|
| Status |
Public on Jan 27, 2021 |
| Title |
HaCaT_SM_vs_HaCaT [aCGH] |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
HaCaT_SM
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: SM-resistant
cell type: human keratinocyte 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 |
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).
|
| |
|
| Channel 2 |
| Source name |
human keratinocyte cell line
|
| Organism |
Homo sapiens |
| Characteristics |
reference cell line: untreated HaCaT cell line
cell type: human keratinocyte 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.
|
| |
|
| Submission date |
Dec 04, 2020 |
| Last update date |
Jan 27, 2021 |
| Contact name |
Hanns Leonhard Kaatsch |
| E-mail(s) |
hannsleonhardkaatsch@bundeswehr.org
|
| Organization name |
Bundeswehr Institute of Radiobiology
|
| Street address |
Neuherbergstraße 11
|
| City |
Munich |
| ZIP/Postal code |
80937 |
| Country |
Germany |
| |
|
| Platform ID |
GPL9777 |
| Series (2) |
| GSE162645 |
Genomic adaptation and mutational patterns in a HaCaT subline resistant to alkylating agents and ionizing radiation [aCGH] |
| GSE162646 |
Genomic adaptation and mutational patterns in a HaCaT subline resistant to alkylating agents and ionizing radiation |
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