|
| Status |
Public on Sep 15, 2009 |
| Title |
MF patient 18 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
Skin tumor, tumor-stage mycosis fungoides
|
| Organism |
Homo sapiens |
| Characteristics |
gender: Female
age: 40
tissue: skin tumor
disease: tumor-stage mycosis fungoides
|
| Treatment protocol |
Skin biopsies were snap frozen.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Total DNA was extracted using the DNeasy Blood & Tissue Kit (Qiagen, Hilden, Germany) following the protocol supplied by the manufacturer.
|
| Label |
Cy5
|
| Label protocol |
0.5µg-1.5 µg of total DNA previously digested were primed with 5 µl Random primers at 95ºC for 3 min. Then the primed DNA was mixed with the Labeling Master Mix (containing 2 µl Nuclease free water, 10 µl 5X Buffer, 10X dNTP, 3 µl Cy3 or Cy5 depending on sample or control DNA labeling and 1µl Exo-Klenow fragment) and incubating at 37ºC for 2 hours.
|
| |
|
| Channel 2 |
| Source name |
Commercial pools of healthy DNA (Promega, Madison, WI, USA)
|
| Organism |
Homo sapiens |
| Characteristics |
gender: Female
tissue: Peripheral blood
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Total DNA was extracted using the DNeasy Blood & Tissue Kit (Qiagen, Hilden, Germany) following the protocol supplied by the manufacturer.
|
| Label |
Cy3
|
| Label protocol |
0.5µg-1.5 µg of total DNA previously digested were primed with 5 µl Random primers at 95ºC for 3 min. Then the primed DNA was mixed with the Labeling Master Mix (containing 2 µl Nuclease free water, 10 µl 5X Buffer, 10X dNTP, 3 µl Cy3 or Cy5 depending on sample or control DNA labeling and 1µl Exo-Klenow fragment) and incubating at 37ºC for 2 hours.
|
| |
|
| |
| Hybridization protocol |
Human cot-1 DNA, Agilent 10x blocking agent and Agilent 2x hybridization buffer were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequentially.
|
| Scan protocol |
Scanned on an Agilent G2565AA scanner. Images were quantified using Agilent Feature Extraction Software (version 8.1).
|
| Description |
MFt 18
|
| Data processing |
Linear normalized background subtracted data obtained from log2 of processed Red signal/processed Green signal. Agilent software was used.
|
| |
|
| Submission date |
Sep 14, 2009 |
| Last update date |
Feb 08, 2012 |
| Contact name |
Rocio Salgado |
| E-mail(s) |
rsalgado@imim.es
|
| Phone |
+00 34 932483521
|
| Fax |
+00 34 932483131
|
| Organization name |
IMIM-Hospital del Mar
|
| Street address |
Passeig Marítim, 25-29
|
| City |
Barcelona |
| ZIP/Postal code |
08003 |
| Country |
Spain |
| |
|
| Platform ID |
GPL5477 |
| Series (1) |
| GSE18098 |
Genetic characterization of tumor-stage mycosis fungoides |
|
