|
| Status |
Public on Dec 31, 2018 |
| Title |
PlacentaBiopsy3_P106 |
| Sample type |
genomic |
| |
|
| Source name |
Placenta tissue
|
| Organism |
Homo sapiens |
| Characteristics |
dna sample: multi cells
quartet: P106
conception method: IVF
tissue: Placenta tissue
birthweight at delivery: AGA
|
| Treatment protocol |
Full-thickness placental blocks of around 1 cm were taken from the placenta and stored at -80 °C for subsequent DNA extraction. The maturity and health of the term placenta were confirmed by histological examination.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
A total of 9 mL of peripheral venous blood from parents and 4 mL of umbilical cord blood were collected into ethylenediaminetetraacetic acid-containing tubes (BD Vacutainer, Becton, Dickinson and Co) for DNA extraction. DNA was isolated from blood and the placental tissue using PureLink® Genomic DNA Kit (Invitrogen, Life Technologies™) according to manufacturer’s protocol. DNA samples were eluted with 200 µL of PureLink® Genomic Elution Buffer (10 mM Tris-HCl, pH 9.0, 0.1 mM EDTA) and stored at -20 °C until analysis. NanoDrop 2000 (Thermo Fisher Scientific Inc.) was used to assess DNA concentration and purity.
|
| Label |
Cy5, Cy3
|
| 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 |
DNA extracted from placenta tissue.
|
| 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 siCHILD algorithm, which is equipted with haplarithmisis (Zamani Esteki et al. 2015, AJHG).
Image data was analyzed using Genomestudio with genotyping module (Illumina).
|
| |
|
| Submission date |
Jan 10, 2017 |
| Last update date |
Dec 31, 2018 |
| Contact name |
Masoud Zamani Esteki |
| E-mail(s) |
[email protected]
|
| Phone |
+31 43 38 75306
|
| Organization name |
Maastricht University Medical Center
|
| Department |
Clinical Genetics
|
| Lab |
Cellular Genomic Medicine
|
| Street address |
P. Debyelaan 25
|
| City |
Maastricht |
| State/province |
Limburg |
| ZIP/Postal code |
6229 HX |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL22819 |
| Series (1) |
| GSE93353 |
In vitro fertilization does not increase the incidence of de novo copy number alterations in fetal and placental lineages |
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