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Sample GSM1197410 Query DataSets for GSM1197410
Status Public on Jul 30, 2013
Title 2M [aCGH]
Sample type genomic
 
Channel 1
Source name tumor_metastatic
Organism Homo sapiens
Characteristics tissue: metastatic tumor
treatment: chemo
Treatment protocol 1M, 2M, 4M, 9M, 12M received chemo while 10M received radiation.
Growth protocol not applicable
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was extracted from the tumor samples using QIAamp DNA FFPE Tissue Kit (Qiagen, Valencia, CA).
Label Cy5
Label protocol The Genomic DNA ULS labeling kit for FFPE Samples (Agilent) was used to chemically label 1 mg of genomic DNA with either ULS-Cy5 (tumor) or ULS-Cy3 dye (normal/reference DNA) according to the manufacturer’s protocol (Agilent Technologies, Inc., Palo Alto, CA).
 
Channel 2
Source name normal female - control/ reference DNA
Organism Homo sapiens
Characteristics tissue: blood
sample type: normal female reference DNA (control)
Treatment protocol 1M, 2M, 4M, 9M, 12M received chemo while 10M received radiation.
Growth protocol not applicable
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was extracted from the tumor samples using QIAamp DNA FFPE Tissue Kit (Qiagen, Valencia, CA).
Label Cy3
Label protocol The Genomic DNA ULS labeling kit for FFPE Samples (Agilent) was used to chemically label 1 mg of genomic DNA with either ULS-Cy5 (tumor) or ULS-Cy3 dye (normal/reference DNA) according to the manufacturer’s protocol (Agilent Technologies, Inc., Palo Alto, CA).
 
 
Hybridization protocol Equimolar mixture of labeled normal and tumor DNA was applied to the Agilent Human Genome CGH 2x400k Microarray. Hybridization was carried out at 65°C for 40 hours, in a rotating oven at 20 rpm.
Scan protocol CGH-v4_95. Feature extraction v.9.5
Data processing The data quality of each microarray was assessed using the Quality Metrics report generated by the Agilent CGH analytics software (v.3.4). Copy number aberrations were detected using the Aberration Detection Method (ADM-1) algorithm, based on computing significance scores for all genomic intervals. Before calling any aberration the log ratios are normalized by subtracting the expected average µ from all log ratios vi, and then these modified log ratios are divided by the estimated variance σ. This transforms the log ratio scores into a normal distribution with a mean of 0 under the null model assumption.
 
Submission date Jul 29, 2013
Last update date Jul 30, 2013
Contact name Ramakrishna Sompallae
E-mail(s) ramakrishnas@gmail.com
Phone 319 353 5548
Organization name University of Iowa
Department Iowa Institute of Human Genetics
Lab Bioinformatics
Street address 285 Newton Road, 5292 CBRB
City Iowa City
State/province IA
ZIP/Postal code 52240
Country USA
 
Platform ID GPL9777
Series (2)
GSE49324 Identification of neural stem cell gene expression signatures associated with disease progression in alveolar soft part sarcoma by integrated molecular profiling [aCGH]
GSE49327 Identification of neural stem cell gene expression signatures associated with disease progression in alveolar soft part sarcoma by integrated molecular profiling

Data table header descriptions
ID_REF
VALUE Lowess normalized log2 tumor/normal ratio

Data table
ID_REF VALUE
4 -0.0524315234273796
5 0.454482298344497
6 -0.900002856201805
7 0.139087174046057
8 -0.246719647609145
9 -0.2636287209019
10 -0.300999802129824
11 0.149105183757509
12 -0.145234921501981
13 -0.42132266062141
14 -0.0980950112790812
15 -0.109795755326966
16 -1.17650007806972
17 -1.36181482312346
18 -2.18248502030793
19 -0.360252681334294
20 -0.222985288565487
21 0.244006174128875
22 -0.226603676419486
23 -0.687543427170718

Total number of rows: 415056

Table truncated, full table size 10260 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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