|
| Status |
Public on Jul 14, 2010 |
| Title |
MB (S16143), aCGH |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
Reference normal tissue of S16143
|
| Organism |
Mus musculus |
| Characteristics |
strain: C3B6F1
genotype: Ptch1+/-
tissue: ear
gender: female
irradiation: 0.1 Gy
|
| Treatment protocol |
Ptch1+/- mice (C3B6F1 background) were irradiated at postnatal day 1 using a Pantak HF-320 X-ray generator (Pantak Ltd., East Haven, CT, USA). Mice were observed daily until moribund and then were killed under ether anesthesia.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was purified by using AllPrep DNA/RNA mini kit (Qiagen, Valencia, CA).
|
| Label |
Cy3
|
| Label protocol |
Fluorescence labeling of DNA was carried out according to the manufacturer’s protocol (version 5) for oligonucleotide array-CGH for genomic DNA analysis (Agilent, Santa Clara, CA, USA). Briefly, 0.4 µg of genomic DNA were digested by AluI and RsaI, then fluorescently labeled by Cy3 or Cy5 using Genomic DNA labeling Kit Plus (Agilent). Clean-up of labeled DNA was carried out with Microcon YM-30 filters (Millopore, Billerica, MA, USA).
|
| |
|
| Channel 2 |
| Source name |
Medulloblastoma of S16143
|
| Organism |
Mus musculus |
| Characteristics |
strain: C3B6F1
genotype: Ptch1+/-
tissue: medulloblastoma
gender: female
irradiation: 0.1 Gy
|
| Treatment protocol |
Ptch1+/- mice (C3B6F1 background) were irradiated at postnatal day 1 using a Pantak HF-320 X-ray generator (Pantak Ltd., East Haven, CT, USA). Mice were observed daily until moribund and then were killed under ether anesthesia.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was purified by using AllPrep DNA/RNA mini kit (Qiagen, Valencia, CA).
|
| Label |
Cy5
|
| Label protocol |
Fluorescence labeling of DNA was carried out according to the manufacturer’s protocol (version 5) for oligonucleotide array-CGH for genomic DNA analysis (Agilent, Santa Clara, CA, USA). Briefly, 0.4 µg of genomic DNA were digested by AluI and RsaI, then fluorescently labeled by Cy3 or Cy5 using Genomic DNA labeling Kit Plus (Agilent). Clean-up of labeled DNA was carried out with Microcon YM-30 filters (Millopore, Billerica, MA, USA).
|
| |
|
| |
| Hybridization protocol |
Cy3- and Cy5-labeled probes were mixed with Mouse Cot I DNA (Invitrogen, Carlsbad, CA), 10x Blocking Agent and 2x Hybridization Buffer included in Agilent Oligo aCGH/ChIP-on-chip Hybridization Kit (Agilent). After denaturation at 95°C for 3 min and succeeding preincubation at 37°C for 30 min, hybridization was done for 40 hours at 65°C in a rotating Agilent hybridization oven.
|
| Scan protocol |
A slide was scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565BA) using two color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um).
|
| Description |
Medulloblastoma was developed in mice after 0.1 Gy irradiation.
|
| Data processing |
The scanned images were analyzed with Feature Extraction Software 9.5.1 (Agilent) using default parameters (protocol CGH-v4_95_Feb07 and Grid: 017823_D_F_20071007) to obtain background-subtracted Processed Signal intensities. Data were analyzed with DNA analytics software v4.0.
|
| |
|
| Submission date |
Dec 08, 2009 |
| Last update date |
Jul 14, 2010 |
| Contact name |
Takashi Takabatake |
| E-mail(s) |
batake@nirs.go.jp
|
| Organization name |
National Institute of Radiological Sciences
|
| Street address |
Anagawa 4-9-1, Inage-ku
|
| City |
Chiba |
| State/province |
Chiba |
| ZIP/Postal code |
263-8555 |
| Country |
Japan |
| |
|
| Platform ID |
GPL9729 |
| Series (2) |
| GSE19382 |
Integrated array-CGH and expression microarray analyses on medulloblastomas in heterozygous Ptch1 mice, aCGH 2 |
| GSE19384 |
Integrated array-CGH and expression microarray analyses on medulloblastomas in heterozygous Ptch1 mice |
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