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Sample GSM848938 Query DataSets for GSM848938
Status Public on Apr 04, 2012
Title DNA methylation analysis of parental cell line
Sample type genomic
 
Channel 1
Source name SW48 colon cancer cells
Organism Homo sapiens
Characteristics sample type: Unmethylated DNA
cell line: SW48
Growth protocol SW48 cell line was cultured in L-15 medium with 10% fetal bovine serum and 100 μg/mL Penicillin-Streptomycin solution.
Extracted molecule genomic DNA
Extraction protocol 5 μg of DNA was digested with 100 units of SmaI for 16 h (all restriction enzymes were from New England Biolabs), followed by digestion with 20 units of XmaI for 6 h. DNA fragments were then precipitated with ethanol.
Label Cy3
Label protocol Incorporation of amino-allyl dUTP (aa-dUTP; Sigma) into 600 ng each of tumor DNA and normal DNA was conducted using the Bioprime DNA-labeling system protocol (Life Technologies) (Weinmann et al. 2002).
 
Channel 2
Source name SW48 colon cancer cells
Organism Homo sapiens
Characteristics sample type: Methylated DNA
cell line: SW48
Growth protocol SW48 cell line was cultured in L-15 medium with 10% fetal bovine serum and 100 μg/mL Penicillin-Streptomycin solution.
Extracted molecule genomic DNA
Extraction protocol 5 μg of DNA was digested with 100 units of SmaI for 16 h (all restriction enzymes were from New England Biolabs), followed by digestion with 20 units of XmaI for 6 h. DNA fragments were then precipitated with ethanol.
Label Cy5
Label protocol Incorporation of amino-allyl dUTP (aa-dUTP; Sigma) into 600 ng each of tumor DNA and normal DNA was conducted using the Bioprime DNA-labeling system protocol (Life Technologies) (Weinmann et al. 2002).
 
 
Hybridization protocol Microarray protocols including the hybridization and post-hybridization procedures are according to protocols developed by DeRisi et al. (1996), except for washing steps, which were extended to 10 min each to decrease background.
Scan protocol Agilent whole genome array (G4497A) that was scanned using the Agilent G2505B scanner
Description SW48 colon cancer cells (parental cells of YB5)
Data processing Two-step global lowess normalization was done using the background-subtracted median intensity of each spot
 
Submission date Dec 13, 2011
Last update date Apr 04, 2012
Contact name Noel J-M Raynal
Organization name Temple University
Department Fels Institute for Cancer and Molecular Biology
Street address 3307 N. Broad Street
City Philadelphia
State/province Pennsylvania
ZIP/Postal code 19140
Country USA
 
Platform ID GPL9886
Series (2)
GSE34427 DNA methylation analysis of Colon Cancer cell line SW48
GSE34429 Expression and DNA methylation of colon cancer cell lines

Data table header descriptions
ID_REF
VALUE normalized log10 ratio Cy5/Cy3

Data table
ID_REF VALUE
1 -1.11E-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 -8.35E-01
13 -2.42E-02
14 1.12E-02
15 -6.08E-01
16 -3.17E-02
17 -2.30E-02
18 6.15E-01
19 -1.43E-02
20 -1.30E-01

Total number of rows: 44674

Table truncated, full table size 667 Kbytes.




Supplementary file Size Download File type/resource
GSM848938.txt.gz 10.8 Mb (ftp)(http) TXT
Processed data included within Sample table
Processed data are available on Series record

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