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Status
Public on May 27, 2003
Title
Kc167_Homotypic_R3_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). 40ug 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
896.254211
36.69643
11800
7.672077
925.788879
21.035715
9000
11.704076
0
1.032953
0.413750277
0.413750277
2
958.229187
58.30357
9600
7.338577
902.81012
16.125
7900
20.085805
0
0.942165
0.276505446
0.276505446
3
1436.613647
191.142853
13200
5.102461
1310.815796
13.392858
11400
30.970556
0
0.912434
0.191139176
0.191139176
4
1350.956909
20.535715
11600
29.328595
1234.305542
9.017858
10800
38.344312
0
0.913653
0.211941747
0.211941747
5
4490.696777
75
14500
25.46944
4618.793457
22.267857
12600
61.611007
0
1.028525
0.316755737
0.316755737
6
4917.716309
71
14100
34.03059
4967.040527
24.285715
12300
62.831437
0
1.01003
0.298501612
0.298501612
7
1758.625977
52.142857
12300
15.216547
1495.175415
10.357142
11400
46.300788
0
0.850195
0.067593256
0.067593256
8
1649.950439
67.839287
12100
11.65518
1551.151245
17.107143
11900
35.368324
0
0.94012
0.211292081
0.211292081
9
1235.142822
43.625
10500
11.538205
1169.141235
27.982143
8500
14.832133
0
0.946564
0.275021574
0.275021574
10
1291.540771
46.57143
9800
10.222279
1017.01062
20.946428
9400
12.99786
0
0.78744
0.015873489
0.015873489
11
1418.638306
96.089287
9400
8.494974
1243.136963
11.803572
7300
40.518125
0
0.876289
0.143545008
0.143545008
12
1167.729736
138.196426
11100
4.554158
1194.528687
19.821428
8700
20.831628
0
1.02295
0.389964779
0.389964779
13
1833.067261
53.482143
11900
12.252132
1586.968384
16.928572
9500
31.589731
0
0.865745
0.098563305
0.098563305
14
1668.484497
165.571426
16100
5.708886
1636.692993
18.464285
11400
36.424478
0
0.980946
0.275863626
0.275863626
15
2503.335693
263.410706
13700
7.048895
2031.613159
20.892857
13700
35.946331
0
0.811562
0.017173653
0.017173653
16
2496.515869
170.25
12600
9.198226
1963.503784
21.321428
13100
30.345625
0
0.786498
-0.027936327
-0.027936327
17
8088.699219
132.732147
14300
33.596719
7341.746582
12.160714
13800
168.69816
0
0.907655
0.139584489
0.139584489
18
7673.506348
51.642857
15200
72.594913
7730.149902
14.410714
14000
145.801618
0
1.007382
0.289961844
0.289961844
19
3285.393555
89.535713
15500
18.011469
2955.507813
22.928572
12800
53.788142
0
0.89959
0.132373145
0.132373145
20
3601.446777
112.85714
14100
16.253045
3076.541016
20.089285
12200
50.471418
0
0.854251
0.051263213
0.051263213
16896 1848 Kbytes .Supplementary file Size Download File type/resource GSM6161_Cy3.Tif.gz
6.4 Mb
(ftp) (http) TIFF
GSM6161_Cy5.Tif.gz
5.2 Mb
(ftp) (http) TIFF
