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Sample GSM1057131 Query DataSets for GSM1057131
Status Public on Sep 22, 2015
Title SCC Sample S17
Sample type genomic
 
Channel 1
Source name Lung Squamous Cell Carcinoma
Organism Homo sapiens
Characteristics age: 65
gender: M
time (month): 22
event (1=dead; 0=alive): 1
cell type: squamous cell carcinoma
tissue type: lung
Treatment protocol Tumor cells were scraped using a scalpel and then collected under the direction of pathologists from ten 10-μm thick FFPE slides for each histological lesion.
Extracted molecule genomic DNA
Extraction protocol Genomic DNA (gDNA) was extracted from the tumor cells using a DNeasy Blood & Tissue Kit (Qiagen Inc., Hilden, Germany).
Label Cy5
Label protocol Tumor and reference gDNA (Promega Inc., WI) were labeled with Cy5 and Cy3, respectively, using the Agilent Genomic DNA USL Labeling Kit (Agilent Technologies) for FFPE Samples according to the manufacturer's instructions.
 
Channel 2
Source name Human genomic DNA: Male (Promega)
Organism Homo sapiens
Characteristics reference: Male (Promega)
Treatment protocol Tumor cells were scraped using a scalpel and then collected under the direction of pathologists from ten 10-μm thick FFPE slides for each histological lesion.
Extracted molecule genomic DNA
Extraction protocol Genomic DNA (gDNA) was extracted from the tumor cells using a DNeasy Blood & Tissue Kit (Qiagen Inc., Hilden, Germany).
Label Cy3
Label protocol Tumor and reference gDNA (Promega Inc., WI) were labeled with Cy5 and Cy3, respectively, using the Agilent Genomic DNA USL Labeling Kit (Agilent Technologies) for FFPE Samples according to the manufacturer's instructions.
 
 
Hybridization protocol A total of 500ng of both gDNA samples and human Cot-I DNA was dissolved in the hybridization mixture supplied within the Agilent Oligo array-CGH Hybridization Kit (Agilent Technologies). After denaturation at 95℃ for 3 minutes and incubation at 37℃ for 30 minutes, the mixtures were slowly dispensed onto the gasket. A microarray slide was then placed onto the gasket slide. The samples were hybridized in a hybridization oven at 65℃ and 20 rpm for 40 hours.
Scan protocol Slides were scanned with the Agilent Scanner System, and the Feature Extraction 12.0 (Agilent Technologies) was used for data extraction.
Data processing Data were normalized with quantile method with limma package in R (version 2.12.0).
 
Submission date Dec 23, 2012
Last update date Sep 22, 2015
Contact name Dongmei Lin
Organization name Cancer Hospital, CAMS
Department Pathology
Street address Panjiayuannanli 17, Chaoyang District
City Beijing
ZIP/Postal code 100021
Country China
 
Platform ID GPL8841
Series (1)
GSE43131 Genomic copy number aberrations in primary lung squamous cell carcinoma

Data table header descriptions
ID_REF
VALUE Quantile normalized log2 ratio (tumor/reference).

Data table
ID_REF VALUE
A_14_P100000 0.02838
A_14_P100001 0.18338
A_14_P100002 -0.51876
A_14_P100003 0.154755
A_14_P100004 0.0811
A_14_P100005 0.17503
A_14_P100006 -0.06249
A_14_P100007 -0.02208
A_14_P100008 -0.15269
A_14_P100009 -0.31384
A_14_P100010 0.15662
A_14_P100011 -0.02711
A_14_P100012 0.09155
A_14_P100013 0.00589
A_14_P100014 -0.24782
A_14_P100015 -0.08723
A_14_P100016 -0.01042
A_14_P100017 -0.378885
A_14_P100018 -0.27318
A_14_P100019 0.12742

Total number of rows: 42494

Table truncated, full table size 898 Kbytes.




Supplementary file Size Download File type/resource
GSM1057131_S17.txt.gz 4.6 Mb (ftp)(http) TXT
Processed data included within Sample table

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