Two independent sets of breast cancers with matched protein lysates and formalin-fixed, paraffin-embedded (FFPE) sections were utilized: TCGA (n = 885) and MDACC (n = 63). For the TCGA cohort, only a subset of cases with RPPA data was available with matched unstained FFPE sections (n = 109).
Breast cancer cell lines (T47D, MCF7) were obtained from the MD Anderson Characterized Cell Line Core facility (Houston, TX). The identities of all cell lines were verified using AmpF/STR Identifier kit (Applied Biosystems) by the core facility and used within 6 months of obtaining the cell lines. The lines were cultured in DMEM supplemented with 5% fetal bovine serum (FBS) at 37°C in 5% carbon dioxide atmosphere. Cell lines were routinely tested for Mycoplasma infection using a MycoTect Kit (Invitrogen).
MDA-MB-134 (ATCC) and Sum44PE (Asterand) cells were cultured as previously described (16 (link)). The cell lines were authenticated annually by PCR RFLP analyses and confirmed to be Mycoplasma negative at the University of Pittsburgh Cell Culture and Cytogenetics Facility (Pittsburgh, PA).
Cancer tissues from the University of Utah (A.W.) were mastectomy specimens from patients without prior therapy. Normal specimens were collected from matched grossly uninvolved tissues. Tissues were collected and de-identified using approved IRB#10924.
Breast cancer cell lines (T47D, MCF7) were obtained from the MD Anderson Characterized Cell Line Core facility (Houston, TX). The identities of all cell lines were verified using AmpF/STR Identifier kit (Applied Biosystems) by the core facility and used within 6 months of obtaining the cell lines. The lines were cultured in DMEM supplemented with 5% fetal bovine serum (FBS) at 37°C in 5% carbon dioxide atmosphere. Cell lines were routinely tested for Mycoplasma infection using a MycoTect Kit (Invitrogen).
MDA-MB-134 (ATCC) and Sum44PE (Asterand) cells were cultured as previously described (16 (link)). The cell lines were authenticated annually by PCR RFLP analyses and confirmed to be Mycoplasma negative at the University of Pittsburgh Cell Culture and Cytogenetics Facility (Pittsburgh, PA).
Cancer tissues from the University of Utah (A.W.) were mastectomy specimens from patients without prior therapy. Normal specimens were collected from matched grossly uninvolved tissues. Tissues were collected and de-identified using approved IRB#10924.
