|
| Status |
Public on Jan 14, 2024 |
| Title |
African Cheetah 08 |
| Sample type |
genomic |
| |
|
| Source name |
Captive African Cheetah
|
| Organism |
Acinonyx jubatus |
| Characteristics |
tissue: Blood
Sex: female
age: 24 months
developmental stage: Newly indepenent
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted from whole blood samples using commercial DNA extraction kits according to instructions
|
| Label |
Bisulfite converted
|
| Label protocol |
DNA was bisulfite converted using a commercial kit according to instructions
|
| |
|
| Hybridization protocol |
The EpiTYPER® Assay methylation analysis was run in three phases, starting with 1) PCR using T7-promoter tagged reverse primers to amplify the target regions while preserving the bisulfite-induced sequence changes and treatment of PCR product with Shrimp-Alkaline Phospatase. 2) In vitro transcription was performed, and 3) the resulting RNA transcripts were specifically cleaved at uracil residues. The resulting fragments differed in size and mass, depending on the sequence changes generated through bisulfite treatment, and through enzymatic cleavage of uracils. The resulting fragments were loaded onto a SpectroCHIP® Array (Chip) that was placed in the MASSarray (MALDI-TOF) mass spectrometer for data acquisition. Results showed individual peaks for the generated fragments.
|
| Scan protocol |
Fragmentation pattern was analysed for mass for each fragment (based on size) and the peak height, which corresponds to the percentage of methylation compared to an internal control. The output was automatically loaded into a database for data analysis with EpiTYPER® software.
|
| Description |
Cheetah EDARADD.txt, Cheetah ELOVL2.txt, Cheetah FHL2.txt, Cheetah GRIA2.txt, Cheetah ITGA2B.txt, Cheetah PENK.txt
SAMN31850919
Source: SANBI Biobank, Location: South Africa
|
| Data processing |
The EpiTYPER® software was used to call the β-value of methylation level for each peak corresponding to a specific CpG as a value between 0 and 1 indicating the percentage of methylation detected
|
| |
|
| Submission date |
Jan 04, 2024 |
| Last update date |
Jan 14, 2024 |
| Contact name |
Louis Stéphane Le Clercq |
| E-mail(s) |
leclercq.l.s@gmail.com
|
| Organization name |
University of the Free State
|
| Department |
Department of Genetics
|
| Lab |
Conservation Genetics
|
| Street address |
Genetics building, 205 Nelson Mandela Dr, Park West
|
| City |
Bloemfontein |
| State/province |
FS |
| ZIP/Postal code |
9301 |
| Country |
South Africa |
| |
|
| Platform ID |
GPL32927 |
| Series (1) |
| GSE252541 |
Methylation-based markers for the estimation of age in African Cheetah, Acinonyx jubatus |
|
| Relations |
| BioSample |
SAMN31850919 |
