Array design description

The array design describes the characteristics of the arrays used in the experiment. The section consists of two parts describing the array as a whole and its design elements (e.g. its spots). The description of the design elements is separated into three different classes: feature, identifying the location on the array; reporter, describing the nucleotide sequence belonging to it; and composite sequence, summarizing the corresponding gene, exon or splice-variant. Additionally information about control elements is to be provided. This second part of the array design description will typically be provided as a spreadsheet or tab-delimited file. Often it will be available from the array providers, in which case they can simply be referenced. Sometimes this part might be difficult to acquire, for instance if commercial array manufacturers only provide information on the composite sequence level and not about the reporters. However, it was recently agreed that this part definitely belongs to MIAME and is necessary when providing information about the array and its elements.

1. The minimum information about the array design includes:

• the platform type (e.g. spotted glass array, in situ synthesized array);

• surface and coating specifications (e.g. glass, membrane);

• physical dimension of array support (e.g. of the slide);

• the number of features on the array;

• availability (for commercial arrays) or production protocol for the array.

2. The minimum information about the features includes:

• a reference to the corresponding reporter(s).

3. The minimum information about the reporters includes:

• the type of reporter (e.g. cDNA, synthetic oligonucleotide);

• single or double-stranded;

• the sequence, accession numbers in DDBJ/EMBL/GenBank and primer pair information;

• the approximate length if the exact sequence is unknown;

• clone information (id, provider, date, availability);

• a protocol describing the production of the element in case of a custom-made array;

• a reference to the corresponding composite sequence(s).

4. The minimum information about the composite sequences includes:

• the reference sequence;

• links to appropriate databases (e.g. SWISS-PROT) if relevant.

5. The minimum information about control elements includes:

• the position of the feature (the coordinate on the array);

• the control type (e.g. spiking, normalization);

• the control qualifier (endogenous, exogenous).

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