|
| Status |
Public on Nov 09, 2009 |
| Title |
Patient 3 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
test - DNA isolated from laser captured microdissected formalin-fixed, paraffin-embedded tissue.
|
| Organism |
Homo sapiens |
| Characteristics |
gender: female
tissue: lobular intraepithelial neoplasia grade 3 (LIN3)
|
| Treatment protocol |
Whole genome amplification by GenomePlex (Sigma).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Sections of formalin-fixed paraffin-embedded (FFPE) specimens cut at 7-8um 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 10ul TE, pH 9, and 0.5ul proteinase K (20mg/ml) for 48h at 55degC . After inactivation of proteinase K at 99degC for 10min, the digest was stored at -20degC . 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 |
reference - 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 7-8um 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 10ul TE, pH 9, and 0.5ul proteinase K (20mg/ml) for 48h at 55degC . After inactivation of proteinase K at 99degC for 10min, the digest was stored at -20degC . 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 42degC 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 um resolution using an Agilent scanner. PMT settings: 100/100
|
| Description |
Array CGH analysis of a female patient with pleomorphic/necrotic lobular intraepithelial neoplasia (LIN3).
|
| 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 |
Feb 09, 2009 |
| Last update date |
Oct 15, 2009 |
| 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) |
| GSE14803 |
Positioning of Necrotic Lobular Intraepithelial Neoplasias within the sequence of breast carcinoma progression |
|
