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Status
Public on May 27, 2003
Title
Kc167_Homotypic_Q3_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 15.75 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) 95-75, Cy5(633 nm) 95-65 (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)
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
832.105774
68.64286
10400
4.786912
529.294739
22.428572
9500
9.757873
0
0.636091
-0.436795533
-0.436795533
2
620.042114
87.89286
9500
3.253115
511.263733
16.928572
9100
11.731119
0
0.824563
0.030799804
0.030799804
3
1109.814575
44.964287
12400
11.423335
1319.327148
16.767857
10700
32.899172
0
1.188782
0.242918837
0.242918837
4
1148.785767
139.589279
12600
3.814474
1137.844238
20.464285
12200
17.838465
0
0.990476
-0.008509102
-0.008509102
5
3548.553955
114.785713
14800
11.420741
3712.628418
41.285713
14800
33.71791
0
1.046237
-0.037569025
-0.037569025
6
3638.020752
76.285713
14500
21.573658
3621.604248
48.767857
14400
36.401901
0
0.995488
-0.109307675
-0.109307675
7
953.942017
103.39286
13800
5.1436
977.529419
44.714287
13600
8.172655
0
1.024726
0.083974728
0.083974728
8
1207.768677
131.982147
13400
6.110303
1312.776001
50.232143
12500
10.922534
0
1.086943
0.104834468
0.104834468
9
789.759644
191.107147
10400
3.076957
583.981323
22.125
10700
9.987407
0
0.739442
-0.232332607
-0.232332607
10
711.288269
145.767853
11100
2.817429
579.184204
33.535713
11400
5.63265
0
0.814275
-0.061575731
-0.061575731
11
405.036041
90.071426
11100
2.25635
249.452057
20.928572
7300
4.495508
0
0.615876
-0.012770391
-0.012770391
12
432.435181
122.64286
10800
2.118181
271.116882
24.535715
7700
4.527129
0
0.626954
-0.042307797
-0.042307797
13
1192.412598
140.517853
14300
5.494616
1089.530273
72.446426
13200
9.09542
0
0.913719
-0.124198664
-0.124198664
14
1229.713013
233.25
10800
4.167099
1059.446167
61.67857
13000
9.83084
0
0.861539
-0.209344782
-0.209344782
15
2015.19165
180.535721
12000
9.789293
1451.710205
46.375
13800
13.708949
0
0.720383
-0.553362955
-0.553362955
16
1556.936646
92.464287
14200
10.028369
1700.523804
14.535714
12600
39.405704
0
1.092224
0.057152256
0.057152256
17
12650.2002
78.678574
15000
78.894762
13024.50977
32.892857
15700
155.220299
0
1.029589
-0.085800502
-0.085800502
18
11201.31836
118.178574
15400
44.916135
13182.69824
20.857143
14900
212.132654
0
1.176888
0.103778266
0.103778266
19
2984.779297
153.267853
14500
12.268824
3328.810547
15.357142
13200
72.745589
0
1.115262
0.06292769
0.06292769
20
3091.480713
123.60714
15600
13.652658
3136.506836
44.910713
14600
40.297186
0
1.014565
-0.074179537
-0.074179537
16896 1847 Kbytes .Supplementary file Size Download File type/resource GSM6158_Cy3.Tif.gz
7.2 Mb
(ftp) (http) TIFF
GSM6158_Cy5.Tif.gz
5.9 Mb
(ftp) (http) TIFF
