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Sample GSM4956163 Query DataSets for GSM4956163
Status Public on Jan 27, 2021
Title HaCaT_SM [aCGH]
Sample type genomic
 
Channel 1
Source name HaCaT_SM
Organism Homo sapiens
Characteristics cell line: sulfur mustard (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 GM12878 cell line
Organism Homo sapiens
Characteristics 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.
 
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

Data table header descriptions
ID_REF
VALUE Normalized log2 ratio (Cy3/Cy5) representing test/reference.

Data table
ID_REF VALUE
1 2.42E-02
2 0.00E+00
3 0.00E+00
4 -1.67E-01
5 1.61E-02
6 2.98E-02
7 4.42E-02
8 1.46E-01
9 -2.34E-02
10 -8.34E-02
11 -1.63E-01
12 1.26E-01
13 8.77E-02
14 7.30E-02
15 5.00E-02
16 1.07E-01
17 -2.04E-01
18 1.23E-01
19 2.43E-02
20 2.32E-01

Total number of rows: 420288

Table truncated, full table size 6659 Kbytes.




Supplementary file Size Download File type/resource
GSM4956163_IRB_20_Cy_3_HACAT_SM_Cy5_12878.txt.gz 44.0 Mb (ftp)(http) TXT
Processed data included within Sample table

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