|
| Status |
Public on May 05, 2010 |
| Title |
Patient 3 LIN |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
DNA isolated from laser captured microdissected formalin-fixed, paraffin-embedded tissue.
|
| Organism |
Homo sapiens |
| Characteristics |
gender: female
tissue: lobular intraepithelial neoplasia
|
| Treatment protocol |
Whole genome amplification by GenomePlex (Sigma).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Sections of formalin-fixed paraffin-embedded (FFPE) specimens cut at 7-8µm were mounted on special foil-coated slides (Molecular Devices, San Diego, USA). The sections were then deparaffinized with Xylene, processed in decreasing concentrations of ethanol and stained with haematoxylin. Lasercapture microdissection for both lesions was performed at multiple sites using Veritas Arcturus. Cells were digested in 10µl TE, pH 9, and 0.5µl proteinase K (20mg/ml) for 48h at 55°C. After inactivation of proteinase K at 99°C for 10min, the digest was stored at -20°C. Without any further purification, the complete digest was used for whole genome amplification by means of the WGA (Whole Genome Amplification) kit from Sigma.
|
| Label |
Alexa Fluor 3
|
| Label protocol |
DNA was labelled by random priming according Invitrogens recommendation (Invitrogen BioPrime® Total Genomic Labeling System).Detailed protocols are available at our website (Molecular Cytogenetics at the Max Planck Institute for Molecular Genetics)
|
| |
|
| Channel 2 |
| Source name |
DNA pool isolated from laser captured microdissected formalin-fixed, paraffin-embedded healthy tissue.
|
| Organism |
Homo sapiens |
| Characteristics |
gender: female
tissue: mammary tissue without histomorphological changes obtained from reduction mammoplasty specimens
|
| Treatment protocol |
Whole genome amplification by GenomePlex (Sigma).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Sections of formalin-fixed paraffin-embedded (FFPE) specimens cut at 7-8µm were mounted on special foil-coated slides (Molecular Devices, San Diego, USA). The sections were then deparaffinized with Xylene, processed in decreasing concentrations of ethanol and stained with haematoxylin. Lasercapture microdissection for both lesions was performed at multiple sites using Veritas Arcturus. Cells were digested in 10µl TE, pH 9, and 0.5µl proteinase K (20mg/ml) for 48h at 55°C. After inactivation of proteinase K at 99°C for 10min, the digest was stored at -20°C. Without any further purification, the complete digest was used for whole genome amplification by means of the WGA (Whole Genome Amplification) kit from Sigma.
|
| Label |
Alexa Fluor 5
|
| Label protocol |
DNA was labelled by random priming according Invitrogens recommendation (Invitrogen BioPrime® Total Genomic Labeling System).Detailed protocols are available at our website (Molecular Cytogenetics at the Max Planck Institute for Molecular Genetics)
|
| |
|
| |
| Hybridization protocol |
Hybridization was done overnight at 42°C in a slide booster (Advalytix, Brunnthal, Germany). Detailed protocols are available at our website (Molecular Cytogenetics at the Max Planck Institute for Molecular Genetics)
|
| Scan protocol |
Slides were scanned at 10 µm resolution using an Agilent scanner. PMT settings: 100/100
|
| Description |
Array CGH analysis of a female patient with classic lobular intraepithelial neoplasia (LIN).
|
| Data processing |
TIFF images were analysed by Genepix 5.0 (Axon Instruments, Union City, CA) and raw intensities (gpr files) were imported into CGHPRO (Chen at al.,2005).Background intensities were not subtracted. Signal intensities were normalized by subgridd LOWESS. Aberrations were defined by Circular Binary Segmentation in combination with log2 ratio threshold of 0.15 and -0.15, respectively.
|
| |
|
| Submission date |
Sep 21, 2009 |
| Last update date |
Apr 09, 2010 |
| Contact name |
Reinhard Ullmann |
| E-mail(s) |
[email protected]
|
| Phone |
00493084131251
|
| Organization name |
MPIMG
|
| Department |
Human Molecular Genetics
|
| Lab |
Molecular Cytogenetics
|
| Street address |
Ihnestr.73
|
| City |
Berlin |
| ZIP/Postal code |
14195 |
| Country |
Germany |
| |
|
| Platform ID |
GPL5114 |
| Series (1) |
| GSE18187 |
Array comparative genomic hybridization analysis of flat epithelial atypia (DIN1a) and lobular intraepithelial neoplasia |
|
