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Series GSE108838 Query DataSets for GSE108838
Status Public on Jan 08, 2018
Title A unique pair of microarray datasets for microRNA profiling: data with careful design (Dataset A)
Organism Homo sapiens
Experiment type Non-coding RNA profiling by array
Summary We set out to demonstrate the logistic feasibility of careful study design in microarray studies and the level of scientific benefits it can provide, in comparison with post-hoc data adjustment such as normalization, for preventing confounding handling effects and improving the accuracy and reproducibility of disease-relevant biomarker detection. Towards this end, we conducted a study of microRNA expression using endometroid endometrial cancer tumors (n=96) and serous ovarian cancer tumors (n=96) that were all primary, untreated, and collected in 2000-2012 at Memorial Sloan Kettering Cancer Center. The same set of tumor tissue samples were profiled twice using the Agilent microRNA microarrays with different study designs.
 
Overall design In the first study, arrays were assigned to tumor samples using blocked randomization and they were processed by one experienced technician in one single run. In the second study, the arrays were assigned to the tumor samples in the order of their collection and they were handled by two technicians (the first of whom handled the first dataset) in five batches (with each batch on a separate date). This design mimicked typical practice. This dataset is from the first study.
Tumor type: advanced serous ovarian cancer or endometrioid endometrial cancer.
 
Contributor(s) Qin LX
Citation(s) 24788100, 29762551
Submission date Jan 07, 2018
Last update date May 23, 2018
Contact name Li-Xuan Qin
E-mail(s) qinl@mskcc.org
Phone 646-717-0515
Organization name Memorial Sloan Kettering Cancer Center
Department Epidemiology and Biostatistics
Street address 485 Lexington Ave
City New York
State/province New York
ZIP/Postal code 10017
Country USA
 
Platforms (1)
GPL15159 Agilent-031181 Unrestricted_Human_miRNA_V16.0_Microarray 030840 (Probe Name version)
Samples (192)
GSM2913987 tumor_ovarian [JB5011V], Dataset A
GSM2913988 tumor_ovarian [JB5143V], Dataset A
GSM2913989 tumor_endometrial [JB4870E], Dataset A
This SubSeries is part of SuperSeries:
GSE109059 Blocking and randomization to improve molecular biomarker discovery
Relations
BioProject PRJNA428875

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
GSE108838_RAW.tar 1.5 Gb (http)(custom) TAR (of TXT)
Processed data included within Sample table

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