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Chip types: Mapping50K_Hind240 & Mapping50K_Xba240

Affymetrix press release: New Affymetrix Arrays with 100,000 SNPs Available for Early Technology Access Customers, April 5, 2004.

The so called 100K SNP chip set, which consists of two chip types Mapping50K_Hind240 and Mapping50K_Xba240, interrogates 116,204 (=57244+58960) SNPs.

Mapping50K_Hind240

> cdf <- AffymetrixCdfFile$byChipType("Mapping50K_Hind240")
> cdf
AffymetrixCdfFile:
Path: annotationData/chipTypes/Mapping50K_Hind240
Filename: Mapping50K_Hind240.CDF
Filesize: 53.43MB
Chip type: Mapping50K_Hind240
Dimension: 1600x1600
Number of cells: 2560000
Number of units: 57299
Cells per unit: 44.68
Number of QC units: 9

Mapping50K_Xba240

> cdf <- AffymetrixCdfFile$byChipType("Mapping50K_Xba240")
> cdf
AffymetrixCdfFile:
Path: annotationData/chipTypes/Mapping50K_Xba240
Filename: Mapping50K_Xba240.CDF
Filesize: 55.03MB
Chip type: Mapping50K_Xba240
Dimension: 1600x1600
Number of cells: 2560000
Number of units: 59015
Cells per unit: 43.38
Number of QC units: 9

Enzymes

One array uses the HindIII restriction enzyme and the other XbaI. Both are palindromic (in the DNA sense).

 Enzyme  | Recognition   | Cut                |
         | sequence      |                    |
-----------------------------------------------
 HindIII | 5'AAGCTT      | 5'---A  AGCTT---3' |
         | 3'TTCGAA      | 3'---TTCGA  A---5' |
         | Unique: 1     | Unique:            |
-----------------------------------------------
 XbaI    | 5'TCTAGA      | 5'---T  CTAGA---3' |
         | 3'AGATCT      | 3'---AGATC  T---5' |
         | Unique: 1     | Unique: 1          |
-----------------------------------------------

Resources

By aroma-project.org:

By Affymetrix.com:

By dChip.org: