|
| Status |
Public on Nov 19, 2012 |
| Title |
Breast cancer, Mm4236_16_R39-2_05 (44k) |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
peripheral blood, circulating tumor cell (CTC)
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: peripheral blood
type of isolated tumor cells: circulating tumor cell (CTC)
disease state: metastatic breast cancer
patient identifier: Mm4236
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
For the single cells: All samples were amplified using the GenomePlex® Single Cell Whole Genome Amplification Kit (Sigma-Aldrich, Missouri, USA) according to the manufacturer's instructions with some modifications. Clean up was performed according to the manufacturer's instructions with the Gen elute™ PCR clean up kit (Sigma-Aldrich, Missouri, USA). DNA concentrations were measured using the NanoDrop® ND-1000 (Thermo Fisher Scientific, Delaware, USA). For the 3 primary tumors: Primary tumor DNA was extracted using an ABI 341 Nucleic Acid Purification System (Applied Biosystems, Carlsbad, CA, USA) according to the manufacturer's protocol.
|
| Label |
Cy5
|
| Label protocol |
1.25ug (244K) or 750ng (44K) of amplified DNA from single cells and reference were labeled using the Agilent DNA Labeling Kit PLUS (containing random primers, 10X dNTPs, exo-Klenow-polymerase, buffer and Cy3- and Cy5-dUTPs). Test samples were labeled with Cy5 and reference with Cy3. The standard protocol (Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis v.3.0) was followed.
|
| |
|
| Channel 2 |
| Source name |
Human reference DNA
|
| Organism |
Homo sapiens |
| Characteristics |
gender: female
donor: multiple anonymous donors
sample type: reference
vendor; catalog#: Promega (Madison, WI, USA); cat.# G1521
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
For the single cells: All samples were amplified using the GenomePlex® Single Cell Whole Genome Amplification Kit (Sigma-Aldrich, Missouri, USA) according to the manufacturer's instructions with some modifications. Clean up was performed according to the manufacturer's instructions with the Gen elute™ PCR clean up kit (Sigma-Aldrich, Missouri, USA). DNA concentrations were measured using the NanoDrop® ND-1000 (Thermo Fisher Scientific, Delaware, USA). For the 3 primary tumors: Primary tumor DNA was extracted using an ABI 341 Nucleic Acid Purification System (Applied Biosystems, Carlsbad, CA, USA) according to the manufacturer's protocol.
|
| Label |
Cy3
|
| Label protocol |
1.25ug (244K) or 750ng (44K) of amplified DNA from single cells and reference were labeled using the Agilent DNA Labeling Kit PLUS (containing random primers, 10X dNTPs, exo-Klenow-polymerase, buffer and Cy3- and Cy5-dUTPs). Test samples were labeled with Cy5 and reference with Cy3. The standard protocol (Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis v.3.0) was followed.
|
| |
|
| |
| Hybridization protocol |
Cot-1 DNA, Agilent blocking agent and Hybridization buffer were added to the Cy3 and Cy5 labeled gDNA mix. Hybridization to microarray rotating in a hybridization oven at 65ºC for 40 hrs (244K) or 20 hrs (44K). Washing of microarrays with Agilent wash buffer 1 and 2, and NO acetonitrile or Agilent Stabilization and Drying Solution.
|
| Scan protocol |
Images were scanned with the Agilent Microarray Scanner (Agilent Technologies, Santa Clara, CA).
|
| Description |
Mm4236_16_R39-2_05
Metastatic breast cancer patient.
|
| Data processing |
Feature Extraction 10.5.1.1. Lowess normalization was performed.
|
| |
|
| Submission date |
Nov 19, 2012 |
| Last update date |
Nov 19, 2012 |
| Contact name |
Randi Mathiesen |
| E-mail(s) |
randi.mathiesen@rr-research.no
|
| Phone |
+4745290525
|
| Organization name |
Institute for cancer research Oslo University Hospital Radiumhospitalet
|
| Department |
Dept. of genetics
|
| Street address |
Montebello
|
| City |
Oslo |
| ZIP/Postal code |
0310 |
| Country |
Norway |
| |
|
| Platform ID |
GPL8841 |
| Series (1) |
| GSE27574 |
High-resolution analysis of copy number changes in circulating and disseminated tumor cells in breast cancer patients |
|
