to design methods for standard ways of summarising spot quality.
9. experiment as a whole (i.e., set of related hybridisations)
• author (submitter), data
• platforms used;
• comparative or absolute measurements,
• single or multiple hybridisations,
• single or multiple arrays,
• For multiple hybridisations we have subtypes:
• time course,
• other ordered,
• other unordered
• relationship between samples (free text)
• We can also classify the experiments by the type of the question that has been asked:
• the aim of the experiment (free text) plus one of the following:
• effect of gene knock-out
• errect of gene knock-in (transgenics)
• shock
• dose response
• normal vs. diseased comparison
• treated vs. untreated comparison
• other
• brief description
• quality related indicators
• publication (if exists)
• number of replicates