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Sample GSM107664 Query DataSets for GSM107664
Status Public on Aug 08, 2007
Title WT_vs_DNMT3b
Sample type RNA
 
Channel 1
Source name Wild type HCT116
Organism Homo sapiens
Characteristics HCT116 human colorectal cancer cell line
Biomaterial provider Bert Vogelstein
Treatment protocol None
Growth protocol McCoy's 5A medium with 10% BCS and 1x P/S
Extracted molecule total RNA
Extraction protocol TriZol extraction followed by RNeasy clean-up with on-column DNase treatment
Label Cy5
Label protocol Agilent Low RNA Input Linear Amplification Kit using manufacturer's recommended protocol
 
Channel 2
Source name DNMT3b deficient HCT116
Organism Homo sapiens
Characteristics HCT116 human colorectal cancer cell line
Biomaterial provider Bert Vogelstein
Treatment protocol None
Growth protocol McCoy's 5A medium with 10% BCS and 1x P/S
Extracted molecule total RNA
Extraction protocol TriZol extraction followed by RNeasy clean-up with on-column DNase treatment
Label Cy3
Label protocol Agilent Low RNA Input Linear Amplification Kit using manufacturer's recommended protocol
 
 
Hybridization protocol Agilent Gene Expression Hybridization Kit using manufecturer's recommended protocol
Scan protocol Microarrays are scanned with Agilent G2565BA microarray scanner under default settings recommended by Agilent Technologies for expression microarrays with 100% PMT and 10 micrometer resolutions. Data are extracted using Feature Extraction Software v8.1 (Agilent Technologies) under default settings for expression microarrays
Description None
Data processing log ratio of red signal to green signal was calculated after background subtraction and loess normalization as implemented in the Limma package from Bioconductor
 
Submission date May 02, 2006
Last update date Aug 08, 2007
Contact name Wayne Yu
E-mail(s) wyu8@jhmi.edu
Phone (410)502-7970
Fax (410)955-8780
Organization name Johns Hopkins University
Department Cancer Center
Street address 417 N. Caroline St.
City Baltimore
State/province MD
ZIP/Postal code 21231
Country USA
 
Platform ID GPL1708
Series (1)
GSE4763 Identity of the human cancer cell DNA hypermethylome revealed by gene expression profiling

Data table header descriptions
ID_REF
VALUE -[INV_VALUE]
INV_VALUE log2 Ratio of background subtracted Cy5 intensity to background subtracted Cy3 intensity after loess normalization

Data table
ID_REF VALUE INV_VALUE
1 5.69738 -5.697378
2 0.117399 -0.117399
3 -0.004804 0.004804
4 0.207728 -0.207728
5 -0.0633 0.0633
6 -0.046239 0.046239
7 6.96462 -6.964617
8 0.189995 -0.189995
9 0.165259 -0.165259
10 0.099356 -0.099356
11 0.296237 -0.296237
12 -0.349952 0.349952
13 0.094246 -0.094246
14 7.05317 -7.053173
15 0.573347 -0.573347
16 0.470558 -0.470558
17 -0.068351 0.068351
18 0.11772 -0.11772
19 -0.501716 0.501716
20 -0.694048 0.694048

Total number of rows: 43931

Table truncated, full table size 1050 Kbytes.




Supplementary file Size Download File type/resource
GSM107664.txt.gz 10.3 Mb (ftp)(http) TXT
Processed data included within Sample table

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