Affymetrix - Copy Number Analysis



		Sample Data Sets for Copy Number Analysis

The Affymetrix GeneChip® Chromosome Copy Number Analysis Tool (CNAT) identifies genome-wide chromosomal gains and losses at high resolution. For more information regarding the Copy Number Analysis Tool, see the CNAT product page.

COPY NUMBER SAMPLE DATA

500K: Nine Tumor/Normal Pairs and Chromosome X Titration Data
500K: Normal data – HapMap Samples
100K: Breast cancer cell lines

500K: Nine Tumor/Normal Pairs and Chromosome X Titration Data

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The sample data set consists of nine Tumor/Normal Pairs derived from human cancer cell lines and X Chromosome titration set (3X, 4X, and 5X).

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Please refer to the 500K Sample Data for Copy Number Analysis README file for important information on this data set

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The data consists of Data Transfer Tool (DTT1.1) Archive files which can be restored in GCOS.

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If needed, download DTT 1.1 from the DTT product page.

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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

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There are 48 HapMap samples available here:
http://www.affymetrix.com/support/technical/
sample_data/500k_data.affx

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The full 270 HapMap dataset CEL files can be downloaded from
http://www.hapmap.org/downloads/raw_data/affy500k/

To restore this dataset to your GCOS system, download the associated 270 XML files available here and follow the instructions in the README file:

270 EXP Files (zip, 1.4 MB)

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
•		Please refer to the 100K Sample Data for Copy Number Analysis README file 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.
•		Download the X Chromosome titration set for 100K (244 MB - includes file listed below)
100K_Titration_Data.DTT
•		Download the Copy Number Sample Data ZIP file (110 MB - includes files listed below)
SKBR3.DTT MCF7.DTT ZR75-30.DTT Ref103.DTT