|
| Status |
Public on Jul 14, 2010 |
| Title |
MB11 (S14843), aCGH |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
Reference normal tissue of S14843
|
| Organism |
Mus musculus |
| Characteristics |
strain: C3B6F1
genotype: Ptch1+/-
tissue: ear
gender: female
irradiation: 1.5 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, 1 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 S14843
|
| Organism |
Mus musculus |
| Characteristics |
strain: C3B6F1
genotype: Ptch1+/-
tissue: medulloblastoma
gender: female
irradiation: 1.5 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, 1 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 mouse after 1.5 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 |
GPL9727 |
| Series (2) |
| GSE19381 |
Integrated array-CGH and expression microarray analyses on medulloblastomas in heterozygous Ptch1 mice, aCGH 1 |
| GSE19384 |
Integrated array-CGH and expression microarray analyses on medulloblastomas in heterozygous Ptch1 mice |
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