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Sample GSM7808 Query DataSets for GSM7808
Status Public on Dec 07, 2003
Title HCT116-CloneK 4Gy 6hr 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 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 = ChipNo12263223_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 1045.022461 221.2327575 810.533325 151.5086215 -0.014682515 -0.014682515
2 1117.517822 221.2327575 924.391724 151.5086215 0.087217963 0.087217963
3 666.333313 221.2327575 434.067413 151.5086215 -0.314651627 -0.314651627
4 544.897949 221.2327575 465.119049 151.5086215 SB1:LI1 0.291254847 0.291254847
5 608.046509 221.2327575 442.474579 151.5086215 -0.071025722 -0.071025722
6 599.555542 221.2327575 491.047607 151.5086215 0.17758507 0.17758507
7 393.117645 221.2327575 420.888885 151.5086215 SB1:LI1 0.991028852 0.991028852
8 471.214294 221.2327575 461.726196 151.5086215 SB1:LI1 0.648674856 0.648674856
9 661.79364 221.2327575 379.58139 151.5086215 -0.600402196 -0.600402196
10 471 221.2327575 445.202118 151.5086215 SB1:LI1 0.573119103 0.573119103
11 662.779419 221.2327575 515.596497 151.5086215 0.052571132 0.052571132
12 447.101135 221.2327575 411.386353 151.5086215 SB1:LI1 0.546605834 0.546605834
13 601.702148 221.2327575 377.641785 151.5086215 SB2 -0.400823263 -0.400823263
14 617.716675 221.2327575 295.609192 151.5086215 SB2:LI2 -1.092487617 -1.092487617
15 449.7258 221.2327575 281.567566 151.5086215 SB1:SB2:LI1:LI2 -0.441210094 -0.441210094
16 549.767883 221.2327575 386.754089 151.5086215 SB1:LI1 -0.1336667 -0.1336667
17 618.114258 221.2327575 403.384613 151.5086215 -0.31049627 -0.31049627
18 474.176483 221.2327575 457.482147 151.5086215 SB1:LI1 0.612353993 0.612353993
19 562.408447 221.2327575 566.947388 151.5086215 LI1 0.609726051 0.609726051
20 683.140015 221.2327575 531.906982 151.5086215 0.049015937 0.049015937

Total number of rows: 19200

Table truncated, full table size 1439 Kbytes.




Supplementary data files not provided

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