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Sample GSM536315 Query DataSets for GSM536315
Status Public on Apr 22, 2010
Title SCLC 3
Sample type genomic
 
Channel 1
Source name Clinical sample
Organism Homo sapiens
Characteristics gender: F
age: 63
sclc/carcinoid: SCLC
sclc primary tumor/metastasis: Primary tumor
bronchial/gi carcinoid: N/A
origin of sample: Lung/nodulectomy
growth pattern of cell line: N/A
pathological review: Small cell lung carcinoma
Treatment protocol n/a
Growth protocol n/a
Extracted molecule genomic DNA
Extraction protocol Total genomic DNA was isolated from cell lines, cytology specimens or deparaffinated FFPE specimens using reagents of the DNeasy Blood and Tissue Kit, QIAquick PCR Purification Kit (Qiagen, Gaithersburg, MD) as well as Dako Target Retrieval Solution (Dako, Carpinteria, CA) in protocols optimized for maximum yield from the various types of samples.
Label Cy5
Label protocol 500ng sample and reference genomic DNA were fragemented by incubation at 95'C up to 10 min and then were labeled with Cy5 and Cy3, respectively at 85'C for 30 min. Labeled DNA were purified using Agilent KREApure column. Degree of labeling was determined by measuring the absorbance at A260nm(DNA), A550nm(Cy3), and A650nmCy5).
 
Channel 2
Source name Promega male human genomic DNA
Organism Homo sapiens
Characteristics gender: M
reference: Promega male human genomic DNA
Treatment protocol n/a
Growth protocol n/a
Extracted molecule genomic DNA
Extraction protocol Total genomic DNA was isolated from cell lines, cytology specimens or deparaffinated FFPE specimens using reagents of the DNeasy Blood and Tissue Kit, QIAquick PCR Purification Kit (Qiagen, Gaithersburg, MD) as well as Dako Target Retrieval Solution (Dako, Carpinteria, CA) in protocols optimized for maximum yield from the various types of samples.
Label Cy3
Label protocol 500ng sample and reference genomic DNA were fragemented by incubation at 95'C up to 10 min and then were labeled with Cy5 and Cy3, respectively at 85'C for 30 min. Labeled DNA were purified using Agilent KREApure column. Degree of labeling was determined by measuring the absorbance at A260nm(DNA), A550nm(Cy3), and A650nmCy5).
 
 
Hybridization protocol Appropriate equal amoung of Cy5-labeled sample and Cy3-labeled reference DNAwere mixed to a 22ul final volumn. 61ul Hybridization Master Mix (1mg/ml Cot-1 DNA 5ul, Agilent 100X blocking agent 1ul, and Agilent 2X HiRPM Hybridization buffer 55ul) was added and incubated at 95'C for 3 min folloed by 37'C for 30min. 27ul of Agilent-CGHBlock was then added and mixed. The hybridization sample mixture was applied onto the microarray gasket well and was covered by a microarray slide. The slide was incubated in a 65'C rotator rack for 40 hours. After hybridization, slide was washed sequential.
Scan protocol Scanned on an Agilent DNA microarray scanner
Images were quantified using Agilent Feature Extraction Software v10.5
Description n/a
Data processing Agilent Feature Extraction Software v10.5 was used for background subtraction and data processing. Data were normalized using Linear method.
 
Submission date Apr 22, 2010
Last update date Apr 22, 2010
Contact name Jih-Hsiang Lee
E-mail(s) leej15@mail.nih.gov
Organization name National Cancer Institute
Department Medical oncology branch
Street address 9000 Rockville Pike, building 10 8N254
City Bethesda
State/province MD
ZIP/Postal code 20852
Country USA
 
Platform ID GPL10123
Series (1)
GSE21468 Array CGH-based Characterization of Genetic Alterations in Pulmonary Neuroendocrine Tumors

Data table header descriptions
ID_REF
VALUE Log2(Cy5/Cy3) per feature using processed signals

Data table
ID_REF VALUE
1 3.90E-02
2 0.00E+00
3 0.00E+00
4 0.00E+00
5 0.00E+00
6 0.00E+00
7 0.00E+00
8 0.00E+00
9 0.00E+00
10 0.00E+00
11 0.00E+00
12 0.00E+00
13 0.00E+00
14 0.00E+00
15 0.00E+00
16 0.00E+00
17 0.00E+00
18 0.00E+00
19 0.00E+00
20 0.00E+00

Total number of rows: 180880

Table truncated, full table size 2793 Kbytes.




Supplementary file Size Download File type/resource
GSM536315_SCLC_3.txt.gz 18.7 Mb (ftp)(http) TXT
Processed data included within Sample table

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