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Sample GSM927253 Query DataSets for GSM927253
Status Public on May 10, 2013
Title Non-smoker female, NSCLC, aCGH [PAT1T]
Sample type genomic
 
Channel 1
Source name human genomic female DNA: Promega G1521
Organism Homo sapiens
Characteristics reference: pooled female genomic DNA
Extracted molecule genomic DNA
Extraction protocol genomic DNA prep: Standard protocol by phenol extraction
Label Cy3
Label protocol 3 µg of gDNA were digested each 0.5 µl of AluⅠ(10U/ µl) and RsaⅠ(10U/µl) restriction enzyme at 37°C for 120 min, 65°C for 20 min then fluorescent labeled at 37°C for 120 min, 65°C for 10 min in Exo-Klenow Fragment enzyme and 2.5mM each dNTP with 1.0mM Cyanine 3-dUTP and 1.0mM Cyanine 5-dUTP
 
Channel 2
Source name Non-smoker female, NSCLC
Organism Homo sapiens
Characteristics disease: Adenocarcinoma, NSCLC
patient: 1
tissue type: tumor
Stage: IIA
gender: female
age: 44 years
smoker: non-smoker
Extracted molecule genomic DNA
Extraction protocol genomic DNA prep: Standard protocol by phenol extraction
Label Cy5
Label protocol 3 µg of gDNA were digested each 0.5 µl of AluⅠ(10U/ µl) and RsaⅠ(10U/µl) restriction enzyme at 37°C for 120 min, 65°C for 20 min then fluorescent labeled at 37°C for 120 min, 65°C for 10 min in Exo-Klenow Fragment enzyme and 2.5mM each dNTP with 1.0mM Cyanine 3-dUTP and 1.0mM Cyanine 5-dUTP
 
 
Hybridization protocol Hybridization was performed using Oligo aCGH Hybridization Kit at 65℃ and 20 rpm for 40 hours, enclosed in Agilent SureHyb-enabled hybridization chambers
Scan protocol Images were scanned on the Agilent G2505 C Scanner and quantified using the Agilent Feature Extraction Software (version 10.7.3.1).
Data processing Agilent Feature Extraction Software (version 10.7.3.1) was used for background subtraction and LOWESS normalization.
 
Submission date May 04, 2012
Last update date May 10, 2013
Contact name Sanghyuk Lee
E-mail(s) sanghyuk@ewha.ac.kr
Phone +82-42-879-8511
Fax +82-42-879-8519
URL http://www.kobic.re.kr
Organization name KRIBB
Department KOBIC
Street address 125 Gwahak-ro
City Daejeon
ZIP/Postal code 305-806
Country South Korea
 
Platform ID GPL10153
Series (2)
GSE37759 A high dimensional deep sequencing study of non-small cell lung adenocarcinoma in never-smoker Korean females [aCGH]
GSE37765 A high dimensional deep sequencing study of non-small cell lung adenocarcinoma in never-smoker Korean females

Data table header descriptions
ID_REF
VALUE Normalized log2 ratio (Cy5/Cy3) represents test/reference

Data table
ID_REF VALUE
1 -0.116485586
2
3 -0.60338164
4 0.237947184
5 0.085688485
6 -0.170661246
7 -0.116592087
8 -0.294429284
9 -0.408738238
10 0.030199764
11 0.116943576
12 -0.322650255
13 -0.093707824
14 0.224254287
15 -0.115243866
16 -0.105791265
17 -0.171402272
18 -0.109675246
19 -0.261043528
20 -0.278315666

Total number of rows: 974016

Table truncated, full table size 18265 Kbytes.




Supplementary file Size Download File type/resource
GSM927253_US84703596_252364210703_S01_CGH_107_Sep09.txt.gz 101.1 Mb (ftp)(http) TXT
Processed data included within Sample table

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