|
| Status |
Public on Apr 29, 2023 |
| Title |
arrayCGH data from patient 3976 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
pediatric patient samples
|
| Organism |
Homo sapiens |
| Characteristics |
subarray: 1
subject: patient 3976
|
| 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) |
R.Hagelaar@prinsesmaximacentrum.nl
|
| 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 |
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