S288c Genome Chip

 

1lq files

Affymetrix 1lq files

 

The 1lq file describes what is on the chip; x,y location, sequence, chromosome location, etc. The file is an internal affymetrix format and usually not released. However, it contains the most complete description of what is physically on the chip. 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 with the sequence written 5' to 3' is available here. I have used the convention of giving files with the probe sequence written 5' to 3' a .SGTC1lq file name suffix. The header also notes that the sequence is written 5' to 3'. Writing the probe sequences 5' to 3' will shift the position of the mm base in the probe in probes where the MM probe has an asymmetrical position. This changes the POS fields. In .SGTC1lq files made on March 15, 2005 or later the XPOS and POS fields have been recalculated to match the MM position in the 5' to 3' written probes.

Some of the S288c tiled probes are shorter than 25 bp on the tiling chip. This is due to constraints in the number of steps in the synthesis steps to make the chip. Certain probes need to be shortened to meet these constraints. These are usually low complexity probes. The number of probes with shortened length is small. For the S288c tiled genome, the probe lengths and # of probes (PM only) of that length are: 25: 2,955,345, 24: 2, 23: 55,760, 22: 4, 21: 5,740, 19: 755

The last probe at the end of some chromosomes have incorrect expos values because the probes were shortened due to being at the end of the sequence. I have corrected the expos of these probes in the SGTC1lq file as of March 15 2005. I have also verified the expos of all S288c tiling probes.

Available 1lq files:

file name
(downloadable, zipped)
Description
S.cerevisiae_tiling.1lq.zip Original 1lq file(and name) from Affymetrix. Probe sequences are written 3' to 5'!!!. S288c probe locations are mapped relative to Version 1 of the S288c sequence in this file.
S.cerevisiae_tiling.SGTC1lq.zip Probe sequences are written 5' to 3'. S288c probe locations are mapped relative to Version 1 of the S288c sequence in this file.
S.cerevisiae_tiling_rotated.SGTC1lq.zip Probe sequences are written 5' to 3'. x,y positions in file are transformed so they so they align with the image produced by the upgraded 7G scanner. S288c probe locations are mapped relative to Version 1 of the S288c sequence in this file.
2005Jan_Yeast_tiling.SGTC1lq.zip Probe sequences are written 5' to 3'. S288c probe locations are mapped relative to 2005Jan version of the S288c sequence in this file. The zip archive contains the 2005Jan_Yeast_tiling.SGTC1lq file description of the tiling chip and the 2005JanYeastTilng.rejected.SGTC1lq file, a list of the rejected probes as a result of the mapping to the new version of the yeast genome sequence

For sequences mapped to new versions of the yeast genomic sequence, there are probes on the chip that no longer correspond to sequence in the new yeast genome due to the revisions in the sequence. In the .SGTC1lq files these probes are indicated by a giving the original EXPOS a negative value. Software that processes 1lq files may not be able to deal with negative values in the EXPOS field, so you may need to prefilter this file. However I thought it important to include all probes on the chip in the SGTC1lq file. A file .rejected.SGTC1lq is included in the zip archive that lists the probes no longer mapped to the genome.

A Brief description of the fields in this file:

Column Name Description
x the x position of the feature on the chip
y the y position of the feature on the chip
sequence the probe sequence on the chip 3 PRIME to 5 PRIME in .1lq files, 5' to 3' in SGTC1lq files.
destype a number describing the type of feature, negative or positive number indicates weather probe hybs. to sense or antisense target (relative to original sequence specified in design). last (the ones digit) digit tells about mismatch, 1 = perfect match probe, 2 = single probe, no mismatch (perfect match) , 3 = mismatch probe.
feature almost are "control", affy's docs should say what it is used for
Qualifier name useful to user, e.g. at_F1_chr1_at, for a probe set. suffix _at = "antisense target", _st = "sense target"
Expos location of probe mismatch base in seq named in Qualifier
PLEN probe length
POS position of mismatch in probe
CBASE complement to base in probe at mismatch position (this appears to refer to the PM probe, since its value is the same for PM and MM probes from the same probe pair)
PBASE base in probe at mismatch position
TBASE base in target at mismatch position
IPBASE another field - does not seem to be used.
UNIT an integer unique to Qualifier(probe set)
BLOCK another field - does not seem to be used.
ATOM integer unique to a probe or probe pair if mismatch probes are included. ATOM is unique within UNIT, so UNIT combined with ATOM will give a unique identifier for a probe pair on a chip