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| Status |
Public on Aug 08, 2008 |
| Title |
MCL 01-10814 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source Name |
Classic MCL
|
| Organism(s) |
Homo sapiens |
| Characteristics |
Lymph node tissue, 56yo male, classic MCL
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Proteinase K digestion, phenol extraction, ethanol precipitation
|
| Label |
Cy3
|
| Label protocol |
random priming
|
| |
|
| Channel 2 |
| Source Name |
pooled normal male genomic DNA
|
| Organism(s) |
Homo sapiens |
| Characteristics |
pool of at least 8 individuals purchased from Novagen
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
unknown, purchased from Novagen, San Diego, CA
|
| Label |
Cy5
|
| Label protocol |
random priming
|
| |
|
| |
| Hybridization protocol |
DIG easy, 45ºC, 40hr
|
| Scan protocol |
Applied Precision AutoE CCD scanner, 9.675um
|
| Description |
MCL 01-10814
|
| Data processing |
Applied Precision SoftWoRx analysis software, Scale factor=1, median background normalization. Stepwise normalization procedure (Khojasteh M., et al BMC Bioinformatics 6, 274)
|
| |
|
| Submission date |
Oct 19, 2007 |
| Contact name |
Ronald J deLeeuw |
| E-mail(s) |
rdeleeuw@bccrc.ca
|
| Phone |
6046758111
|
| Fax |
6046758232
|
| Organization name |
BC Cancer Research Centre
|
| Department |
Cancer Genetics
|
| Lab |
Lam Lab
|
| Street address |
675 W. 10th Ave.
|
| City |
Vancouver |
| State/province |
British Columbia |
| ZIP/Postal code |
V5Z 1L3 |
| Country |
Canada |
| |
|
| Platform ID |
GPL2616 |
| Data table header descriptions |
| ID_REF |
|
| Spot Mean Intensity (w595) |
|
| Spot Mean Intensity (w685) |
|
| Background Median Intensity (w595) |
|
| Background Median Intensity (w685) |
|
| Spot Normalized Intensity (w595) |
|
| Spot Normalized Intensity (w685) |
|
| Spot SNR (w595) |
|
| Spot SNR (w685) |
|
| Spot Ratio (w595) |
|
| Spot Ratio (w685) |
|
| Spot Log2 Ratio (w595) |
|
| VALUE |
processed/normalized data used for analysis; ratio of (MCL/reference DNA) |
| Data table |
| ID_REF |
Spot Mean Intensity (w595) |
Spot Mean Intensity (w685) |
Background Median Intensity (w595) |
Background Median Intensity (w685) |
Spot Normalized Intensity (w595) |
Spot Normalized Intensity (w685) |
Spot SNR (w595) |
Spot SNR (w685) |
Spot Ratio (w595) |
Spot Ratio (w685) |
Spot Log2 Ratio (w595) |
VALUE |
| 1 |
7142.47 |
3410.19 |
412.5 |
697.5 |
6729.97 |
2712.694 |
355.909 |
145.8613 |
0.8334745 |
1.199755 |
-0.26279 |
0.080206 |
| 2 |
3802.77 |
2007.745 |
426 |
705 |
3376.77 |
1302.745 |
46.8994 |
46.414 |
0.8708068 |
1.148321 |
-0.1995755 |
0.02049 |
| 3 |
4113.61 |
2568.482 |
489.5 |
734 |
3624.11 |
1834.482 |
7.16036 |
9.42793 |
0.6636944 |
1.506665 |
-0.591409 |
0.4096 |
| 4 |
1797.301 |
1193.542 |
428 |
710 |
1369.301 |
483.542 |
3.092063 |
2.6767 |
0.9513589 |
1.051092 |
-0.07193843 |
-0.093748 |
| 5 |
8508.51 |
4308.42 |
449 |
716 |
8059.51 |
3592.42 |
82.5917 |
79.4506 |
0.7537057 |
1.326732 |
-0.4079266 |
0.205894 |
| 6 |
4039.45 |
2074.149 |
455 |
723 |
3584.45 |
1351.149 |
168.5677 |
72.6752 |
0.8912503 |
1.121981 |
-0.1660976 |
-0.015713 |
| 7 |
8025.71 |
3816.45 |
461 |
722 |
7564.71 |
3094.448 |
377.799 |
160.1589 |
0.8212754 |
1.217576 |
-0.2840621 |
0.084692 |
| 8 |
2023.128 |
1395.477 |
451 |
722 |
1572.128 |
673.477 |
72.0919 |
38.4557 |
0.7842329 |
1.275087 |
-0.3506459 |
0.182302 |
| 9 |
6366.72 |
3550.59 |
448 |
724 |
5918.72 |
2826.589 |
272.1946 |
116.7667 |
0.7034689 |
1.421478 |
-0.5074415 |
0.308765 |
| 10 |
10764.88 |
4957.41 |
437 |
715 |
10327.88 |
4242.41 |
388.821 |
326.53 |
0.8178589 |
1.222663 |
-0.2900762 |
0.054371 |
| 11 |
8274.62 |
3994.06 |
443.5 |
705 |
7831.12 |
3289.06 |
330.348 |
243.3403 |
0.7998934 |
1.250123 |
-0.3221203 |
0.088519 |
| 12 |
7507.93 |
3535.61 |
442 |
711 |
7065.93 |
2824.611 |
358.072 |
178.323 |
0.8404081 |
1.189857 |
-0.250838 |
0.009365 |
| 13 |
10972.18 |
5533.92 |
455 |
709 |
10517.18 |
4824.92 |
505.516 |
236.1286 |
0.7322993 |
1.365515 |
-0.4494947 |
0.187873 |
| 14 |
11365.01 |
5145.23 |
454 |
716 |
10911.01 |
4429.23 |
320.31 |
215.484 |
0.8275923 |
1.208283 |
-0.2730079 |
0.009683 |
| 15 |
8449.99 |
4227.14 |
449 |
722 |
8000.99 |
3505.14 |
137.7036 |
108.3376 |
0.7668629 |
1.303969 |
-0.3829595 |
0.126575 |
| 16 |
12452.53 |
5543.7 |
454 |
718.5 |
11998.53 |
4825.2 |
599.391 |
218.9658 |
0.8353965 |
1.196995 |
-0.2594669 |
-0.013848 |
| 17 |
14223.74 |
6610.51 |
458.5 |
727.5 |
13765.24 |
5883.01 |
593.618 |
291.8071 |
0.786075 |
1.272099 |
-0.3472612 |
0.049055 |
| 18 |
9980.14 |
4807.6 |
460 |
723.5 |
9520.14 |
4084.1 |
382.963 |
163.2413 |
0.7831172 |
1.276904 |
-0.3526998 |
-0.011839 |
| 19 |
9978.59 |
4482.71 |
454 |
721.5 |
9524.59 |
3761.21 |
481.827 |
220.3977 |
0.8507436 |
1.175402 |
-0.2332037 |
-0.04122 |
| 20 |
10681.56 |
4768.79 |
460.5 |
723.5 |
10221.06 |
4045.29 |
640.972 |
216.1495 |
0.8488405 |
1.178037 |
-0.2364345 |
-0.044658 |
Total number of rows: 53856
Table truncated, full table size 5456 Kbytes.
| Supplementary file |
Size |
Download |
File type/resource |
| GSM238859.txt.gz |
2.4 Mb |
(ftp)(http) |
TXT |
| Raw data included within Sample table |
| Raw data provided as supplementary file |
| Processed data included within Sample table |
|
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