Tiling data viewed in affy's IGB software (Marina & Lior's data)
|S288c Genome||1 probe every 8 bp on each strand offset by 4 bp.
Version 1, current as of late 2003, of the S288c sequence was used for tiling and arrayed on the tiling chip. The mitochondrial genome sequence used to design the tiling chip is here. SGD did not release a version of the yeast sequence that corresponds to the Version 1. So some of the S288c chromosomes have official versions in Genbank that correspond to the chromosome sequence on the chip, and some do not. The versions page lists the corresponding GenBank accession for each chromosome. The differences between the "chip" chromosomes and the current Genbank versions are detailed here. Data files have been created for the Version 1 sequence and the current GenBank version of the S288 genome sequence. 3,039,046 probe pairs.
|YJM789 polymorphic probes.||Identified by Ted Jones. The polymorphic YJM789 oligos for the tiling chip were based on comparison of YJM789 version 1 to this sequence. 127,813 probes|
|YJM789 sequences not present in S288c||1 probe every 8 bp on each strand offset by 4 bp.
See the "unique" YJM page for a more detailed description of these pages. 4,564 probe pairs
|S288c Splice Junction probes||1 probe every bp both directions. 7,359 probe pairs|
|Tag probes||16,271 Tag probes and their reverse complements.|
|Random 25-mer probes||25-mer probes with random sequence and various distributions of GC richness. 10,647 probes.|
|Non-Yeast controls||1 probe every bp for sequences AF159801, AF159803, AF168390, AF191028, AF198054, AF247559, deleted_thr_3, deleted_thr_5, deleted_trp, NM_002046, present_thr, present_trp, X56062 and X58149. 14,535 probe pairs|
* QC BioB, C, D and Cre Control block (in both senses)
* QC tag Control block (in both senses)
* oligo 213/948 checkerboards approx every 1mm in chip
* oligo 213/948 stripes approx every 1mm in chip
* Text reading "Genechip S cerevisiae Tiling Array"
* Oligo 213 cross at center of chip
The stripes and checkerboards divide the chip surface into 1mm by 1mm square regions. These small regions can be scanned separately and the stripes and checkerboards can be used to join their images together in software to create a virtual image of the entire chip.
DNA sequence of S288c. Different versions are provided, including the version used to tile the chip and the current version in GenBank.
The GFF files are one way to store annotation data for genomic sequence data. They can be used with the Integrated Genome Browser (IGB) when viewing tiling chip data. Besides the standard gene structure type GFF files, GFF files have been produced to allow visualization in IGB analysis of some of the custom features on the chip. These include the unique YJY789 sequence and the Arabidopsis cDNA controls. Also, a gff file has been produced that shows the location of all the probes that are repeated in the genome.