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Series GSE109058 Query DataSets for GSE109058
Status Public on Jan 10, 2018
Title A unique pair of microarray datasets for microRNA profiling: data without careful design (Dataset B)
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 the purpose of reducing the impact of handling effects on the accuracy and reproducibility of microarray data analysis. 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 (Human miRNA V16.0), once with uniform handling and careful design for the allocation of arrays to samples and the second study without.
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, arrays were assigned to tumor samples in the order of sample collection and they were handled by two technicians (the first of whom handled the first dataset) in multiple batches (with each batch on a separate date), mimicking typical practice. Dataset B is from the second study.
Tumor type: advanced serous ovarian cancer versus endometrioid endometrial cancer; batch: processing batches, Batch 1 to Batch 5.
Contributor(s) Qin LX
Citation(s) 24788100, 29762551
Submission date Jan 10, 2018
Last update date May 23, 2018
Contact name Li-Xuan Qin
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)
GSM2928821 tumor_endometrial [JB1245E], Dataset B
GSM2928822 tumor_endometrial [JB1394E], Dataset B
GSM2928823 tumor_endometrial [JB1437E], Dataset B
This SubSeries is part of SuperSeries:
GSE109059 Blocking and randomization to improve molecular biomarker discovery
BioProject PRJNA429511

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
GSE109058_RAW.tar 1.5 Gb (http)(custom) TAR (of TXT)
Processed data included within Sample table

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