A pair of datasets for microRNA expression profiling to examine the use of careful study design for assigning arrays to samples

Scientific Data
Li-Xuan QinDouglas A Levine

Abstract

We set out to demonstrate the logistic feasibility of careful experimental design for microarray studies and its level of scientific benefits for improving the accuracy and reproducibility of data inference. Towards this end, we conducted a study of microRNA expression using endometrioid endometrial tumours (n=96) and serous ovarian tumours (n=96) that were primary, untreated, and collected from 2000 to 2012 at Memorial Sloan Kettering Cancer Center. The same set of tumour tissue samples were profiled twice using the Agilent microRNA microarrays: once under an ideal experimental condition with balanced array-to-sample allocation and uniform handling; a second time by mimicking typical practice, with arrays assigned in the order of sample collection and processed by two technicians in multiple batches. This paper provides a detailed description of the generation and validation of this unique dataset pair so that the research community can re-use it to investigate other statistical questions regarding microarray study design and data analysis, and to address biological questions on the relevance of microRNA expression in gynaecologic cancer.

References

Nov 14, 2000·Journal of Cellular Biochemistry·E E SchadtW H Wong
Nov 28, 2002·Nature Genetics·Gary A Churchill
Sep 8, 2005·Journal of Clinical Oncology : Official Journal of the American Society of Clinical Oncology·Richard Simon
Oct 18, 2013·Nature·Lisa M McShaneBarbara A Conley
Feb 1, 2014·Nature·Francis S Collins, Lawrence A Tabak
May 3, 2014·Clinical Cancer Research : an Official Journal of the American Association for Cancer Research·Li-Xuan QinDouglas A Levine

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Citations

Jul 11, 2021·Briefings in Bioinformatics·Ai Ni, Li-Xuan Qin
Aug 12, 2021·JCO Precision Oncology·Yilin WuLi-Xuan Qin

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Methods Mentioned

BETA
Feature Extraction

Software Mentioned

R
Feature Extraction

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