disease state: nonmetastatic breast cancer tissue: primary breast tumor er status: ER- her2 status: Her2+ age: 32 yr
Treatment protocol
The 19 HER2+ breast cancer brain metastatic specimens were fresh-frozen biopsies obtained from the M.D. Anderson Cancer Center between 1998 and 2001. The HER2+ primary breast cancer specimens were fresh-frozen biopsies obtained from the Massachusetts General Hospital in 2006.
Growth protocol
Not applicable.
Extracted molecule
total RNA
Extraction protocol
4,000–5,000 malignant epithelial cells were procured by laser capture microdissection using a PixCell IIe system (Molecular Devices, Mountain View, CA, USA) as described in PubMed ID: 19187537. Total RNA was isolated from captured cells using the PicoPure RNA isolation kit (Molecular Devices), then amplified by T7 RNA amplification (RiboAmp; Molecular Devices).
Label
biotin
Label protocol
According to manufacturer's instructions (Affymetrix, Santa Clara, CA, USA).
Hybridization protocol
According to manufacturer's instructions (Affymetrix, Santa Clara, CA, USA).
Scan protocol
According to manufacturer's instructions (Affymetrix, Santa Clara, CA, USA). The scanner model used to scan the arrays was an Affymetrix GeneChip Scanner 3000-7G.
Description
MGH1104
Data processing
MAS5.0 as implemented by Bioconductor package simpleaffy, version 2.14.05.
