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E-GEOD-32518 - Expression data from paired matched breast cancer Fine needle aspiration (FNA) or Core needle biopsies (CBX)

Status
Released on 31 October 2011, last updated on 14 November 2011
Organism
Homo sapiens
Samples (74)
Array (1)
Protocols (6)
Description
Paired FNA and CBX specimens were prospectively collected from 37 breast cancers before any systemic therapy during a biomarker discovery study at The University of Texas M. D. Anderson Cancer Center. We identified 293 probe sets overexpressed in core biopsies; these included five highly coexpressed gene clusters (metagenes) corresponding to immune functions and extracellular matrix components. We compared gene expression profiles of pairs of fine-needle (stroma-poor) and core-needle (stroma-rich) biopsies from 37 cancers to identify stroma-associated genes Pre-treatment paird matched FNA and CBX from primary tumors were obtained and RNA extracted and hybridized to afymetrix microarrays according to manufacturer protocol.
Experiment type
transcription profiling by array 
Contacts
TAKAYUKI IWAMOTO <tiwamoto@mdanderson.org>, Giampaolo Bianchini, Lajos Pusztai, Takayuki Iwamoto, Yuan Qi
Citation
Molecular anatomy of breast cancer stroma and its prognostic value in estrogen receptor-positive and -negative cancers. Bianchini G, Qi Y, Alvarez RH, Iwamoto T, Coutant C, Ibrahim NK, Valero V, Cristofanilli M, Green MC, Radvanyi L, Hatzis C, Hortobagyi GN, Andre F, Gianni L, Symmans WF, Pusztai L. , PMID:20805453
MIAME
PlatformsProtocolsVariablesProcessedRaw
Files
Investigation descriptionE-GEOD-32518.idf.txt
Sample and data relationshipE-GEOD-32518.sdrf.txt
Raw data (2)E-GEOD-32518.raw.1.zip, E-GEOD-32518.raw.2.zip
Processed data (1)E-GEOD-32518.processed.1.zip
Array designA-AFFY-33.adf.txt
R ExpressionSetE-GEOD-32518.eSet.r
Links