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Sample GSM5381073 Query DataSets for GSM5381073
Status Public on Aug 18, 2021
Title Mother_Family6225
Sample type genomic
 
Source name Cow ovarian tissue pedigree Family6225
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 Family6225
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

Data table header descriptions
ID_REF
VALUE Genotypes: AA,AB,BB or NC (No Call)
B Allele Freq
Log R Ratio

Data table
ID_REF VALUE B Allele Freq Log R Ratio
ARS-BFGL-BAC-11602 NC 0.02546532 -0.1528438
ARS-BFGL-BAC-13205 BB 0.9964278 -0.09537879
ARS-BFGL-BAC-19353 BB 1 -0.2695215
ARS-BFGL-BAC-27150 NC 1 0.08100387
ARS-BFGL-BAC-31012 NC 1 0.4864954
ARS-BFGL-BAC-32700 NC 1 -0.2003234
ARS-BFGL-BAC-35028 AA 0 0.2439077
ARS-BFGL-BAC-35948 NC 0 0.1287109
ARS-BFGL-NGS-100012 BB 1 0.3962784
ARS-BFGL-NGS-100232 NC 1 -0.005839866
ARS-BFGL-NGS-100372 AB 0.5387005 -0.05250726
ARS-BFGL-NGS-100549 AA 0 0.05564636
ARS-BFGL-NGS-100941 AA 0 0.279882
ARS-BFGL-NGS-101104 AB 0.5249833 -0.02911175
ARS-BFGL-NGS-101164 BB 1 -0.07854746
ARS-BFGL-NGS-101368 AB 0.5150694 -0.05623098
ARS-BFGL-NGS-101923 AA 0 0.3604609
ARS-BFGL-NGS-102643 AB 0.4755673 0.391173
ARS-BFGL-NGS-102677 BB 1 -0.01467442
ARS-BFGL-NGS-102692 AB 0.4580317 -0.081746

Total number of rows: 65530

Table truncated, full table size 2488 Kbytes.




Supplementary file Size Download File type/resource
GSM5381073_3999767056_R08C01_Grn.idat.gz 5.2 Mb (ftp)(http) IDAT
GSM5381073_3999767056_R08C01_Red.idat.gz 5.3 Mb (ftp)(http) IDAT
Processed data included within Sample table
Processed data are available on Series record

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