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Title: Identification of circadian-related gene expression profiles in entrained MCF7      
dateReleased:
04-01-2016
description:
Cancer cells have broken circadian clocks as compared to their normal tissue counterparts. Moreover, it has been shown in breast cancer that disruption of common circadian oscillations are associated to worse prognosis. Numerous studies focused at conical circadian genes in breast cancer cell lines have suggested that there are no mRNA circadian-like oscillations. Nevertheless, cancer cell lines have not been extensively characterized and it is unknown to what extent the circadian oscillations are disrupted. We have chosen representative breast cancer cell lines (MCF-10A, MCF-7, ZR-75-30, MDA-MB-231, and HCC-1954) in order to determine the degree which the circadian clock is damaged. We used serum shock to synchronize the circadian clocks in culture. Our aim was to observe the time course of gene expression using cDNA microarrays in the noncancerous MCF-10A and the cancerous MCF-7 cells and characterize specific genes in other cell lines. We used a cosine function to select highly correlated profiles. Some of the identified genes were validated by qPCR and further evaluated in the other breast cancer cell lines. Interestingly, we observed that breast cancer and noncancerous cultured cells are able to generate specific circadian expression profiles in response to the serum shock. The rhythmic genes suggested via microarray and measured in each particular subtype suggest that each breast cancer cell type respond differently to the circadian synchronization. Future results could identify circadian-like genes that are altered in breast cancer and noncancerous cells which can be used to propose novel treatments. Breast cell lines are potential models for in vitro studies of circadian clocks and clock-controlled pathways. There are 8 total samples representing 0 to 28 hours in 4 hour intervals in MFC-7 breast cancer epitheleal cell line.
privacy:
not applicable
aggregation:
instance of dataset
ID:
E-GEOD-76368
refinement:
raw
alternateIdentifiers:
76368
keywords:
functional genomics
dateModified:
04-11-2016
availability:
available
types:
gene expression
name:
Homo sapiens
ID:
A-GEOD-21250
name:
Human Exonic Evidence Based Oligonucleotide (HEEBO) array [hoas.gal]
accessURL: https://www.ebi.ac.uk/arrayexpress/files/E-GEOD-76368/E-GEOD-76368.raw.1.zip
storedIn:
ArrayExpress
qualifier:
gzip compressed
format:
TXT
accessType:
download
authentication:
none
authorization:
none
accessURL: https://www.ebi.ac.uk/arrayexpress/files/E-GEOD-76368/E-GEOD-76368.processed.1.zip
storedIn:
ArrayExpress
qualifier:
gzip compressed
format:
TXT
accessType:
download
authentication:
none
authorization:
none
accessURL: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE76368
storedIn:
Gene Expression Omnibus
qualifier:
not compressed
format:
HTML
accessType:
landing page
primary:
true
authentication:
none
authorization:
none
abbreviation:
EBI
homePage: http://www.ebi.ac.uk/
ID:
SCR:004727
name:
European Bioinformatics Institute
homePage: https://www.ebi.ac.uk/arrayexpress/
ID:
SCR:002964
name:
ArrayExpress

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