|
| Status |
Public on Aug 18, 2021 |
| Title |
Mother_BAC_E04 |
| Sample type |
genomic |
| |
|
| Source name |
Cow ovarian tissue pedigree BAC_E04
|
| Organism |
Bos taurus |
| Characteristics |
tissue: Ovarian
|
| Treatment protocol |
Single blastomeres of bovine preimplantation embryos were dissociated and whole genome amplified as described previously (Destouni et al., 2016)). Briefly, zona pellucida was removed by pronase treatment and single blastomeres were disassociated and picked individually.
|
| Growth protocol |
Embryos were in vitro produced according to previously described methods (Catteeuw et al., 2017).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Extraction of gDNA from sperm and ovarian tissue was performed using the Qiagen DNeasy Blood and Tissue kit according to the manufacturer's protocol (sperm: user-developed protocol for purification of total DNA from animal sperm using the DNeasy® Blood & Tissue Kit; protocol 2). Single blastomere and whole-embryo DNA was whole-genome amplified using the REPLI-g SC kit (Qiagen) according to the manufacturer's instructions with full or half reaction volumes and a 3 h incubation reaction.
|
| Label |
Cy5/Cy3
|
| Label protocol |
200 ng of gDNA and 600 ng of whole-genome amplified DNA was used as input for processing the samples according to the manufacturer's protocol of BovineHD BeadChip arrays using Infinium HD whole-genome genotyping assay (Illumina Inc., USA).
|
| |
|
| Hybridization protocol |
According to the manufacturer's protocol of Infinium HD Assay for BovineHD BeadChip arrays.
|
| Scan protocol |
The scanning of the bead-chips was performed on an iScan, using the iScan Control software (Illumina, USA) according to the manufacturer's protocol of BovineHD BeadChip arrays using Infinium HD whole-genome genotyping assay (Illumina Inc., USA)
|
| Description |
Genomic DNA extracted from cow ovarian tissue was genotyped using BovineHD BeadChip arrays (Illumina).
Cow gDNA in the pedigree BAC_E04
|
| Data processing |
Samples were genotyped using the BovineHD BeadChip arrays using Infinium HD whole-genome genotyping assay (Illumina Inc., USA. The genotypes, B allele frequencies and LogR values were processed by the Genotyping module of GenomeStudio software. The discrete genotypes were determined using a threshold of 0,75. We subsequently analysed these data with haplarithmisis adapted for bovine (Zamani Esteki et al. 2015, AJHG).
Genotypes: AA,AB,BB or NC (No Call); BAF: B-allele frequency; logR: log2ratio
|
| |
|
| Submission date |
Jun 14, 2021 |
| Last update date |
Aug 18, 2021 |
| Contact name |
Joris R. Vermeesch |
| E-mail(s) |
joris.vermeesch@kuleuven.be
|
| Organization name |
KU Leuven
|
| Department |
Department of Human Genetics
|
| Lab |
Laboratory for Cytogenetics and Geome Research
|
| Street address |
Herestraat 49 box 606
|
| City |
Leuven |
| ZIP/Postal code |
3000 |
| Country |
Belgium |
| |
|
| Platform ID |
GPL21267 |
| Series (1) |
| GSE178156 |
Single-cell genome-wide concurrent haplotyping and copy-number profiling through genotyping-by-sequencing in bovine embryos |
|
