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Sample GSM7833 Query DataSets for GSM7833
Status Public on Nov 29, 2003
Title Unirradiated HCT116-CloneK PartA 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 = ChipNo12144787_19k2iiA
 
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 GPL353
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
1 629.03772 118.043106 1077.694458 367.75 -0.514184318
2 642.592224 118.043106 1277.033936 367.75 -0.048798572
3 416.112244 118.043106 1094.875 367.75 0.314454613
4 443.689667 118.043106 846.776306 367.75 SB2 -0.817116812
5 1251.467285 118.043106 1522.21875 367.75 -0.714445943
6 1252.631592 118.043106 1225.666626 367.75 -1.275654977
7 546.531921 118.043106 1180.507935 367.75 0.021103206
8 568.836182 118.043106 1190.764648 367.75 -0.026836143
9 507.061218 118.043106 1249.861084 367.75 0.323343625
10 477.08548 118.043106 900.021729 367.75 SB2 -0.676082721
11 484.535706 118.043106 1109.728394 367.75 0.058983592
12 622.130432 118.043106 1406.32605 367.75 0.260746763
13 756.883911 118.043106 1414.164185 367.75 -0.067079293
14 689.921082 118.043106 1548.714233 367.75 0.313328046
15 4707.560547 118.043106 9082.336914 367.75 0.469204691
16 6295.799805 118.043106 10523.68262 367.75 0.266878348
17 5521.844727 118.043106 10713.10547 367.75 0.487265315
18 4454.547852 118.043106 10021.67285 367.75 0.702536221
19 609.337341 118.043106 1333.705933 367.75 0.161668663
20 597.020203 118.043106 1044.382324 367.75 -0.525123565

Total number of rows: 19200

Table truncated, full table size 1205 Kbytes.




Supplementary data files not provided

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