Dataset features

Specifications


Application: Gene expression microarray analysis
Number of samples: 9
Release date: Dec 31 2010
Last update date: Oct 29 2018
Access: Public
Diseases: Breast Neoplasms, Neoplasms
Chemicals: Estrogens, Nucleotides, Progesterone, Tyrosine
Dataset link Identification of the receptor tyrosine kinase AXL in triple negative breast cancer as a novel target for the human miR-34a microRNA (gene expression)

Experimental Protocol


MDA-MB-231 cells were transfected in 6-well dishes (600,000 cells) with either AllStar negative control, Qmimic, or Dmimic at 10 nM final concentration using Lipofectamine™ 2000 (Invitrogen; Carlsbad, CA). All transfections were performed in triplicate. Forty-eight hours post-transfection, total RNA was isolated from each sample using Qiagen’s miRNeasy extraction kit (Qiagen; Germantown, MD). Total RNA samples were sent to the Laboratory of Molecular Technology (National Cancer Institute at Frederick; Frederick, MD), for processing on Affymetrix GeneChip Human Genome U133 Plus 2.0 microarrays (Affymetrix; Santa Clara, CA). Expression values were normalized using Robust Multichip Averaging (RMA). Only gene probes (AllStar vs. Mimic) that passed a log2 1.5-fold change, p < 0.05 threshold using an Empirical Bayes moderated t statistics with a Benjamini-Hochberg correction for the false discovery rate were reported. All analyses were performed with Bioconductor packages AFFYGUI and LIMMA on a R environment.

Repositories


GEO

GSE21832

ArrayExpress

E-GEOD-21832

BioProject

PRJNA129329

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Contact


Mark Mackiewicz