|
| Status |
Public on Mar 11, 2013 |
| Title |
SNP010XHM2 |
| Sample type |
genomic |
| |
|
| Source name |
whole genome amplification product of trophectoderm cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: trophectoderm cells
karyotype of patient donor: 46,XX,t(9;13)(q32;q14)
karyotype classification: reciprocal translocation
analysis result: 46,XX
result classification: normal female
|
| Treatment protocol |
Blastocyst cultivation and biopsy reference to clinical standard procedure. The normal/balance embryos detected by SNP-array would been transfer to patients as clinical standard procedure.
|
| Growth protocol |
None.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Whole genome amplification of the biopsied trophectoderm cells was performed using a WGA4 GenomePlex Single Cell Whole Genome Amplification kit (Sigma-Aldrich, MO, USA) according to the manufacturer's instructions.
|
| Label |
Biotin
|
| Label protocol |
DNA was restriction digested, PCR amplified, fragmented, and labeled according to the manufacturer's instructions.
|
| |
|
| Hybridization protocol |
DNA was hybridized to each array according to the manufacturer's instructions. The arrays were then washed using Affymetrix Fluidics Stations.
|
| Scan protocol |
The arrays were scanned using the GeneChip Scanner 7G.
|
| Description |
Whole genome amplification DNA.
Hybridized to 250K_Nsp SNP array.
|
| Data processing |
The array image was acquired using Affymetrix GeneChip® Operating Software (GCOS version 1.4). Copy number values for individual SNPs were extracted and converted from CEL files into signal intensities using GTYPE 4.1 and Affymetrix Copy Number Analysis Tool (CNAT 4.0.1) softwares. Genomic Smoothing analysis was performed by using the smoothing window of 0 Mb, and inferred copy number states were derived from a Hidden Markov Model (HMM) based algorithm implemented in CNAT 4.0.1. Circular Binary Segmentation (Ohlsen et al., 2004) was applied using the DNAcopy package for R Bioconductor on raw data.
|
| |
|
| Submission date |
Mar 09, 2013 |
| Last update date |
Mar 20, 2013 |
| Contact name |
xiong bo |
| Organization name |
xiangya
|
| Street address |
xiangya road
|
| City |
changsha |
| ZIP/Postal code |
410001 |
| Country |
China |
| |
|
| Platform ID |
GPL3718 |
| Series (1) |
| GSE44994 |
SNP microarray-based PGS significantly improves the clinical outcome for translocation carriers |
|
