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Status |
Public on Sep 15, 2009 |
Title |
MF patient 13 |
Sample type |
genomic |
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Channel 1 |
Source name |
Skin tumor, tumor-stage mycosis fungoides
|
Organism |
Homo sapiens |
Characteristics |
gender: Male age: 63 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 |
2 µg of total DNA previously digested were primed with 20 µl 2.5X Random primers at 95ºC for 5 min. Then the primed DNA was mixed with 10X Buffer, 3 µl Cy3 or Cy5 depending on sample or control DNA labeling and 1µl Exo-Klenow fragment) and incubating at 37ºC for 2 hours.
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|
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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 |
2 µg of total DNA previously digested were primed with 20 µl 2.5X Random primers at 95ºC for 5 min. Then the primed DNA was mixed with 10X Buffer, 3 µl Cy3 or Cy5 depending on sample or control DNA labeling and 1µl Exo-Klenow fragment) and incubating at 37ºC for 2 hours.
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|
|
|
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 13
|
Data processing |
Linear normalized background subtracted data obtained from log2 of processed Red signal/processed Green signal. Agilent software was used.
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Submission date |
Sep 14, 2009 |
Last update date |
Sep 14, 2009 |
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 |
GPL2879 |
Series (1) |
GSE18098 |
Genetic characterization of tumor-stage mycosis fungoides |
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