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Sample GSM7807 Query DataSets for GSM7807
Status Public on Dec 07, 2003
Title HCT116-CloneK 4Gy 6hr 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 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 6 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 = ChipNo12263219_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
GSE525 HCT116-CloneK cells 6 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 3893.703613 595.732758 4444.484375 292.870697 0.267026244 0.267026244
2 3458.104004 595.732758 4328.257813 292.870697 0.442425 0.442425
3 2292.175049 595.732758 971.064514 292.870697 -0.622367433 -0.622367433
4 1518.565186 595.732758 697.971436 292.870697 SB2 -0.269713964 -0.269713964
5 2170.151611 595.732758 838.904785 292.870697 -0.735809592 -0.735809592
6 2285.888916 595.732758 705.120667 292.870697 SB2 -1.124882005 -1.124882005
7 2458.782715 595.732758 801.253723 292.870697 -1.051547674 -1.051547674
8 2631.608643 595.732758 942.326538 292.870697 -0.929678587 -0.929678587
9 2077.620605 595.732758 1009.419373 292.870697 -0.371165738 -0.371165738
10 1497.62854 595.732758 1086.588257 292.870697 0.449587842 0.449587842
11 2097.363525 595.732758 1020.970581 292.870697 -0.373944117 -0.373944117
12 1704.714233 595.732758 1455.305542 292.870697 0.540645657 0.540645657
13 1122.875 595.732758 734.459473 292.870697 SB1 0.626149847 0.626149847
14 1003.117676 595.732758 585.884644 292.870697 SB1:SB2 0.579496004 0.579496004
15 1078.446411 595.732758 438.631592 292.870697 SB1:SB2:LI2 -0.377652567 -0.377652567
16 1101.065552 595.732758 558.75 292.870697 SB1:SB2 0.169511775 0.169511775
17 1361.681763 595.732758 756.138916 292.870697 SB1 0.135990161 0.135990161
18 1648.923096 595.732758 927.909119 292.870697 -0.001698504 -0.001698504
19 1711.648193 595.732758 1250.197021 292.870697 0.333599575 0.333599575
20 1825.162842 595.732758 1040.205078 292.870697 -0.058801912 -0.058801912

Total number of rows: 19200

Table truncated, full table size 1447 Kbytes.




Supplementary data files not provided

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