Application of affymetrix array and massively parallel signature sequencing for identification of genes involved in prostate cancer progression

Asa J Oudes¹ , Jared C Roach¹ , Laura S Walashek² , Lillian J Eichner¹ , Lawrence D True³ , Robert L Vessella² and Alvin Y Liu¹^,2

¹Institute for Systems Biology, Seattle, USA

²Department of Urology, University of Washington, Seattle, USA

³Department of Pathology, University of Washington, Seattle, USA

author email corresponding author email

BMC Cancer 2005, 5:86doi:10.1186/1471-2407-5-86


Published:	22 July 2005

Additional files

Additional File 1:

PCR primer sequences. Nucleic acid sequences of PCR primer pairs for C4-2 specific, LNCaP specific, and MPSS zero genes.

Format: XLS Size: 28KB Download file

This file can be viewed with: Microsoft Excel Viewer

Additional File 2:

Overall Affymetrix and MPSS merge results. List of GeneIDs detected by Affymetrix and MPSS expression profiling of C4-2 and LNCaP cell lines with corresponding signal or tpm data. Empty cells indicate absence of data. Columns contain the following data: GeneID (NCBI GeneID), X_P (Affymetrix present call 1 or absent call 0), X_S (Affymetrix raw signal), X_tpm (MPSS tpm for the gene), where X = cell line. Cell lines are labeled as follows: LN = LNCaP and C42 = C4-2.

Format: XLS Size: 1.6MB Download file

This file can be viewed with: Microsoft Excel Viewer

Additional File 3:

C4-2 specific genes. Genes determined to be unique to C4-2 cells by Affymetrix signal and MPSS tpm. Gene expression was tested by RT-PCR, and PLD1, ACAS2L, CA1, ITM2A, CA9, CARD14, GPR54 were detected in C4-2 and not in LNCaP. Columns contain the following data: GeneID (NCBI GeneID), X_S (Affymetrix raw signal), X_tpm (MPSS tpm), X_RT (RT-PCR result, positive + or negative -), where X = cell line. Cell lines are labeled as follows: LN = LNCaP and C42 = C4-2.

Format: XLS Size: 12KB Download file

This file can be viewed with: Microsoft Excel Viewer

Additional File 4:

LNCaP specific genes. Genes determined to be unique to LNCaP cells by Affymetrix signal and MPSS tpm. Gene expression was tested by RT-PCR, and ETV1, PAK1, EPHA7, HELLS, were detected in LNCaP and not in C4-2. Columns contain the following data: GeneID (NCBI GeneID), X_S (Affymetrix raw signal), X_tpm (MPSS tpm), X_RT (RT-PCR result, positive + or negative -), where X = cell line. Cell lines are labeled as follows: LN = LNCaP and C42 = C4-2.

Format: XLS Size: 18KB Download file

This file can be viewed with: Microsoft Excel Viewer