HaCaT cells were kindly provided by Prof. Dr. N. Fusenig (German Cancer Research Center, Heidelberg, Germany) and cultivated in Dulbecco’s Modified Eagle Medium supplemented with glutamine and 10 % fetal bovine serum (Gibco, Carlsbad, CA). Cells were maintained at 37 °C and 5 % CO2 in a humidified atmosphere. For cell passaging, HaCaT were detached with 0.05 % trypsin in 1 mM EDTA (Gibco, Carlsbad, CA) for 5 min and reseeded in fresh culture medium twice a week. Human lymphoblastoid cells (GM12878, suspension cells) were obtained from Corriell Institute for medical Research (Camden, New Jersey, USA). Cells were cultivated at 37°C / 5% CO2 in RPMI-1640 2mM L-glutamine and Eagle´s Minimum Essential Medium.
Extracted molecule
genomic DNA
Extraction protocol
DNA was isolated using the QIAGEN® Blood & Cell Culture DNA Midi Kit (QIAGEN, Cat No./ID: 13343, Hilden, Germany).
Label
Cy3
Label protocol
Labelling of DNA and hybridization onto a 400k SurePrint G3 Human CGH Array (Agilent; G4448A-021850) were performed according to the manufacturer’s recommendations (Agilent® Oligonucleotide Array-Based CGH for Genomic DNA Analysis Enzymatic Labeling for Blood, Cells, or Tissues, ProtocolVersion 7.3 March 2014).
reference cell line: GM12878 cell type: human lymhoblastoid cell
Growth protocol
HaCaT cells were kindly provided by Prof. Dr. N. Fusenig (German Cancer Research Center, Heidelberg, Germany) and cultivated in Dulbecco’s Modified Eagle Medium supplemented with glutamine and 10 % fetal bovine serum (Gibco, Carlsbad, CA). Cells were maintained at 37 °C and 5 % CO2 in a humidified atmosphere. For cell passaging, HaCaT were detached with 0.05 % trypsin in 1 mM EDTA (Gibco, Carlsbad, CA) for 5 min and reseeded in fresh culture medium twice a week. Human lymphoblastoid cells (GM12878, suspension cells) were obtained from Corriell Institute for medical Research (Camden, New Jersey, USA). Cells were cultivated at 37°C / 5% CO2 in RPMI-1640 2mM L-glutamine and Eagle´s Minimum Essential Medium.
Extracted molecule
genomic DNA
Extraction protocol
DNA was isolated using the QIAGEN® Blood & Cell Culture DNA Midi Kit (QIAGEN, Cat No./ID: 13343, Hilden, Germany).
Label
Cy5
Label protocol
Labelling of DNA and hybridization onto a 400k SurePrint G3 Human CGH Array (Agilent; G4448A-021850) were performed according to the manufacturer’s recommendations (Agilent® Oligonucleotide Array-Based CGH for Genomic DNA Analysis Enzymatic Labeling for Blood, Cells, or Tissues, ProtocolVersion 7.3 March 2014).
Hybridization protocol
Samples were hybridized on a whole genome array (Agilent®, Santa Clara, CA, USA; SurePrint G3 Human Genome CGH Microarray 2x400K, 5.3 kb spacing).
Scan protocol
Agilent® Oligonucleotide Array-Based CGH for Genomic DNA Analysis, Version 7.3 March 2014; Agilent® G2505C; Scan Control Version A.8.1.3; resolution 3 µm; 16 bit TIFF; no XDR; Images were quantified using Agilent Feature Extraction Software (version 12.0).
Data processing
Agilent Feature Extraction Software (v 12.0) was used for background subtraction and LOWESS normalization.
