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Sample GSM7852 Query DataSets for GSM7852
Status Public on Dec 08, 2003
Title Unirradiated HCT116-CloneK PartB R1
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 unirradiated 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. Their total mRNA was collected 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 = ChipNo12167477_19k2iiB
 
Submission date Jul 11, 2003
Last update date May 28, 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 GPL354
Series (2)
GSE522 X-radiation (XR) sensitive HCT116-CloneK: XR at 0 and 4 Gy
GSE523 Unirradiated HCT116-CloneK cells

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 Ratio (Log2)(Regression SubArray Normalised)(LogIntensity)(SubArray Bkgd Subtracted)

Data table
ID_REF CH1_MEAN CH1_BKD CH2_MEAN CH2_BKD FLAGS VALUE
1 493.176483 175.6293105 903.049988 399.6465605 SB2 -0.01958434
2 594.41333 175.6293105 1009.75 399.6465605 0.168679186
3 557.987488 175.6293105 1114.5 399.6465605 0.709640839
4 447.230774 175.6293105 953.56665 399.6465605 SB2 0.513874646
5 771.758606 175.6293105 1088.071411 399.6465605 -0.023971202
6 788.166687 175.6293105 1061.583374 399.6465605 -0.162684605
7 574.531616 175.6293105 820.703674 399.6465605 SB2 -1.05684452
8 479.623535 175.6293105 1157.400024 399.6465605 1.179655708
9 540.616272 175.6293105 954.304321 399.6465605 SB2 0.091564958
10 744.949158 175.6293105 914.06897 399.6465605 SB2 -0.788844381
11 625.766663 175.6293105 1892.5 399.6465605 1.97809725
12 551.986328 175.6293105 1165.153809 399.6465605 0.895373415
13 1349.810059 175.6293105 1681.294067 399.6465605 0.316030915
14 1458.640747 175.6293105 1517.142822 399.6465605 -0.073248006
15 17809.06641 175.6293105 15025.81348 399.6465605 0.26265489
16 15761.18848 175.6293105 14274.21777 399.6465605 0.363062115
17 1744.41272 175.6293105 2292 399.6465605 0.590956197
18 2181.796143 175.6293105 2317.729736 399.6465605 0.259158801
19 4948.836426 175.6293105 5309.733398 399.6465605 0.514032367
20 8821.958984 175.6293105 7861.681152 399.6465605 0.291490857

Total number of rows: 19200

Table truncated, full table size 1202 Kbytes.




Supplementary data files not provided

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