cDNAs for the 32k chip were selected using two different but similar methods:

	a)   cDNAs selected for the previous 16k chip were included in the 32k chip.
	      see "http://web.uvic.ca/grasp/microarray/16k_selection.html" for selection details.

	b)   Other cDNAs were selected as described below.

	c)   Based on Assembly of 435,000 ESTs (81,000 contigs)  and 1100 mRNA clones from Atlantic salmon
		and > 100,000 ESTs from Rainbow trout

	d)   Date: 06/09

b)   Additional cDNA selection.
    ----------------------------

  i)   Appropriate clustered cDNAs (contigs) were chosen.
  ii)  From the selected contigs, constituent cDNAs were chosen.

i) Contig selection criteria:

	1) includes at least one clone from koop lab

	2) good BlastX hit - important (if really good, accept singleton contig)

	3) good quality contig - less important:
	   a) few conflicting positions
	   b) few singleton positions
	   c) no interior singleton positions (potential chimeric sites)
	   (and no point between two positions which is crossed only by one sequence)
	   d) at least 2 members in contig (from at least 2 plates, and preferably
	   from at least 2 libraries)

	4) nothing with >= 94% identity to another sequence on the chip (the existing
	16K plus any new ones) (not counting Rainbow trout orthologs... they can
	be more than 94% similar)

	5) no tRNA, ribosomal, mitochondrial sequences (we already have as much of
	those as we need)

	6) After clones have been chosen as per the above rules, choose others
	fairly freely, keeping in mind point 4 (not too similar), to get a wide
	variety of stuff on the chip.

ii)   cDNAs selection criteria:

	1) from RGB/RGB2, RGA, EVD, EVE, or EVF (except that EVD seems to be mainly
	5' -> 3' sequences, and we prefer 3' -> 5', so probably not much from it

	2) no SSH sequences

	3) high similarity to consensus of contig (allow 20bp at ends for poor trimming)

	4) at 3' end of contig

	5) correct (3' -> 5') orientation (highly preferable)

	6) koop lab clone (critical)

	7) clone length approx 1.5kb

	8) minimize number of plates needed (i.e. if we have 5 clones to choose among
	in a contig, choose one that's on a plate we already need, say)

iii)   Rainbow trout clones
	Dr. Caird Rexroad provided over 1000 clones from genes not found in Atlantic
	salmon transcripts.