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Sample GSM1197419 Query DataSets for GSM1197419
Status Public on Jul 30, 2013
Title 10P [aCGH]
Sample type genomic
 
Channel 1
Source name tumor_primary
Organism Homo sapiens
Characteristics tissue: primary tumor
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 -0.423894390054194
5 0.938826179685639
6 -0.744308701216944
7 -0.186489026471182
8 0.0632489802486422
9 -0.572580488598212
10 0.445937890355098
11 -0.46340240610345
12 -0.0359802637478361
13 -0.130713736826154
14 -0.766579137706878
15 -0.026611754039096
16 0.146042032831415
17 -0.246261709024999
18 -0.612497320718201
19 -0.916866263746302
20 -0.168883153447432
21 0.613642647778514
22 0.179703431582226
23 -0.848258549905541

Total number of rows: 415056

Table truncated, full table size 10268 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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