|
| Status |
Public on Sep 08, 2010 |
| Title |
MPNST tumor (rp mutation) vs normal tail tissue, replicate 28 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
Tumor from adult fish
|
| Organism |
Danio rerio |
| Characteristics |
FISH strain: Zebrafish TAB strain
age: 8-24 months
tissue: Peripheral nerve sheath
tumor type: MPNST
mutation type: rp mutation
|
| Growth protocol |
Fish were kept according to standard conditions described in: The Zebrafish Book: A Guide for the Laboratory use of Zebrafish (Danio rerio), Monte Westerfield - 1995 - Univ. of Oregon Press
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was isolated according to the reference Zhang et al, 2010 (submitted). Briefly, samples were digested in lysis buffer with 10ug/ml proteinase K. Following DNA isolation, the samples were cleaned by phenol-choloroform extraction and ethonal precipitation.
|
| Label |
Cy5
|
| Label protocol |
5 µg genomic DNA was used for probe labeling with DNA polymerase I Klenow exo-. The reactions were carried according to the manufacturer's (Agilent) manual.
|
| |
|
| Channel 2 |
| Source name |
Normal tail from adult fish (reference)
|
| Organism |
Danio rerio |
| Characteristics |
strain: Zebrafish TAB strain
age: 8-24 months
tissue: tail
|
| Growth protocol |
Fish were kept according to standard conditions described in: The Zebrafish Book: A Guide for the Laboratory use of Zebrafish (Danio rerio), Monte Westerfield - 1995 - Univ. of Oregon Press
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was isolated according to the reference Zhang et al, 2010 (submitted). Briefly, samples were digested in lysis buffer with 10ug/ml proteinase K. Following DNA isolation, the samples were cleaned by phenol-choloroform extraction and ethonal precipitation.
|
| Label |
Cy3
|
| Label protocol |
5 µg genomic DNA was used for probe labeling with DNA polymerase I Klenow exo-. The reactions were carried according to the manufacturer's (Agilent) manual.
|
| |
|
| |
| Hybridization protocol |
Agilent aCGH/chip-on-chip hybridization Kit was used for hybridization at 65° celsius, and labeled samples were loaded onto microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequentially with Agilent Washing buffer A and B.
|
| Scan protocol |
Scanned on an Agilent G2505B scanner.
Images were quantified using Agilent Feature Extraction Software (version v 9.1.3.1).
|
| Description |
G1_2-3_TN
|
| Data processing |
Agilent Feature Extraction Software (v 9.1.3.1) was used for background subtraction and LINEAR normalization.
Agilent control spots and probes were excluded. Normalized log10 ratio (Cy5/Cy3) representing test/reference in original FE output were converted to log2 ratios. Also, probe values for dye-swap samples C_2-2 and G1_1-1 were multiplied by -1 to correct the dye swap, so that data is usable as is.
|
| |
|
| Submission date |
Aug 17, 2010 |
| Last update date |
Sep 08, 2010 |
| Contact name |
Sebastian Hoersch |
| Organization name |
Massachusetts Institute of Technology
|
| Department |
David H. Koch Institute for Integrative Cancer Research at MIT
|
| Lab |
Bioinformatics and Computing Core
|
| Street address |
77 Massachusetts Avenue (E18-366)
|
| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02474 |
| Country |
USA |
| |
|
| Platform ID |
GPL10797 |
| Series (1) |
| GSE23666 |
Highly Aneuploid Zebrafish Malignant Peripheral Nerve Sheath Tumors have Genetic Alterations Similar to Human Cancers |
|
