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Sample GSM7801 Query DataSets for GSM7801
Status Public on Dec 07, 2003
Title HCT116-CloneK 4Gy 10min R1
Sample type RNA
 
Channel 1
Source name Control HCT116-Clone10 cells (Cy5)
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name XR sensitive HCT116-CloneK cells (Cy3)
Organism Homo sapiens
Extracted molecule total RNA
 
 
Description A cDNA microarray between X-radiation (XR) sensitive cell clone HCT116-Clone K and unirradiated control HCT116-Clone10 cells, a cell clone which has similar XR response with parental HCT116 cells. HCT116-CloneK cells were treated with XR at dose 4 Gy. Their total mRNA was collected 10 minutes after XR from different batches and pooled together. RNA extraction was done using Rneasy Mini kit (Qiagen Inc.). Total mRNA from HCT116-CloneK or HCT116-Clone10 was labeled either with Cy5 or Cy3. This experiment was repeated three times with one of them was a reciprocal labeling. The arrays were scanned with ScanArray Express (Packard Bioscience). Acquired images were analyzed using QuantArray software version 3.0 (Packard Bioscience). The data was transformed with an Excel VBA macro Normaliser2 software (Institute for Biological Sciences, NRC, Ottawa, ON, Canada). Normaliser2 filtered the data by identifying problems with a spot on the array (flagging), which was then removed from the data set according to the set threshold i.e. spot intensity signal/sub array background less than 2.5, less than 5% spot intensity, and ignore spots with streak or damage.
Note: FLAGS: IF, Ignore Filter; SB1 or 2, Substract Background CH1 or CH2; LI1 or 2, Low Intensity CH1 or CH2; HI1 or 2, High Intensity CH1 or CH2. VALUE: Ratio (Log2)(Regression SubArray Normalised)(LogIntensity)(SubArray Bkgd Subtracted).
Keywords = X-radiation (XR), XR sensitive, colorectal cancer cells, HCT1116
Lot batch = ChipNo12256957_19k3A
 
Submission date Jul 10, 2003
Last update date Nov 21, 2005
Contact name Felix M. Mesak
E-mail(s) Felix.Mesak@orcc.on.ca
Phone 1-613-737 7700 ext. 6940-42
Fax 1-613-247 3524
Organization name Ottawa Regional Cancer Centre
Department Centre for Cancer Therapeutics
Lab Dr. Cheng E. Ng
Street address 503 Smyth Rd. 3rd Floor
City Ottawa
State/province ON
ZIP/Postal code K1H 1C4
Country Canada
 
Platform ID GPL350
Series (2)
GSE522 X-radiation (XR) sensitive HCT116-CloneK: XR at 0 and 4 Gy
GSE524 HCT116-CloneK cells 10 minutes after XR treatment at 4 Gy

Data table header descriptions
ID_REF
CH1_MEAN CH1 Mean Intensity
CH1_BKD CH1 Background (Subarray Median)
CH2_MEAN CH2 Mean Intensity
CH2_BKD CH2 Background (Subarray Median)
FLAGS IF, Ignore Filter; SB1 or 2, Subtract Background CH1 or CH2; LI1 or 2, Low Intensity CH1 or CH2; HI1 or 2, High Intensity CH1 or CH2
VALUE same as UNF_VALUE but with flagged values removed
UNF_VALUE Ratio (Log2)(Regression SubArray Normalised)(LogIntensity)(SubArray Bkgd Subtracted)

Data table
ID_REF CH1_MEAN CH1_BKD CH2_MEAN CH2_BKD FLAGS VALUE UNF_VALUE
1 2957.161865 232.612068 2529.353027 325.327576 -0.111090077 -0.111090077
2 2666.468994 232.612068 2584.560547 325.327576 0.098596334 0.098596334
3 700.058838 232.612068 959.466675 325.327576 0.069766296 0.069766296
4 567.106384 232.612068 781.405396 325.327576 SB1:SB2:LI1 -0.072424336 -0.072424336
5 604.017883 232.612068 879.157898 325.327576 0.144801744 0.144801744
6 650.708313 232.612068 752.269226 325.327576 SB2 -0.519460311 -0.519460311
7 635.666687 232.612068 824.080017 325.327576 -0.171805844 -0.171805844
8 813.253357 232.612068 2831.153809 325.327576 2.362559441 2.362559441
9 743.239136 232.612068 978.974365 325.327576 -0.000247739 -0.000247739
10 710.085693 232.612068 933.918396 325.327576 -0.038830307 -0.038830307
11 1115.277832 232.612068 938.451599 325.327576 IF -0.911204326
12 1150.086914 232.612068 1318.795898 325.327576 IF -0.05181244
13 710.5 232.612068 987 325.327576 IF 0.118490704
14 589.099976 232.612068 818.090881 325.327576 -0.017591985 -0.017591985
15 557.659973 232.612068 827.416687 325.327576 SB1:LI1 0.151160838 0.151160838
16 478.625 232.612068 847.714294 325.327576 SB1:LI1 0.628228177 0.628228177
17 525.578918 232.612068 1372.599976 325.327576 SB1:LI1 1.695130726 1.695130726
18 1057.777832 232.612068 1681.3125 325.327576 IF 0.691057779
19 840.112366 232.612068 970.888916 325.327576 -0.27446518 -0.27446518
20 1090.166626 232.612068 1053.115356 325.327576 -0.544469318 -0.544469318

Total number of rows: 19200

Table truncated, full table size 1455 Kbytes.




Supplementary data files not provided

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