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Sample GSM4095016 Query DataSets for GSM4095016
Status Public on Oct 01, 2020
Title P3_cell-line_passage_12
Sample type genomic
 
Channel 1
Source name Cell Line
Organism Homo sapiens
Characteristics sample type: Cell Line
gender: Male
Growth protocol patient specimen were: 1) flash frozen on dry ice after surgical removal or 2) mechanically cut, seeded on agar coated flasks (0.85%) and allowed to form spheroids for up to 2 weeks at 37°C under 5% CO2 and atmospheric oxygen in DMEM medium, 10% FBS, 2mM L-Glutamine, 0.4mM NEAA and 100U/ml Pen-Strep (all from Lonza). Spheroids (generation 0) with a diameter of 300-1000 µm were then implanted in the brain of immunodeficient mice (NOD/Scid, Nude or NSG; 6 spheroids per mice). Cell lines were derived from xenotransplanted mice by papain-based enzymatic digestion of PDOX tissue and cultured in serum-free medium based on Neurobasal® base medium (Life Technologies) supplemented with 1 x B27 (Life Technologies) 2 mM L-Glutamine, 30 U/ml Pen-Step, 1 U/ml Heparin (Sigma), 20 ng/ml bFGF (Miltenyi, 130-093-841) and 20 ng/ml EGF (Provitro, 1325950500).
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was isolated from patient tissue, spheroid cultures or cell lines using the AllPrep DNA/RNA Mini Kit® (Qiagen) following manufacturer’s instructions for “Simultaneous purification of genomic DNA and total RNA from animal tissues”.
Label Cy5
Label protocol For Agilent-021529 platform 2µg, for Agilent-021850 and Agilent-028081 platform 1µg, for Agilent-030587 platform 500ng and for Agilent-021924 platform 250ng of genomic DNA were digested with RSA1 and Alu1 (Agilent) to generate 200-500bp large fragments. The BioPrime aCGH Genomic labeling Kit (Life Technologies) and Cy3 and Cy5 dyes (GE Healthcare) were used following standard protocols for Agilent aCGH (CGH enzymatic protocol v6.2; Ref # G4410-90010).
 
Channel 2
Source name Reference DNA
Organism Homo sapiens
Characteristics sample type: Reference DNA
gender: Female
catalog no: G1521
Growth protocol patient specimen were: 1) flash frozen on dry ice after surgical removal or 2) mechanically cut, seeded on agar coated flasks (0.85%) and allowed to form spheroids for up to 2 weeks at 37°C under 5% CO2 and atmospheric oxygen in DMEM medium, 10% FBS, 2mM L-Glutamine, 0.4mM NEAA and 100U/ml Pen-Strep (all from Lonza). Spheroids (generation 0) with a diameter of 300-1000 µm were then implanted in the brain of immunodeficient mice (NOD/Scid, Nude or NSG; 6 spheroids per mice). Cell lines were derived from xenotransplanted mice by papain-based enzymatic digestion of PDOX tissue and cultured in serum-free medium based on Neurobasal® base medium (Life Technologies) supplemented with 1 x B27 (Life Technologies) 2 mM L-Glutamine, 30 U/ml Pen-Step, 1 U/ml Heparin (Sigma), 20 ng/ml bFGF (Miltenyi, 130-093-841) and 20 ng/ml EGF (Provitro, 1325950500).
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was isolated from patient tissue, spheroid cultures or cell lines using the AllPrep DNA/RNA Mini Kit® (Qiagen) following manufacturer’s instructions for “Simultaneous purification of genomic DNA and total RNA from animal tissues”.
Label Cy3
Label protocol For Agilent-021529 platform 2µg, for Agilent-021850 and Agilent-028081 platform 1µg, for Agilent-030587 platform 500ng and for Agilent-021924 platform 250ng of genomic DNA were digested with RSA1 and Alu1 (Agilent) to generate 200-500bp large fragments. The BioPrime aCGH Genomic labeling Kit (Life Technologies) and Cy3 and Cy5 dyes (GE Healthcare) were used following standard protocols for Agilent aCGH (CGH enzymatic protocol v6.2; Ref # G4410-90010).
 
 
Hybridization protocol Similarly treated amounts of reference; Female or Male gDNA pool (Promega) were processed as sample genomic DNAs and hybridized with the Agilent Oligo aCGH Hybridization Kit to the corresponding platform array at 65°C for 24h or 48h respectively.
Scan protocol Microarray slides were scanned using an Agilent 2565C DNA scanner
Description P3_C15
Data processing The tif images were analyzed with Agilent Feature Extraction version 12.5, using default settings
normalised log ratio Cy5/Cy3 representing test/reference; transformed logratio matrix with 0 - unaltered, 1 - gain, -1 - loss, 2 - amplification, -2 - deletion
 
Submission date Sep 24, 2019
Last update date Oct 01, 2020
Contact name Ann-Christin Hau
E-mail(s) ann-christin.hau@lns.etat.lu
Organization name Laboratoire National de sante
Department National Center of Pathology
Street address 1, Rue Louis Rech
City Luxembourg
ZIP/Postal code 3555
Country Luxembourg
 
Platform ID GPL11357
Series (1)
GSE137959 Copy-Number abberation profiles of glioma patient tissue samples and corresponding xenografted tumor samples as well as cell lines derived there-of

Data table header descriptions
ID_REF
VALUE normalized log10 ratio Cy5/Cy3

Data table
ID_REF VALUE
1 2.783823838e-001
2 5.906898108e-001
3 5.403490033e-001
4 1.643739680e-001
5 3.234006350e-001
6 4.292607406e-001
7 2.738563605e-001
8 1.345525145e+000
9 2.680731000e-001
10 1.285799753e-001
11 1.129943593e-001
12 2.750727019e-001
13 9.288186138e-001
14 2.340904702e-001
15 1.284922473e-001
16 3.994689330e-001
17 -1.508191651e-001
18 1.396448342e-001
19 1.650032162e-001
20 5.536450890e-001

Total number of rows: 420152

Table truncated, full table size 9917 Kbytes.




Supplementary file Size Download File type/resource
GSM4095016_P3_C15_252808110978_1_1.txt.gz 43.6 Mb (ftp)(http) TXT
Raw data provided as supplementary file
Processed data included within Sample table
Processed data are available on Series record

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