S288c Genome Tiling Chip

 

Tiling data viewed in affy's IGB software (Marina & Lior's data)

Sequences on the tiling chip
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
Manufacturing controls * QC BioB, C, D and Cre Control block (in both senses)
* QC tag Control block (in both senses)
Boring controls * 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.
   
Chip Analysis and data files
Described briefly below are several data formats and software applications that should be useful in analysis of tiling chip data. links are given, below and in the menu at left, to pages that describe each data type in more detail and provide links to download the data. If the data format contains S288c genomic sequence or coordinates, different versions are available that correspond to the "Version 1" used to tile the chip and the current Version of the S288c sequence produced by SGD and released to genbank. The current version will be updated semi-annually.

Affymetrix .1lq file

Affymetrix has released the commercial version of thier 5 micron scanner. It no longer rotates chip images after scanning. Analyzing chips with the upgraded 7G scanner requires a different set of files compared to the original set released with the tiling chip.
The .1lq file describes what is on the chip; x,y location, sequence, chromosome location, etc. Please note, the sequence in this file is written 3' to 5', so if you want to use this information, be warned. The best advice is to never use this file for data analysis. A version of this file is provided with the sequence written 5' to 3'. A version has been made that maps the probe positions to the current genome coordinates.

DNA Sequences (FASTA format)

DNA sequence of S288c. Different versions are provided, including the version used to tile the chip and the current version in GenBank.

Sequence Annotations - Genbank, SGD and other (GFF format)

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.

bpmap files (GTRANS input files)


These files contain probe locations, both the x,y chip coordinates and the chromosome coordinates. The bpmap files are inputs, along with cel files for chip analysis with GTRANS. There are rotated versions of these files for the updated 7G scanner.

Chip Analysis Software

Descriptions of programs developed at SGTC and from other sources. Instructions for running and/or links for downloading programs and needed data files

Notes about Version Names


SGD and/or GenBank have not released versions of the yeast genome with version numbers or dates. FIles that refer to "current sequence" will have a date as part of the name of the file and will use the sequence that is current in GenBank as of that date. A web page on this site will keep a list of the dates used and the genbank accession numbers and gi numbers that go along with the dates. SInce the version of the sequence on the chip can not be associated with any specific release date, the files that contain this sequence will be referred to as ver1 (version 1) in the file names. Individual chromosomes have unique version numbers in Genbank