|
| Status |
Public on Oct 05, 2023 |
| Title |
Periferal blood father [PL455_Father] |
| Sample type |
genomic |
| |
|
| Source name |
Periferal blood
|
| Organism |
Homo sapiens |
| Characteristics |
gender: Male
family member: Father
tissue: Periferal blood
|
| Treatment protocol |
The two tissues were mechanically separated and the yield of chorionic cytotrophoblast cells was increased by maceration of chorionic villi under an Axiovert 200 inverted microscope (Carl Zeiss, Germany) and treatment with 70% acetic acid for 3-5 min followed by three washes of the obtained cell suspension with PBS according to a modified protocol (Simoni, G. et al. Efficient direct chromosome analyses and enzyme determinations from chorionic villi samples in the first trimester of pregnancy. Human Genetics 63, 349-357 (1983)).
|
| Growth protocol |
The tissues were chopped with scissors to small fragments, and long-term cultures were set up in 25 cm2 flasks with 5 mL of DMEM/F12 (1:1) medium (Gibco) supplemented with 20% fetal bovine serum (HyClone), 1% MEM NEAA solution (Gibco), 1% Pen-Strep (Gibco). Tissues were incubated at 37°C with once-weekly medium renewal.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted using a standard phenol-chloroform extraction method that allows for the isolation of up to 900 ng DNA from the tissues. Likewise, genomic DNA was extracted from peripheral blood of parents using the standard phenol-chloroform method.
|
| Label |
Cy3, Cy5
|
| Label protocol |
The samples were not labelled before the hybridization. The staining is based on post-hybridization Cy5/Cy3 labelling by extension, according to the manual of Infinium II Assay (Illumina, USA).
|
| |
|
| Hybridization protocol |
According to the manual of Infinium II Assay (Illumina, USA).
|
| Scan protocol |
The scanning of the bead-chips was performed on an iScan, using the iScan Control software (Illumina, USA)
|
| Description |
PL455.adj
|
| Data processing |
The genotypes, B allele frequencies and LogR values were processed by the Genotyping module of GenomeStudio software. We subsequently fed these data into haplarithmisis (Zamani Esteki et al. 2019, Nature medicine).
Image data was analyzed using Genomestudio with genotyping module (Illumina). Subsequently, genotype calls (AA,AB,BB,or NC (no call), SNP B-allele frequency values, LogR.
|
| |
|
| Submission date |
Mar 24, 2023 |
| Last update date |
Oct 05, 2023 |
| Contact name |
Rick Essers |
| E-mail(s) |
rick.essers@mumc.nl
|
| Organization name |
Maastricht University Medical Centre (MUMC+)
|
| Department |
Clinical Genetics
|
| Street address |
P. Debyelaan 25
|
| City |
Maastricht |
| State/province |
Limburg |
| ZIP/Postal code |
6229HX |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL28939 |
| Series (2) |
| GSE228150 |
Prevalence of chromosomal alterations in first-trimester spontaneous pregnancy loss |
| GSE228151 |
Prevalence of chromosomal alterations in first-trimester spontaneous pregnancy loss |
|
