|
| Status |
Public on Feb 02, 2016 |
| Title |
VUB31_D_08 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
hESC culture
|
| Organism |
Homo sapiens |
| Characteristics |
sample: Single hESC
assayed molecule: Amplified DNA
density group: high
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Extraction was done following standard 24sure v3 protocol. In brief, 2.5µl extraction buffer and 5µl extraction cocktail were added per sample, followed by 10min incubation at 75°C and 4min at 95°C.
|
| Label |
Cy5
|
| Label protocol |
Labelling was done following standard 24sure v3 protocol. In brief, samples were mixed with 5µl of random primers and denaturated for 5min at 94°C. Afterwards, samples were mixed with 12µl of Cy3/Cy5 labelling master mix and incubated at 37°C for 4 hours.
|
| |
|
| Channel 2 |
| Source name |
female/male reference
|
| Organism |
Homo sapiens |
| Characteristics |
sample: reference
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Extraction was done following standard 24sure v3 protocol. In brief, 2.5µl extraction buffer and 5µl extraction cocktail were added per sample, followed by 10min incubation at 75°C and 4min at 95°C.
|
| Label |
Cy3
|
| Label protocol |
Labelling was done following standard 24sure v3 protocol. In brief, samples were mixed with 5µl of random primers and denaturated for 5min at 94°C. Afterwards, samples were mixed with 12µl of Cy3/Cy5 labelling master mix and incubated at 37°C for 4 hours.
|
| |
|
| |
| Hybridization protocol |
After ethanol precipitation, samples were dissolved in hybridization mix at 75°C for 10 minutes, and incubated overnight at 47°C on the arrays in closed incubation chambers with 50% formamide. The slides were washed 10min in 2xSSC/0.05% Tween20, 10 min 1xSSC, 5min 0.1%SSC at 60°C and 1min in 0.1%SSC at RT
|
| Scan protocol |
Agilent dual laser DNA microarray scanner G2566AA was used for scanning the arrays, data was stored as .TIFF files
|
| Description |
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample_vs_female_reference: 130724-829045B_bottom_Cy5_female_fused.txt, sample_vs_male_reference:130724-829045B_bottom_Cy5_male_fused.txt
|
| Data processing |
.TIFF files were imported in, and processed by, BlueFuse Multi 3.1.
|
| |
|
| Submission date |
Jun 06, 2014 |
| Last update date |
Feb 03, 2016 |
| Contact name |
Kurt Jacobs |
| E-mail(s) |
[email protected]
|
| Organization name |
Vrije Universiteit Brussel (VUB)
|
| Department |
Faculty of Medicine and Pharmacy
|
| Lab |
Research Group Reproduction and Genetics
|
| Street address |
Laarbeeklaan 103
|
| City |
Brussels |
| ZIP/Postal code |
1090 |
| Country |
Belgium |
| |
|
| Platform ID |
GPL17760 |
| Series (1) |
| GSE58281 |
Genomic instability in human embryonic stem cells is associated to culture density and medium acidification. |
|
