Exon data from recent publications

Identification of Genetic Variants Contributing to Cisplatin-Induced Cytotoxicity using a Genome-wide Approach
Huang, Rong Stephanie; Duan, Shiwei; Shukla, Sunita J.; Kistner, Emily; Clark, Tyson A.; Chen, Tina X.; Scweitzer, Anthony C.; Blume, John E.; Dolan, M. Eileen
Data stored at GEO GSE7761 

A Novel Genome-Wide Approach to Identify Genetic Variant that Contribute to Etoposide-Induced Cytotoxicity
R. S. Huang, S. Duan, W. K. Bleibel, E. O. Kistner, W. Zhang, T. A. Clark, N. Cox and M. E. Dolan
Data stored at GEO 7792 

Exon array data set

Chip

Sample set

AGCC flat files*

EC results*

APT results

Human Exon 1.0 ST

Tissues + Mixture

Tissues 
(662 MB)
Tissue mixtures 
(408 MB)
(contents)

(updated May 2008)

Tissues 
(1.2 GB)
Tissue mixtures 
(788 MB)
(contents)

(updated May 2008)

Download 
(750 MB)
contents

Human Exon 1.0 ST

Colon Cancer

Download 
(379 MB)
contents

(updated May 2008)

Download 
(757 MB)
contents

(updated May 2008)

Download 
(292 MB)
contents

Mouse Exon 1.0 ST

Tissues

Download 
(720 MB)
contents

(updated May 2008)

Download 
(1.12 GB)
contents

(updated May 2008)

Download 
(416 MB)
contents

Rat Exon 1.0 ST

Tissues

Download 
(693 MB)
contents

(updated May 2008)

Download 
(1 GB)
contents

(updated May 2008)

Download 
(345 MB)
contents

 

Description of downloads

  • GCOS flat files: This zip file contains XDA format CEL files and GCOS XML files. These files are intended for use with Expression Console and other Exon Array analysis software. They are not intended for import into GCOS systems.

  • AGCC flat files: This zip file contains AGCC format CEL files and AGCC ARR sample attribute files generated from the GCOS Flat Files. These files are intended for use with Expression Console and other Exon Array analysis software. They are not intended for import into GCOS systems. The files were generated using a beta version of DEC (software for converting files).

  • EC results: This is an Expression Console Study Zip which can be extracted within the Expression Console application. It includes AGCC format CEL files and AGCC ARR sample attribute files. EC generated results in AGCC CHP format are also included.

    • For HG-U133 Plus 2.0, PLIER, RMA, and MAS5 results are included.
    • For the Exon Arrays, RMA results for Core (ie RefSeq supported) genes, Core exons, and all exons are included. DABG values for exon-level results are also provided.

  • APT results: This zip file contains text result files generated using apt-probeset-summarize which is a command line program included in the Affymetrix Power Tools (APT) package.

    • For HG-U133 Plus 2.0, PLIER and RMA results are included.
    • For the Exon Arrays, RMA, PLIER, and IterPLIER Core (ie RefSeq supported) gene-level results are included. Exon-level results for both Core exons and all exons using RMA, PLIER, and DABG are also provided.

* Archive contains beta version AGCC CEL and ARR files generated by a beta version of DEC.

** Due to the size of this zip study, you must manually unzip the files rather than using the unzip study feature in Expression Console.

Description of sample sets (tissues/mixtures)

This data set contains a collection of 11 tissues along with several mixtures of three tissues. The RNA samples are from a commercial source. The 11 tissues listed below have three assay replicates each.

Tissues
breast liver spleen
cerebellum muscle testes
heart pancreas thyroid
kidney prostate  

 

There are four mixtures with five assay replicates for each mixture. The mixtures are proportioned as follows:

Mixtures
 

Mix 1

Mix 2

Mix 3

Mix 4

Heart

0

0

0.33

0.33

Testes

0.5

0.33

0.33

0.17

Cerebellum

0.5

0.67

0.33

0.5

 

Tissues

This data set contains a collection of 11 tissues. The RNA samples are from a commercial source. The 11 tissues listed below have three assay replicates each.

Tissues
breast liver spleen
cerebellum muscle testes
heart pancreas thyroid
kidney prostate  

 

Colon cancer:
This data set contains a collection of 10 paired normal/cancer samples from colon tissue. The RNA samples are from a commercial source.