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Sample GSM7815 Query DataSets for GSM7815
Status Public on Dec 07, 2003
Title HCT116-CloneK 4Gy 24hr PartA R3
Sample type RNA
 
Channel 1
Source name Control HCT116-Clone10 cells (Cy3)
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name XR sensitive HCT116-CloneK cells (Cy5)
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 24 hours 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 = ChipNo12263227_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
GSE526 HCT116-CloneK cells 24 hours 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
1 603.615356 172.3706895 803.099976 167.6379315 0.665479959 0.665479959
2 727.20752 172.3706895 713.226074 167.6379315 0.07931972 0.07931972
3 376.688324 172.3706895 424.029846 167.6379315 SB1 0.418184518 0.418184518
4 437.954559 172.3706895 525.8125 167.6379315 0.527864185 0.527864185
5 358.924988 172.3706895 516.857117 167.6379315 SB1 1.000472693 1.000472693
6 430.612244 172.3706895 569.638916 167.6379315 SB1 0.736822172 0.736822172
7 482.083344 172.3706895 398.600006 167.6379315 SB2:LI2 -0.334414467 -0.334414467
8 571.520813 172.3706895 368.412689 167.6379315 SB2:LI2 -0.904890776 -0.904890776
9 536.564514 172.3706895 503.345459 167.6379315 -0.022241393 -0.022241393
10 480.197174 172.3706895 626.944458 167.6379315 0.67796485 0.67796485
11 370.494843 172.3706895 538.320007 167.6379315 SB1 1.000733803 1.000733803
12 409.153076 172.3706895 353.28183 167.6379315 SB1:SB2:LI2 -0.265901997 -0.265901997
13 624.380981 172.3706895 308.059509 167.6379315 SB2:LI2 -1.606246922 -1.606246922
14 418.470581 172.3706895 295.789459 167.6379315 SB1:SB2:LI2 -0.862614091 -0.862614091
15 389.444458 172.3706895 358.537323 167.6379315 SB1:SB2:LI2 -0.099773275 -0.099773275
16 600.392883 172.3706895 358.711853 167.6379315 SB2:LI2 -1.077939458 -1.077939458
17 350.039459 172.3706895 487.555542 167.6379315 SB1 0.942946 0.942946
18 355.644745 172.3706895 446.685699 167.6379315 SB1 0.698606126 0.698606126
19 597.412292 172.3706895 791.188416 167.6379315 0.658759093 0.658759093
20 813.5 172.3706895 774.777771 167.6379315 0.026813827 0.026813827

Total number of rows: 19200

Table truncated, full table size 1449 Kbytes.




Supplementary data files not provided

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