Samples used extract preparation and labeling

A sample is the labeled nucleic acid that is used together with an array in the hybridization process. The MIAME section about samples describes their biological origins as well as treatments performed on the initial material and resulting products from each intermediate step.

1. The minimum information about the biological origin of a biomaterial is:

• the name of the organism (NCBI taxonomy);

• the sample provider;

• developmental stage;

• genetic variation (e.g. gene knockout, transgenic variation);

• individual genetic characteristics (e.g. disease alleles, polymorphisms);

• animal/plant strain or line;

• disease state or normal;

• links to clinical information (if available).

2. The minimum information about biomaterial manipulations is:

• growth conditions;

• in vivo treatments (organism or individual treatments);

• in vitro treatments (cell culture conditions);

• treatment type (e.g. small molecule, heat shock, cold shock);

• separation technique (e.g. none, trimming, micro-dissection);

3. The minimum information about hybridization extract preparation is:

• the extraction method;

• nucleic acid extracted (total RNA, mRNA or genomic DNA);

• amplification (e.g. none, RNA polymerase, PCR).

4. The minimum information about the labeling process is:

• the amount of nucleic acids labeled;

• label incorporation method.

5. The minimum information about added external controls is:

• the element on the array expected to hybridize to a spiking control;

• spike type (e.g. oligonucleotide, plasmid DNA, transcript);

• spike qualifier (e.g. concentration, expected ratio).

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