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RNA profiling from ovarian FFPE specimens

ABSTRACT: To study feasibility of gene expression profiling from FFPE tissues using NuGen amplified mRNA hybridized on Affymetrix GeneChip Human Gene 1.0 ST arrays, we designed a pilot study utilizing samples from prostate cancer cohort. We selected samples from large-scale epidemiologic studies and clinical trials representative of a wide variety of fixation times, block ages and block storage conditions.

ORGANISM(S): Homo sapiens

PROVIDER: GSE54807 | GEO | 2014/07/01

SECONDARY ACCESSION(S): PRJNA237800

REPOSITORIES: GEO

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RNA profiling from prostate FFPE specimens

2014-07-01 | GSE54808 | GEO

RNA profiling from ovarian FFPE specimens

Project description:To study feasibility of gene expression profiling from FFPE tissues using NuGen amplified mRNA hybridized on Affymetrix GeneChip Human Gene 1.0 ST arrays, we designed a pilot study utilizing samples from prostate cancer cohort. We selected samples from large-scale epidemiologic studies and clinical trials representative of a wide variety of fixation times, block ages and block storage conditions. Five serous carcinoma and six clear cell carcinoma samples with technical replicates

2014-07-01 | E-GEOD-54807 | biostudies-arrayexpress

RNA profiling from ovarian FFPE specimens (Nanostring)

Project description:To study feasibility of gene expression profiling from FFPE tissues using NanoString nCounter platform, we designed a pilot study utilizing samples from ovarian cancer cohort. We selected samples from large-scale epidemiologic studies and clinical trials representative of a wide variety of fixation times, block ages and block storage conditions.

2014-07-01 | GSE55056 | GEO

RNA profiling from prostate FFPE specimens (Nanostring)

Project description:To study feasibility of gene expression profiling from FFPE tissues using NanoString nCounter platform, we designed a pilot study utilizing samples from prostate cancer cohort. We selected samples from large-scale epidemiologic studies and clinical trials representative of a wide variety of fixation times, block ages and block storage conditions.

2014-07-01 | GSE55055 | GEO

RNA profiling from prostate FFPE specimens

Project description:To study feasibility of gene expression profiling from FFPE tissues using NuGen amplified mRNA hybridized on Affymetrix GeneChip Human Gene 1.0 ST arrays, we designed a pilot study utilizing samples from prostate cancer cohort. We selected samples from large-scale epidemiologic studies and clinical trials representative of a wide variety of fixation times, block ages and block storage conditions. We profiled seven paired tumor and adjacent normal prostate tissue samples from three patients with Gleason score 8, one with Gleason score 7 and three with Gleason 6 disease. 11 samples had two or three technical replicates.

2014-07-01 | E-GEOD-54808 | biostudies-arrayexpress

RNA profiling from ovarian FFPE specimens (Nanostring)

2014-07-01 | E-GEOD-55056 | biostudies-arrayexpress

RNA profiling from prostate FFPE specimens (Nanostring)

Project description:To study feasibility of gene expression profiling from FFPE tissues using NanoString nCounter platform, we designed a pilot study utilizing samples from prostate cancer cohort. We selected samples from large-scale epidemiologic studies and clinical trials representative of a wide variety of fixation times, block ages and block storage conditions. five paired tumor and adjacent normal prostate tissue speciemens with technical replicates

2014-07-01 | E-GEOD-55055 | biostudies-arrayexpress

Gene expression profiling of FFPE breast cancer samples [Illumina DASL WG platform]

Project description:The use of Affymetrix U133 2.0 Plus chips on FFPE samples when coupled with a qPCR-based sample pre-assessment step, yielded satisfactory results from the point of view of biological reliability. When compared with the Illumina DASL WG platform, specifically designed for degraded RNA, the data generated with the Affymetrix platform showed a wider interquartile range (1.32 vs 0.57, p<2.2x10-16) suggesting a superior discriminatory power within samples as indicated by the good agreement with the immunohistiochemically derived ER status. FFPE primary breast cancer samples profiled using Illumina DASL WG platform after RNA amplification with the Nugen WT-Ovation FFPE System

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2020-04-02 | PXD017269 | Pride

Gene expression profiling of FFPE breast cancer samples

Project description:We implemented an optimized processing, using alternative Chip Description Files (CDFs) and fRMA normalization, which improve the quality of downstream analysis. We profiled 44 FFPE primary breast cancer samples using Affymetrix HG-U133 Plus 2.0 microarray platform after RNA amplification with the Nugen WT-Ovation FFPE System

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