cell line: human female reference DNA source: Agilent SureTag Complete DNA labeling kit (Agilent, Part# 5190-3399)
Treatment protocol
Not applicable. Cells are not treated.
Growth protocol
MCF-7 cells were maintained in complete growth medium composed of DMEM-F12 (GIBCO, Life Technologies, Grand Island, NY, USA, no. 11309) supplemented with 10% fetal bovine serum (Atlanta Biologicals, Norcross, GA, USA, no. S11150), 1x nonessential amino acids (GIBCO, Life Technologies, no. 11140), 10μg/mL bovine insulin (Akron Biotech, Boca Raton, FL, USA, no. AK8213) and 0.01mg/ml gentamicin (Invitrogen, Life Technologies, no. 15710) in Bisphenol-A-free culture flasks. Cultures were fed every 2-3 days and passaged when 70-80% confluent. Serum used in both labs was purchased from the same lot.
Extracted molecule
genomic DNA
Extraction protocol
Genomic DNA was prepared using Qiagen QIAamp DNA mini Kit (# 51304) following the manufacturer’s recommended procedure.
Label
Cy3
Label protocol
1 ug gDNA was labeled with Cy5 or Cy3 using Agilent SureTag Complete DNA labeling kit (Agilent, Part# 5190-3399) following the manufacturer’s recommended procedure (Agilent Oliognucleotide Array-Based CGH for “GenomicDNA Analysis: Enzymatic Labeling for Blood, Cells, or Tissues” protocol version 7.3, Part# G4410-90010).
Channel 2
Source name
MCF-7 from ATCC (HTB-22, lot number 59388743) at passage number 150 from Brown University
MCF-7 cells were maintained in complete growth medium composed of DMEM-F12 (GIBCO, Life Technologies, Grand Island, NY, USA, no. 11309) supplemented with 10% fetal bovine serum (Atlanta Biologicals, Norcross, GA, USA, no. S11150), 1x nonessential amino acids (GIBCO, Life Technologies, no. 11140), 10μg/mL bovine insulin (Akron Biotech, Boca Raton, FL, USA, no. AK8213) and 0.01mg/ml gentamicin (Invitrogen, Life Technologies, no. 15710) in Bisphenol-A-free culture flasks. Cultures were fed every 2-3 days and passaged when 70-80% confluent. Serum used in both labs was purchased from the same lot.
Extracted molecule
genomic DNA
Extraction protocol
Genomic DNA was prepared using Qiagen QIAamp DNA mini Kit (# 51304) following the manufacturer’s recommended procedure.
Label
Cy5
Label protocol
1 ug gDNA was labeled with Cy5 or Cy3 using Agilent SureTag Complete DNA labeling kit (Agilent, Part# 5190-3399) following the manufacturer’s recommended procedure (Agilent Oliognucleotide Array-Based CGH for “GenomicDNA Analysis: Enzymatic Labeling for Blood, Cells, or Tissues” protocol version 7.3, Part# G4410-90010).
Hybridization protocol
Agilent SurePrint G3 4X180K ISCA Human CGH+SNP array (Agilent Part # G4890A, AMADID: 029830) following the manufacturer’s recommended procedure (Agilent Oliognucleotide Array-Based CGH for “GenomicDNA Analysis: Enzymatic Labeling for Blood, Cells, or Tissues” protocol version 7.3, Part# G4410-90010).
Scan protocol
The hybridized slides were scanned using Agilent Scanner G2505C and array data was extracted from the scanned image using Agilent Feature Extraction software version 11.5.1.1.
Description
MCF-7 from ATCC (HTB-22, lot number 59388743) at passage number 150 from Brown University vs. human female reference DNA, replicate 1
Data processing
Data were normalized and analyzed with CytoGenomics 3.0.4.1 (64 bit) and implemented default analysis method CGH v2.
