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Status
Public on May 27, 2003
Title
Kc167_Homotypic_R2_1
Sample type
RNA
Channel 1 Source name
Untreated Kc167 cells
Organism
Drosophila melanogaster Extracted molecule
total RNA
Channel 2 Source name
Untreated Kc167 cells
Organism
Drosophila melanogaster Extracted molecule
total RNA
Description
Total RNA was extracted from a dense culture of Kc167 cells which was maintained at 22C in Schneider's Complete Drosophila Medium (Invitrogen, Burlington, ON) supplemented with 5% Fetal Bovine Serum (Invitrogen) and 20ug/mL Gentamicin (Sigma, Oakville, ON) using Trizol Reagent (Invitrogen). 80ug of RNA, quantified by A260 in an Ultrmark plate reader (Biorad, Mississauga, ON), was used in each direct labeling reaction (see http://www.flyarrays.com ) to generate fluorescently labeled cDNA. The respective Cy3 and Cy5 targets were suspended in 75 uL DIG EasyHyb solution (Roche, Mississauga, ON)and were competitively hybridized to the array for 16 hours in a CMT-GAPS hybridization chamber (Corning, Acton, MA). Scanning was performed with a ScanArray 4000 system (Perkin Elmer, Boston, MA) using the following settings: 10uM scan: Cy3(543 nm) 100-72, Cy5(633 nm) 100-62 (laser power-PMT Gain). Quantification was performed using QuantArray v3 software (Perkin Elmer) using the adaptive algorithm without background subtraction. The data in the file is not normalized. The ratio in the Value column was derived from normalized data (not shown) as discussed in the manuscript.
Submission date
Apr 29, 2003
Last update date
Nov 21, 2005
Contact name
Zak Razak
E-mail(s)
z.razak@utoronto.ca Phone
905-569-4664
URL
http://www.flyarrays.com Organization name
University of Toronto
Department
Zoology Department
Lab
Canadian Drosophila Microarray Centre
Street address
3359 Mississauga Road
City
Mississauga
State/province
ON
ZIP/Postal code
L5L 1C6
Country
Canada
Platform ID
GPL311 Series (1)
GSE418 Kc167_Inter-slide_Variability_Test
Data table header descriptions ID_REF
CH1_RAW Raw fluorescence intensity - Cy3
CH1_BKD_RAW Raw background fluorescence intensity - Cy3
CH1_AREA Spot area - Cy3
Ch1_Signal_Noise_Ratio Signal to noise ratio - Cy3
CH2_RAW Raw fluorescence intensity - Cy5
CH2_BKD_RAW Raw background fluorescence intensity - Cy5
CH2_AREA Spot area - Cy5
Ch2_Signal_Noise_Ratio Signal to noise ratio - Cy5
Ignore Quality measure exported from GeneTraffic; flag=1, good=0
Ratio The ratio of CH2_Raw to CH1_Raw
VALUE same as UNF_VALUE but with flagged values removed
UNF_VALUE The log2-transformed ratio of the Lowess-normalized fluorescence values (Ch2/Ch1) exported from GeneTraffic
Data table ID_REF CH1_RAW CH1_BKD_RAW CH1_AREA Ch1_Signal_Noise_Ratio CH2_RAW CH2_BKD_RAW CH2_AREA Ch2_Signal_Noise_Ratio Ignore Ratio VALUE UNF_VALUE 1
1013.064514
51.05357
12400
8.986928
839.166687
19.589285
8400
14.252654
0
0.828345
0.140789828
0.140789828
2
1294.379272
37.160713
8700
12.491102
1043.626709
7.767857
7500
45.082409
0
0.806276
0.05965002
0.05965002
3
1083.32312
156.910721
13000
4.300407
898.481812
34.482143
11000
8.628984
0
0.829376
0.121840558
0.121840558
4
1340.482788
152.964279
14500
5.770041
1232.589722
27.035715
11700
18.228242
0
0.919512
0.22883249
0.22883249
5
3960.993408
67.196426
15300
29.408191
3506.55127
18.678572
12700
62.185797
0
0.885271
0.13589436
0.13589436
6
4796.556152
66.464287
13300
32.502294
3832.360107
12.714286
12500
72.577791
0
0.798982
-0.003369627
-0.003369627
7
1498.959961
61.32143
15000
10.324026
1209.900024
26.303572
12000
15.859697
0
0.80716
0.03021998
0.03021998
8
1566.546265
72.571426
11900
10.375253
1334.701904
18.803572
10400
23.772377
0
0.852003
0.089736947
0.089736947
9
978.642883
50.625
11200
9.867139
796.256104
13.339286
8200
26.653414
0
0.813633
0.128261909
0.128261909
10
1343.734497
186.464279
11300
3.068973
1328.5
16.017857
10200
20.513193
0
0.988663
0.324638229
0.324638229
11
1711.469849
147.982147
8300
7.168687
1663.317505
18.196428
6300
33.448706
0
0.971865
0.263808843
0.263808843
12
1909.987061
44.19643
7700
21.547211
1985.236328
10.517858
5500
47.178146
0
1.039398
0.37527484
0.37527484
13
1558.5802
93.696426
13100
8.228619
1467.722168
20.517857
10800
31.407402
0
0.941705
0.223091869
0.223091869
14
1190.694824
94.75
15400
5.525927
1452.279297
16.107143
11100
34.328588
0
1.219691
0.631216538
0.631216538
15
1756.333374
52.25
13200
14.940822
1606.692261
8.892858
11700
44.767035
0
0.914799
0.176274746
0.176274746
16
1759.433105
54.375
12700
14.06011
1569.093262
11.125
11800
40.193512
0
0.891818
0.138984629
0.138984629
17
7391.127441
57.69643
14100
69.86796
7279.676758
21.357143
13000
78.137757
0
0.984921
0.288574234
0.288574234
18
6963.173828
134.214279
16100
32.48386
7234.51416
15.285714
14000
161.987164
0
1.038968
0.365415066
0.365415066
19
3160.761475
78.964287
13000
14.501641
3087.720459
14.946428
11800
71.143216
0
0.976891
0.269199764
0.269199764
20
4364.585449
40.69643
12300
44.228944
3461.275635
26.125
12700
34.222903
0
0.793037
-0.019959617
-0.019959617
16896 1845 Kbytes .Supplementary file Size Download File type/resource GSM6160_Cy3.Tif.gz
6.4 Mb
(ftp) (http) TIFF
GSM6160_Cy5.Tif.gz
5.0 Mb
(ftp) (http) TIFF
