|
| Status |
Public on May 09, 2012 |
| Title |
Parathyroid adenoma 5 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
Parathyroid adenoma
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: parathyroid adenoma
gender: female
age (years): 57
tumor weight (g): 8.5
plasma parathyroid hormone (ng/l): 358
total calcium (mmol/l): 2.97
ionized calcium (mmol/l): 1.59
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Total genomic DNA was extracted using the DNeasy Blood and Tissue DNA isolation kit (Qiagen AB, Sweden) following the manufacturer’s protocol.
|
| Label |
Cy3
|
| Label protocol |
One microgram of test DNA and normal reference DNA (Promega) were labelled separately with Cy3-dCTP and Cy5-dCTP using a random labelling kit (BioPrime Array CGH Genomic kit; Invitrogen Life Technologies).
|
| |
|
| Channel 2 |
| Source name |
Normal reference DNA (sex-mismatched)
|
| Organism |
Homo sapiens |
| Characteristics |
sample type: reference
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
The normal reference DNA was obtained from Promega.
|
| Label |
Cy5
|
| Label protocol |
One microgram of test DNA and normal reference DNA (Promega) were labelled separately with Cy3-dCTP and Cy5-dCTP using a random labelling kit (BioPrime Array CGH Genomic kit; Invitrogen Life Technologies).
|
| |
|
| |
| Hybridization protocol |
BAC array CGH microarrays were hybridized as described (PMID: 17334996, PMID: 21423728). After hybridization, stringent washing was performed as described in PMID: 21423728.
|
| Scan protocol |
Slides were scanned in an Axon Scanner 4000A (Axon Instruments).
|
| Data processing |
Images were quantified using the GenePix Pro 6.0 package analysis software (Axon instruments) and uploaded at the BioArray Software Environment (BASE; http://www.base.thep.lu.se/) for filtering, normalization and statistical analysis, as described in. First, spots flagged by the GenePix software or disqualified after manual inspection were removed. Subsequently, probes with spot diameter <40 µm or intensity below background were removed. Background-corrected data was obtained by calculating the median foreground and subtracting the median background signal intensity for each channel. Intensity ratios for individual probes were calculated within arrays from background-corrected intensity levels of test sample divided by reference sample and data were normalized using the LOWESS algorith. The data was smoothed using a three-clone sliding window and CGH plotter was used to identify the extent of alterations using a segmentation constant of 7. Log2 ratios for two continuous BAC clones outside the threshold ranges were classified as copy number changes including gain (threshold +0.25), loss (-0.25), amplification (+1) and homozygous loss (-1).
|
| |
|
| Submission date |
May 09, 2012 |
| Last update date |
May 10, 2012 |
| Contact name |
Jamileh Hashemi |
| E-mail(s) |
[email protected]
|
| Organization name |
Karolinska Institutet
|
| Department |
Molecular Medicine & Surgery
|
| Lab |
CMM, L8:01
|
| Street address |
Karolinska University Hospital
|
| City |
Stockholm |
| ZIP/Postal code |
171 76 |
| Country |
Sweden |
| |
|
| Platform ID |
GPL9077 |
| Series (1) |
| GSE36511 |
Genetic characterization of large parathyroid adenomas |
|
