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Sample GSM7814 Query DataSets for GSM7814
Status Public on Dec 07, 2003
Title HCT116-CloneK 4Gy 24hr PartA R2
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 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 = ChipNo12256990_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 2452.702393 312.0689695 1449.559326 123.637932 -0.130666925 -0.130666925
2 2155.078369 312.0689695 1369.080688 123.637932 -0.003698629 -0.003698629
3 1006.777771 312.0689695 419.522125 123.637932 LI2 -0.639129775 -0.639129775
4 636.840027 312.0689695 441.634613 123.637932 SB1:LI1 0.560303179 0.560303179
5 652.095215 312.0689695 349.154938 123.637932 SB1:LI2 0.005606584 0.005606584
6 717.402039 312.0689695 411.173462 123.637932 SB1:LI2 0.097486494 0.097486494
7 743.073181 312.0689695 301.913971 123.637932 SB1:SB2:LI2 -0.670577988 -0.670577988
8 748.653076 312.0689695 298.600006 123.637932 SB1:SB2:LI2 -0.715807514 -0.715807514
9 862.309509 312.0689695 409.057678 123.637932 LI2 -0.353966217 -0.353966217
10 816.707703 312.0689695 536.846863 123.637932 0.29676981 0.29676981
11 1404.75 312.0689695 669.850891 123.637932 -0.421117043 -0.421117043
12 1393.943604 312.0689695 688.54718 123.637932 -0.35893762 -0.35893762
13 879.6875 312.0689695 294.355255 123.637932 SB2:LI2 -1.129380497 -1.129380497
14 923.368408 312.0689695 386.5224 123.637932 LI2 -0.622691662 -0.622691662
15 866 312.0689695 251.629211 123.637932 SB2:LI2 -1.503608571 -1.503608571
16 721 312.0689695 341.404755 123.637932 SB1:LI2 -0.310313833 -0.310313833
17 885.904785 312.0689695 414.954559 123.637932 LI2 -0.385473425 -0.385473425
18 738.488892 312.0689695 366.049988 123.637932 SB1:LI2 -0.218331989 -0.218331989
19 1378.789429 312.0689695 875.477051 123.637932 0.067744402 0.067744402
20 2030.426514 312.0689695 1008.826111 123.637932 -0.388012887 -0.388012887

Total number of rows: 19200

Table truncated, full table size 1452 Kbytes.




Supplementary data files not provided

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