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Sample GSM5526587 Query DataSets for GSM5526587
Status Public on Apr 29, 2023
Title arrayCGH data from patient vu9963
Sample type genomic
 
Channel 1
Source name pediatric patient samples
Organism Homo sapiens
Characteristics subarray: 2
subject: patient vu9963
Extracted molecule genomic DNA
Extraction protocol 10 μg genomic reference or patient DNA was digested with AluI (20 U) and RsaI (20 U) (Invitrogen) overnight at 37°C. Patient genomic DNA (2 μg) and male/female reference DNA (2 μg; Promega) were fragmented by sonification (VibraCell Model VC130; Sonics & Materials, Newtown, CT). DNA fragmentation was verified by agarose gel electrophoresis. Individual reference and experimental samples were then purified using the QIAQuick polymerase chain reaction (PCR) clean-up kit (Qiagen, Valencia, CA).
Label Cy5
Label protocol Labeling reactions with Cy5-dUTP and Cy3-dUTP (PerkinElmer, Wellesley, MA) were performed with 5 μg purified restricted DNA using the Bioprime labeling kit (Invitrogen, Paisley, United Kingdom) according to the manufacturer's instructions. Experimental and reference targets for each hybridization were pooled and mixed with 50 μg human Cot-1 DNA (Invitrogen), 100 μg yeast tRNA (Invitrogen), and 1x hybridization control targets (SP310; Operon Technologies, Alameda, CA) in a final volume of 500 μL in situ hybridization buffer (Agilent Technologies).
 
Channel 2
Source name pediatric patient samples
Organism Homo sapiens
Characteristics subject: control
Extracted molecule genomic DNA
Extraction protocol 10 μg genomic reference or patient DNA was digested with AluI (20 U) and RsaI (20 U) (Invitrogen) overnight at 37°C. Patient genomic DNA (2 μg) and male/female reference DNA (2 μg; Promega) were fragmented by sonification (VibraCell Model VC130; Sonics & Materials, Newtown, CT). DNA fragmentation was verified by agarose gel electrophoresis. Individual reference and experimental samples were then purified using the QIAQuick polymerase chain reaction (PCR) clean-up kit (Qiagen, Valencia, CA).
Label Cy3
Label protocol Labeling reactions with Cy5-dUTP and Cy3-dUTP (PerkinElmer, Wellesley, MA) were performed with 5 μg purified restricted DNA using the Bioprime labeling kit (Invitrogen, Paisley, United Kingdom) according to the manufacturer's instructions. Experimental and reference targets for each hybridization were pooled and mixed with 50 μg human Cot-1 DNA (Invitrogen), 100 μg yeast tRNA (Invitrogen), and 1x hybridization control targets (SP310; Operon Technologies, Alameda, CA) in a final volume of 500 μL in situ hybridization buffer (Agilent Technologies).
 
 
Hybridization protocol The hybridization mixtures were denatured at 95°C for 3 minutes, preincubated at 37°C for 30 minutes, and hybridized to the array in a microarray hybridization chamber (Agilent Technologies) for 14 to 18 hours at 65°C in a rotating oven (Robbins Scientific, Mountain View, CA). The array slides were washed in 0.5x SSC/0.005% Triton X-102 at room temperature for 5 minutes, followed by 5 minutes at 37°C in 0.1x SSC/0.005% Triton X-102.
Scan protocol TIF images were obtained using Agilent scanner (model B and C)
Data processing Images were analyzed using Cytogenomics v.50.0.38 software with the default analysis method: CGH v2 (ADM-2 algortihm). Threshold of 6.0, with a minimum of 3 consecutive aberrant probes and a minimum absolute amplification/deletion average of 0.25 log2ratio
 
Submission date Aug 17, 2021
Last update date Apr 29, 2023
Contact name Rico Hagelaar
E-mail(s) [email protected]
Organization name Princess Maxima Center
Street address Heidelberglaan 25
City Utrecht
ZIP/Postal code 3584CS
Country Netherlands
 
Platform ID GPL9777
Series (2)
GSE182312 Elevated enhancer-oncogene contacts and higher oncogene expression levels by recurrent CTCF inactivating mutations in acute T cell leukemia [Array CGH]
GSE182317 Elevated enhancer-oncogene contacts and higher oncogene expression levels by recurrent CTCF inactivating mutations in acute T cell leukemia

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

Data table
ID_REF VALUE
1 -1.595908796e-002
2 0.000000000e+000
3 0.000000000e+000
4 7.929851568e-002
5 -3.311527344e-002
6 1.326327174e-001
7 -2.907968168e-002
8 -8.884918868e-003
9 3.746717980e-002
10 -7.801597162e-002
11 -4.005813880e-003
12 4.352320019e-002
13 1.284164019e-002
14 -4.288842670e-002
15 3.461370857e-002
16 2.942647772e-002
17 -2.015610344e-002
18 1.226417494e-001
19 -1.814337567e-002
20 2.000750126e-002

Total number of rows: 420288

Table truncated, full table size 9964 Kbytes.




Supplementary file Size Download File type/resource
GSM5526587_252185010438_S01_CGH_105_Dec08_2_ULS_HTU_FE10511_1_2.txt.gz 42.8 Mb (ftp)(http) TXT
Processed data included within Sample table

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