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| Status |
Public on Aug 08, 2008 |
| Title |
MCL 00-13921 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source Name |
Classic MCL
|
| Organism(s) |
Homo sapiens |
| Characteristics |
lymph node tissue, 59yo 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 00-13921
|
| 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 |
2380.329 |
1118.603 |
184 |
302 |
2196.329 |
816.603 |
188.9716 |
62.0822 |
1.445227 |
0.6919047 |
0.5312966 |
0.07942 |
| 2 |
1645.705 |
806.464 |
189 |
312 |
1456.705 |
494.464 |
138.6024 |
38.7884 |
1.58302 |
0.6316784 |
0.6626796 |
0.120312 |
| 3 |
1296.86 |
733.46 |
187 |
311 |
1109.86 |
422.46 |
85.6185 |
35.8707 |
1.411667 |
0.7083538 |
0.4973998 |
-0.044609 |
| 4 |
1085.736 |
659.08 |
184 |
309.5 |
901.736 |
349.58 |
45.864 |
24.81676 |
1.386059 |
0.7214409 |
0.4709888 |
-0.075692 |
| 5 |
1390.265 |
757.031 |
186 |
311 |
1204.265 |
446.031 |
78.2916 |
29.12521 |
1.450799 |
0.6892477 |
0.5368473 |
0.008069 |
| 6 |
1163.563 |
712.708 |
183.5 |
311.5 |
980.063 |
401.208 |
51.6776 |
32.6901 |
1.312603 |
0.761814 |
0.3924311 |
-0.140674 |
| 7 |
1305.535 |
825.525 |
182.5 |
307 |
1123.035 |
518.525 |
78.2689 |
38.3881 |
1.163787 |
0.8592294 |
0.2188265 |
-0.308261 |
| 8 |
1538.905 |
831.262 |
184 |
314 |
1354.905 |
517.262 |
15.7791 |
12.01517 |
1.407499 |
0.7104516 |
0.4931335 |
-0.028644 |
| 9 |
1248.91 |
730.09 |
182 |
311 |
1066.91 |
419.09 |
71.7022 |
31.36778 |
1.36795 |
0.7309912 |
0.4520158 |
-0.066169 |
| 10 |
1876.136 |
934.559 |
184 |
312 |
1692.136 |
622.559 |
127.9104 |
46.7017 |
1.460509 |
0.6846654 |
0.5464708 |
0.117078 |
| 11 |
1995.693 |
1011.467 |
187 |
310 |
1808.693 |
701.467 |
145.7791 |
50.5817 |
1.385503 |
0.7217302 |
0.4704102 |
0.04888 |
| 12 |
1661.298 |
859.821 |
184.5 |
307 |
1476.798 |
552.821 |
111.717 |
35.4786 |
1.435445 |
0.6966201 |
0.5214977 |
0.095008 |
| 13 |
2821 |
1464.051 |
189 |
306 |
2632 |
1158.051 |
230.9873 |
74.8802 |
1.22126 |
0.8187937 |
0.28837 |
-0.103298 |
| 14 |
3081.086 |
1212.257 |
191 |
307 |
2890.086 |
905.257 |
276.0544 |
56.0307 |
1.715491 |
0.5829 |
0.7786215 |
0.388188 |
| 15 |
2010.329 |
1027.904 |
187 |
307.5 |
1823.329 |
720.404 |
166.1568 |
59.7119 |
1.359999 |
0.7352651 |
0.4436054 |
0.037173 |
| 16 |
2124.286 |
1317.078 |
186.5 |
309 |
1937.786 |
1008.078 |
162.9124 |
77.3816 |
1.032907 |
0.9681021 |
0.04671075 |
-0.346988 |
| 17 |
3005.025 |
1410.914 |
186 |
310 |
2819.025 |
1100.914 |
266.0767 |
106.7591 |
1.375927 |
0.7267535 |
0.4604038 |
0.085552 |
| 18 |
2260.218 |
1048.308 |
184 |
308.5 |
2076.218 |
739.808 |
197.1841 |
59.9324 |
1.508008 |
0.6630995 |
0.5926445 |
-0.018053 |
| 19 |
2718.74 |
1294.597 |
184 |
309 |
2534.74 |
985.597 |
263.2125 |
66.1359 |
1.381922 |
0.7236006 |
0.4666764 |
0.006566 |
| 20 |
2375.212 |
1122.088 |
184.5 |
308.5 |
2190.712 |
813.588 |
166.7973 |
56.4067 |
1.446874 |
0.6911172 |
0.5329395 |
0.064043 |
Total number of rows: 53856
Table truncated, full table size 5500 Kbytes.
| Supplementary file |
Size |
Download |
File type/resource |
| GSM238814.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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