Spotted array using PCR fragments of approximately 95% of the genes in the D. melanogaster BDGP genome.
We followed a sequence of decreasingly stringent tests to pick optimal primer pairs for the PCR fragments on the arrays. For each gene, we looked for (first) a 500b to 2kb sequence at the 3’ end and, failing this, (second) two 200b to 500b sequences in:(1) coding sequence, completely within an EST clot, and unduplicated (BLAST<=10^-4); (2) coding sequence, partially within an EST clot, unduplicated; (3) coding sequence, unduplicated; (4) exon, completely within an EST clot, unduplicated; (5) exon, partially within an EST clot, unduplicated; (6) exon, unduplicated; (7) sequence less than 2kb at the 3’ end. See above for the other details about making these arrays.
32 blocks of spots in 4 columns and 8 rows. Block numbering is from left to right and from higher to lower. The 1st block is at the upper left corner. The 4th block is at the higher right corner. The 29th block is at the lower left corner. The 32nd block is at the lower right corner.
The column number of a spot within a block.
The row number of a spot within a block.
The internal ID. Representing the ID for primer pairs.
The CG number for a gene used by Flybase.
Reporter Biosequence Database Entry: The FBgn number used by FlyBase, which is the systematic gene name.
The sequence for the forward primer that is used in the PCR reaction to amplify a gene fragment.
The sequence for the reverse primer that is used in the PCR reaction to amplify a gene fragment.
The predicted sequence (base on Flybase annotation) of the product from the PCR reaction amplifying a gene fragment.