NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Series GSE134051 Query DataSets for GSE134051
Status Public on Jun 17, 2020
Title Differential gene expression analysis by assessing expression variation between tissue specimen of prostate cancer (PCa) and benign prostate hyperplasia (BPH) on a custom expression microarray
Organism Homo sapiens
Experiment type Expression profiling by array
Summary We assessed differential gene expression in tissue specimens of PCa and BPH patients who underwent radical prostatectomy by customized expression microarrays (Agilent).
To detect gene signatures of diagnostic and prognostic value, we assessed fresh frozen radical prostatectomy (RP) samples of PCa and BPH patients by transcriptome-wide sequencing and Agilent custom microarrays.
We stratified PCa patients according to seven clinical risk groups based on Gleason Score (GS), the presence of regional lymph node metastases (pN) and the occurrence of death of disease (DoD): (i) very low risk (group V: GS<7, pN0), (ii) low risk (group L: GS=7, pN0), (iii) medium risk (group M: GS<=7, pN1), (iv) high risk survivors without lymph node infiltration (group H-s: GS>7, pN0), (v) high risk non-survivors without lymph node infiltration (group H-d: GS>7, pN0, DoD), (vi) high risk survivors with lymph node infiltration (group H+s: GS>7, pN1), (vii) high risk non-survivors with lymph node infiltration (group H+d: GS>7, pN1, DoD). For high risk groups adjacent tumor-free prostate tissue samples were obtained (groups H+sf, H-sf, H+df, H+df). The control group contained patients with benign prostate hyperplasia (group C).
Information on the course of the disease, survival of the patients and the cause of death were obtained from the general practitioners or treating urologists or from records of the regional tumor registry. Clinicopathological parameters were obtained by routine histopathological examination of the surgical specimens. Serum levels of the prostate-specific antigen (PSA) were determined preoperatively (Abbott, Wiesbaden, Germany).
Frozen tissue samples were embedded in Tissue-Tek OCT-compound (Sakura Finetek GmbH, Staufen im Breisgau, Germany) and fixed on metal indenters by freezing. Cryo-sections were prepared using a cryo-microtome (Leica Biosystems, Nußloch, Germany) equipped with a microtome blade C35 cooled to -28 °C. For every tissue three stacks of consecutive cryo-sections (10 µm) were generated, each bordered/flanked by HE-stained cryo-sections (4 µm), which were evaluated by a pathologist with regard to tumor and stroma cell content. PCa tissue stacks had to be flanked on either side by sections containing at least 50 % tumor cells to be used for further analyses. Sections of the tissue stacks were immediately transferred to 1 ml Qiazol (Qiagen, Hilden, Germany) and stored at -80 °C until RNA isolation.
 
Overall design Total RNA of RPE-derived freshly frozen tissue of 164 PCa and 39 BPH patients was assessed for gene expression profiling by custom microarrays, including the 48 samples analyzed previously by RNA-seq.
 
Contributor(s) Baretton GB, Bartsch S, Bertram C, Blumert C, Buschmann T, Christ S, Erdmann K, Friedrich M, Froehner M, Fuessel S, Hackermueller J, Horn F, Kreuz M, Loeffler D, Loeffler M, Muders M, Otto D, Puppel S, Rade M, Reiche K, Specht M, Toma MI, Wiedemann K, Wirth M
Citation(s) 32365858
Submission date Jul 09, 2019
Last update date Feb 16, 2021
Contact name Kristin Reiche
E-mail(s) kristin.reiche@izi.fraunhofer.de
Organization name Fraunhofer Institute for Cell Therapy and Immunology
Lab Kristin Reiche
Street address Perlickstr. 1
City Leipzig
ZIP/Postal code 04103
Country Germany
 
Platforms (1)
GPL26898 Agilent-058029 Custom human expression microarray (Probe Name version)
Samples (255)
GSM3934487 prostate_tissue-C-replicate_RIB0034345
GSM3934488 prostate_tissue-C-replicate_RIB0034351
GSM3934489 prostate_tissue-V-replicate_RIB0034387
Relations
BioProject PRJNA553569

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE134051_RAW.tar 2.2 Gb (http)(custom) TAR (of TXT)
GSE134051_processed_data.tsv.gz 267.3 Mb (ftp)(http) TSV
Processed data included within Sample table
Processed data are available on Series record
| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap