|
| Status |
Public on Jun 11, 2019 |
| Title |
aCGH analysis of AM patient-7 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
AM-007_tumor
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: ameloblastoma tumor
Sex: Female
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
For oligo-aCGH, genomic DNA was obtained from both tumor and normal tissues from 8 ameloblastoma patients using proteinase K/RNAse treatment and phenol–chloroform extraction according to standard procedures. DNA concentration was quantified using a NanoDrop-1000 spectrophotometer.
|
| Label |
Cy3
|
| Label protocol |
Labeling and hybridization were performed according to the manufacturer's protocol. Briefly, 2 μg each of patients-derived DNA from tumor and normal counterpart were labeled by random priming with either, Cy3-dUTP or Cy5-dUTP using the Agilent Genomic DNA Labeling Kit PLUS, respectively(Agilent Technologies). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.
|
| |
|
| Channel 2 |
| Source name |
AM-007_normal tissue
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: normal tissue
Sex: Female
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
For oligo-aCGH, genomic DNA was obtained from both tumor and normal tissues from 8 ameloblastoma patients using proteinase K/RNAse treatment and phenol–chloroform extraction according to standard procedures. DNA concentration was quantified using a NanoDrop-1000 spectrophotometer.
|
| Label |
Cy5
|
| Label protocol |
Labeling and hybridization were performed according to the manufacturer's protocol. Briefly, 2 μg each of patients-derived DNA from tumor and normal counterpart were labeled by random priming with either, Cy3-dUTP or Cy5-dUTP using the Agilent Genomic DNA Labeling Kit PLUS, respectively(Agilent Technologies). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.
|
| |
|
| |
| Hybridization protocol |
Cy3-dUTP-labeled tumor-derived DNA or Cy5-dUTP-labeled coppresponding normal DNA were hybridized on a Agilent Human Genome CGH Microarray Kit 2 × 400K. After 40 h of hybridization at 65℃, the slides were washed according to the manufacturer instructions.
|
| Scan protocol |
Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using two color scan setting for 4x00k array slides (Scan Area 61x21.6 mm, Scan resolution 3 um).
|
| Description |
Somatic genomic alterations of ameloblastoma in AM patient-7
|
| Data processing |
The scanned images were analyzed with Feature Extraction Software 11.0.1.1 (Agilent) using default parametersto obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
|
| |
|
| Submission date |
Jun 10, 2019 |
| Last update date |
Jun 11, 2019 |
| Contact name |
Akinobu Ota |
| E-mail(s) |
aota@aichi-med-u.ac.jp
|
| Organization name |
Aichi Medical University School of Medicine
|
| Department |
Biochemistry
|
| Street address |
1-1 Yazakokarimata
|
| City |
nagakute |
| State/province |
Aichi |
| ZIP/Postal code |
4801195 |
| Country |
Japan |
| |
|
| Platform ID |
GPL9777 |
| Series (2) |
| GSE132473 |
Array comparative genomic hybridization (CGH) analysis of ameloblastoma tumor |
| GSE132474 |
Gene expression profiling and aCGH of ameloblastoma tumor |
|
