The GeneChip™ Chromosome Copy Number Analysis Tool (CNAT) identifies genome-wide chromosomal gains and losses at high resolution.

500K: Nine tumor/normal pairs and chromosome X titration data

  • Refer to the 500K sample data for copy number analysis README for important information on this data set. 
  • The data consists of Data Transfer Tool (DTT1.1) archive files which can be restored in GCOS. 
  • If needed, download DTT 1.1 from the DTT product page.
  • Sample data consists of nine tumor/normal pairs derived from human cancer cell lines and X chromosome titration set (3X, 4X, and 5X).

500K copy number sample data

Download the 500K copy number sample data DTT files listed below.
You will need to download each file from the set, prior to clicking the DTT files.

Note: The .D0x notation indicates that the DTT archive file was broken up into multiple files due to the large size. You need to download all DTT files (e.g., Chromosome_X_NSP-DTT and Chromosome_X_NSP-D02) and then launch Data Transfer Tool to restore the chromosome X NSP data to your GCOS system.

500K: normal data – HapMap samples

To restore the data set to your GCOS system, download the associated 270 XML files below and follow the instructions:

100K: Breast cancer cell lines

  • Consists of data from 3 human breast cancer cell lines: SKBR3, MCF7, and ZR75-30 and reference DNA: Ref103
  • The call rate and QC metrics for the samples above can be found in Mapping Array Report.xls
  • Refer to the 100K Sample Data for Copy Number Analysis README for important information on this data set.
  • The data consists of Data Transfer Tool (DTT1.1) Archive files which can be restored in GCOS.
  • If needed, download DTT 1.1 from the DTT page.

  • Download the X chromosome titration set for 100K (Zip, 244 MB) 
    Includes file listed below:
    • 100K_Titration_Data.DTT

  • Download the copy number sample data ZIP file (Zip, 110 MB)
    Includes files listed below:
    • SKBR3.DTT
    • MCF7.DTT
    • ZR75-30.DTT
    • Ref103.DTT