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Sample GSM3868594 Query DataSets for GSM3868594
Status Public on Jun 11, 2019
Title aCGH analysis of AM patient-6
Sample type genomic
 
Channel 1
Source name AM-006_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-006_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-6
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

Data table header descriptions
ID_REF
VALUE log10Ratio

Data table
ID_REF VALUE
4 0.08
5 0.27
6 -0.11
7 -0.08
8 -0.10
9 -0.07
10 -0.01
11 -0.15
12 -0.21
13 -0.01
14 0.00
15 0.09
16 -0.05
17 -0.07
18 -0.44
19 -0.04
20 -0.20
21 0.23
22 -0.06
23 -0.07

Total number of rows: 415056

Table truncated, full table size 4953 Kbytes.




Supplementary file Size Download File type/resource
GSM3868594_US90603642_252185027998_S02_CGH_1100_Jul11_1_2.txt.gz 117.2 Mb (ftp)(http) TXT
Processed data included within Sample table

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