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TranscriptomicsHigh Reproducibility Using Sodium Hydroxide Stripped Long Oligonucleotide DNA Microarrays
Recently, long oligonucleotide (60-70mer) microarrays for two-color experiments have been developed and are gaining widespread use. In addition, when there is limited availability of mRNA from tissue sources, RNA amplification can and is being used to produce sufficient quantities of cRNA for microa...
ORGANISM(S): Homo sapiens 
2010-06-10 | E-GEOD-1706 | biostudies-arrayexpress
TranscriptomicsDown-regulation of SFRP1 in a mammary epithelial cell line
Microarray data to accompany Gauger et al. (2009) Cancer Cell International paper A treated X untreated design was used whereby immortalized human mammary epithelial cell lines (TERT cells) were modified to stably express an siRNA that knocked down SFRP1 expression. These "treated" cells were label...
ORGANISM(S): Homo sapiens 
2010-05-08 | E-GEOD-15948 | biostudies-arrayexpress
TranscriptomicsActivation of Host Wound Responses in Breast Cancer Microenvironment
Cancer progression is mediated by processes that are also important in wound repair. As a result, cancers have been conceptualized as overhealing wounds or "wounds that do not heal," and gene expression signatures reflective of wound repair have shown value as predictors of breast cancer s...
ORGANISM(S): Homo sapiens 
2010-01-06 | E-GEOD-16113 | biostudies-arrayexpress
TranscriptomicsSystematic Bias in Genomic Classification Due to Contaminating Normal Tissue in Breast Tumor Samples
Results: Normal tissue contamination caused misclassification of tumors in all predictors, but different breast cancer predictors showed different susceptibility to normal tissue bias. Sensitivity and negative predictive value (NPV) of the PAM50 assay was improved by accounting for normal tissue. C...
ORGANISM(S): Homo sapiens 
2011-07-18 | E-GEOD-22384 | biostudies-arrayexpress
TranscriptomicsRelationship of mammographic density and gene expression: analysis of normal breast tissue surrounding breast cancer
Purpose: Previous studies of breast tissue gene expression have demonstrated that the extratumoral microenvironment has substantial variability across individuals, some of which can be attributed to epidemiologic factors. To evaluate how mammographic density (MD) and breast tissue composition relat...
ORGANISM(S): Homo sapiens 
2013-10-21 | E-GEOD-49175 | biostudies-arrayexpress
TranscriptomicsNormal breast tissue of obese women is enriched for macrophage markers and macrophage-associated gene expression
Activation of inflammatory pathways is one plausible mechanism underlying the association between obesity and increased breast cancer risk. However, macrophage infiltration and local biomarkers of inflammation in breast adipose tissue have seldom been studied in association with obesity. Gene expres...
ORGANISM(S): Homo sapiens 
2011-11-08 | E-GEOD-33526 | biostudies-arrayexpress
TranscriptomicsInteractions with Fibroblasts are Distinct in Basal-like and Luminal Breast Cancers
Basal-like breast cancers have several well-characterized distinguishing molecular features, but most of these are features of the cancer cells themselves. The unique stromal-epithelial interactions, and more generally, microenvironmental features of basal-like breast cancers, have not been well cha...
ORGANISM(S): Homo sapiens 
2011-05-26 | E-GEOD-26411 | biostudies-arrayexpress
TranscriptomicsRole of HGF in epithelial-stromal cell interactions during progression from benign breast disease to ductal carcinoma in situ
ABSTRACT: Introduction: Basal-like and luminal breast cancers have distinct stromal-epithelial interactions, which likely play a role in progression to invasive cancer. However, little is known about how stromal-epithelial interactions evolve in benign and pre-invasive lesions.Methods: To study epit...
ORGANISM(S): Homo sapiens 
2013-07-12 | E-GEOD-43467 | biostudies-arrayexpress
TranscriptomicsTumor Intrinsic Subtype is Reflected in Cancer-Adjacent Benign Tissue
Introduction: Overall survival of early-stage breast cancer (BC) patients is similar for those who undergo breast conserving therapy (BCT) and mastectomy, however, 10-15% of women undergoing BCT suffer ipsilateral breast tumor recurrence. The risk of recurrence may vary with age or breast cancer sub...
ORGANISM(S): Homo sapiens 
2014-04-30 | E-GEOD-50939 | biostudies-arrayexpress
TranscriptomicsEpigenome analysis of tumor adjacent normal tissue from breast cancer patients
Genome wide DNA methylation profiling of tumor adjacent normal tissue from patients with invasive breast cancer, as well as tissue from women undergoing reduction mammoplasty or prophylactic surgery. The Illumina Infinium 450k Human DNA methylation Beadchip was used to obtain DNA methylation profil...
ORGANISM(S): Homo sapiens 
2015-04-15 | E-GEOD-67919 | biostudies-arrayexpress
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