{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Jean Latimer"],"organism":["Homo sapiens"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-GEOD-25407"],"description":["Breast tumorigenesis involves modulation of gene expression. We used microarrays to detail the global program of gene expression underlying breast tumorigenesis. Three examples of stage I breast tumor and 3 samples of breast reduction mammoplasty tissue were expanded as explant cultures for RNA extraction and hybridization to Affymetrix microarrays."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Nucleic Acid Extraction - Total RNA was extracted using the RNAEasy kit from Qiagen according to manufacturer's instructions.","Labeling - Biotinylated cRNA were prepared using the Affymetrix GeneChip® Expression 3' Amplification One-Cycle Target Labeling and Control Reagents assay (Affymetrix Corp, Santa Clara, CA) starting with 1 ug of purified total RNA.","Growth Protocol - Samples were cultured in MWRI medium and expanded until 10-20 ug of total RNA were obtainable.","Sample Processing - None","Hybridization - Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45°C on Affymetrix Human Genome HGU133 Plus 2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450."],"figure_sub":["MIAME Score","Raw Data","Organization","Assays and Data","Processed Data","MAGE-TAB Files","Array Designs"],"data_protocol":["Image Adquisition - GeneChips were scanned using the Affymetrix Scanner 3000.","Assay Data Transformation - ID_REF = <br>VALUE = PLIER signal intensity","Feature Extraction - The data were analyzed with GeneSpring GX 10.0.1 using the PLIER algorithm and default analysis settings."],"omics_type":["Unknown","Transcriptomics","Genomics","Proteomics"],"pubmed_abstract":["The molecular etiology of breast cancer has proven to be remarkably complex. Most individual oncogenes are disregulated in only approximately 30% of breast tumors, indicating that either very few molecular alterations are common to the majority of breast cancers, or that they have not yet been identified. In striking contrast, we now show that 19 of 19 stage I breast tumors tested with the functional unscheduled DNA synthesis assay exhibited a significant deficiency of DNA nucleotide excision repair (NER) capacity relative to normal epithelial tissue from disease-free controls (n = 23). Loss of DNA repair capacity, including the complex, damage-comprehensive NER pathway, results in genomic instability, a hallmark of carcinogenesis. By microarray analysis, mRNA expression levels for 20 canonical NER genes were reduced in representative tumor samples versus normal. Significant reductions were observed in 19 of these genes analyzed by the more sensitive method of RNase protection. These results were confirmed at the protein level for five NER gene products. Taken together, these data suggest that NER deficiency may play an important role in the etiology of sporadic breast cancer, and that early-stage breast cancer may be intrinsically susceptible to genotoxic chemotherapeutic agents, such as cis-platinum, whose damage is remediated by NER. In addition, reduced NER capacity, or reduced expression of NER genes, could provide a basis for the development of biomarkers for the identification of tumorigenic breast epithelium."],"study_type":["transcription profiling by array"],"species":["Homo sapiens"],"pubmed_title":["Nucleotide excision repair deficiency is intrinsic in sporadic stage I breast cancer."],"pubmed_authors":["Jean Latimer","Stephen Grant","Latimer JJ, Johnson JM, Kelly CM, Miles TD, Beaudry-Rodgers KA, Lalanne NA, Vogel VG, Kanbour-Shakir A, Kelley JL, Johnson RR, Grant SG"],"additional_accession":[]},"is_claimable":false,"name":"Expression data from breast tumors and reduction mammoplasty explants","description":"Breast tumorigenesis involves modulation of gene expression. We used microarrays to detail the global program of gene expression underlying breast tumorigenesis. Three examples of stage I breast tumor and 3 samples of breast reduction mammoplasty tissue were expanded as explant cultures for RNA extraction and hybridization to Affymetrix microarrays.","dates":{"release":"2010-11-17T00:00:00Z","modification":"2023-08-10T08:41:24.896Z","creation":"2022-02-02T12:43:34.687Z"},"accession":"E-GEOD-25407","cross_references":{"GEO":["GSE25407"],"pubmed":["21118987"],"EFO":["EFO_0002768"],"doi":["10.1073/pnas.0914772107"]}}