Measuring Gene Expression in FFPE Tissues

To measure gene expression in archival FFPE tissue specimens, whole-transcriptome amplification using the WT-Ovation FFPE System V2 (NuGEN) was paired with microarray technologies using the GeneChip Human Gene 1.0 ST microarray (Affymetrix) as previously described.^{8 (link), 9 (link)} Expression profiles were processed by regressing out technical variables including mRNA concentration, block age, batch (96-well plate), percentage of probes above background, log-transformed average background signal, and median of the perfect match probes for each probe intensity of the raw data. The residuals were shifted to the original mean expression values and normalized using the robust multi-array average method.^{10 (link), 11 (link)} We mapped gene names to Affymetrix transcript cluster IDs using the NetAffx annotations as implemented in Bioconductor annotation package pd.hugene.1.0.st.v1, resulting in 20,254 unique gene names. Gene expression data are available through Gene Expression Omnibus (GSE79021).

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Ebot E.M., Gerke T., Labbé D.P., Sinnott J.A., Zadra G., Rider J.R., Tyekucheva S., Wilson K.M., Kelly R.S., Shui I.M., Loda M., Kantoff P.W., Finn S., Vander Heiden M.G., Brown M., Giovannucci E.L, & Mucci L.A. (2017). Gene expression profiling of prostate tissue identifies chromatin regulation as a potential link between obesity and lethal prostate cancer. Cancer, 123(21), 4130-4138.

Publication 2017

WT-Ovation FFPE System V2 GeneChip Human Gene 1.0 ST microarray

Gene Gene cluster Gene expression Genechip Human Microarray Mrna Tissue Transcriptome

Corresponding Organization : Harvard University

Other organizations : Moffitt Cancer Center, Dana-Farber Cancer Institute, The Ohio State University, Brigham and Women's Hospital, Boston University, Memorial Sloan Kettering Cancer Center, St. James's Hospital, Trinity College Dublin, Massachusetts Institute of Technology

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Variable analysis

independent variables

WT-Ovation FFPE System V2 (NuGEN) for whole-transcriptome amplification
GeneChip Human Gene 1.0 ST microarray (Affymetrix) for microarray technologies

dependent variables

Gene expression profiles

control variables

MRNA concentration
Block age
Batch (96-well plate)
Percentage of probes above background
Log-transformed average background signal
Median of the perfect match probes for each probe intensity of the raw data

positive controls

None specified

negative controls

None specified

Annotations

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