in situ oligonucleotide synthesis on glass slide platform; 50bp oligo sequences based on custom designed probes to be centered on all Taq1-alpha restriction cut sites (TCGA) in the purple urchin genome
Development of the Restriction Site Tiling Analysis (RSTA) method: Accurate discovery and quantitative genotyping of genome-wide polymorphisms using nucleotide arrays
Data table header descriptions
ID
Row
Col
SubTypeMask
SubTypeName
SEQUENCE
Custom oligonucleotide probe sequences commercially synethesized by Agilent Technologies Inc. Probes in matrix data file are all centered on Taq restriction cut sites (TCGA), bases 24 through 27 of the 50 base pair oligonucleotide sequence.
ProbeUID
ControlType
ProbeName
Unique probe name with 15 characters: Characters 1-6 - unique probe identifier number, Character 7 - indicates presence / absence of a restriction cut site in the center of the probe sequence (X – presence, “_” – absence), Characters 8-9 indicate ProbeType - GE is intergenic, GL is in a GLEAN coding region, UP is an upstream putative regulatory region, RD is a randomly generated probe sequence that does not match anywhere in the genome according to BLASTN, MT is in the mitochondrial genome, DS is a degradation series probe to look for the effect of mutations on binding, RC is in ribosomal DNA, Character 10 is zero, Characters 11-15 is the GLEAN3 reference number.
GeneName
SPOT_ID
GLEAN3Number
GLEAN3 gene numbers with reference to the purple sea urchin genome sequence. http://luria.mit.edu/urchin/seq_lookup.html
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