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Sample GSM7812 Query DataSets for GSM7812
Status Public on Dec 07, 2003
Title HCT116-CloneK 4Gy 6hr PartB 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 = ChipNo12262658_19k3B
 
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 GPL351
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
1 475.319153 213.5 754.025635 312.8879245 SB1:SB2:LI1 0.167584617 0.167584617
2 842.8125 213.5 614.166687 312.8879245 SB2 -1.784062226 -1.784062226
3 833.556702 213.5 1033.797119 312.8879245 -0.192082998 -0.192082998
4 857.875 213.5 971.200012 312.8879245 -0.411099662 -0.411099662
5 1313.46875 213.5 1800.177246 312.8879245 0.284601013 0.284601013
6 1134.74585 213.5 1454.764648 312.8879245 0.064654176 0.064654176
7 524.454529 213.5 648.426697 312.8879245 SB1:SB2:LI1 -0.573108704 -0.573108704
8 715.392883 213.5 801.689636 312.8879245 -0.58652766 -0.58652766
9 1964.512817 213.5 2327.32251 312.8879245 0.160013906 0.160013906
10 1905.394165 213.5 2404.305176 312.8879245 0.277076514 0.277076514
11 490.100006 213.5 775.62793 312.8879245 SB1:SB2:LI1 0.174416811 0.174416811
12 456.773804 213.5 1024.882324 312.8879245 SB1:LI1 1.135336473 1.135336473
13 526.358215 213.5 661.327576 312.8879245 SB1:SB2:LI1 -0.513998285 -0.513998285
14 556.288879 213.5 921.763184 312.8879245 0.358949435 0.358949435
15 1145.644409 213.5 1363.86731 312.8879245 -0.101637978 -0.101637978
16 1110.82605 213.5 1407.354858 312.8879245 0.026270793 0.026270793
17 448.899994 213.5 859.93335 312.8879245 SB1:LI1 0.708390977 0.708390977
18 454.49295 213.5 987.799988 312.8879245 SB1:LI1 1.052639943 1.052639943
19 456.617645 213.5 883 312.8879245 SB1:LI1 0.73619948 0.73619948
20 369.876709 213.5 814.540527 312.8879245 SB1:LI1 1.142542152 1.142542152

Total number of rows: 19200

Table truncated, full table size 1457 Kbytes.




Supplementary data files not provided

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