|
| Status |
Public on Dec 23, 2019 |
| Title |
CGH Tdp2-/-Atm-/- Exp3 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
Thymocytes
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Thymocytes
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNeasy Blood and Tissue Kit (Qiagen) following recommendations of the manufacturer
|
| Label |
Cy5
|
| Label protocol |
1g of DNA was labeled following the standard Agilent protocol: “Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis. Enzymatic Labeling for blood, cells, or tissues” (Version 7.4, August 2015)”. Cy3 and Cy5 were used for control and thymocyte samples, respectively.
|
| |
|
| Channel 2 |
| Source name |
Kidney
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Kidney
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNeasy Blood and Tissue Kit (Qiagen) following recommendations of the manufacturer
|
| Label |
Cy3
|
| Label protocol |
1g of DNA was labeled following the standard Agilent protocol: “Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis. Enzymatic Labeling for blood, cells, or tissues” (Version 7.4, August 2015)”. Cy3 and Cy5 were used for control and thymocyte samples, respectively.
|
| |
|
| |
| Hybridization protocol |
Hybridization was performed during 40 hours at 67ºC. Agilent Mouse Genome CGH Microarray, 2x105K (DesignID=014699) was then used.
|
| Scan protocol |
GenePix pro 7.0 of GenePix 4100A Microarrays Scanner (Molecular Devices, LLC).
|
| Data processing |
The R package snapCGH was used for background subtraction and normalization.
|
| |
|
| Submission date |
Jul 09, 2019 |
| Last update date |
Dec 24, 2019 |
| Contact name |
Felipe Cortés Ledesma |
| E-mail(s) |
fcortes@cnio.es
|
| Organization name |
CNIO
|
| Department |
Molecular Oncology
|
| Lab |
Topology and DNA breaks
|
| Street address |
Melchor Fernández Almagro 3
|
| City |
Madrid |
| State/province |
Madrid |
| ZIP/Postal code |
28029 |
| Country |
Spain |
| |
|
| Platform ID |
GPL4094 |
| Series (1) |
| GSE134054 |
Endogenous topoisomerase II-mediated DNA breaks drive thymic cancer predisposition linked to ATM deficiency |
|
