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Sample GSM1103275 Query DataSets for GSM1103275
Status Public on Mar 21, 2013
Title SNP067CY2
Sample type genomic
 
Source name whole genome amplification product of trophectoderm cells
Organism Homo sapiens
Characteristics cell type: trophectoderm cells
karyotype of patient donor: 45,XY,t(13;14)(q10;q10)
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 have been transferred to patients as clinical stantard ptocedure.
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 Hybridized to 250K_Nsp
Genotype Call (SNP call): AA, AB, BB, NC, and NoCall; 'Signal' = Summarized signal
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 20, 2013
Last update date Mar 21, 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

Data table header descriptions
ID_REF
VALUE Genotypes: AA, AB, BB, No Call
CONFIDENCE
RAS1 Relative allele signal for the data in the first probe group
RAS2 Relative allele signal for the data in the second probe group
P-VALUE AA
P-VALUE AB
P-VALUE BB
P-VALUE NO CALL

Data table
ID_REF VALUE CONFIDENCE RAS1 RAS2 P-VALUE AA P-VALUE AB P-VALUE BB P-VALUE NO CALL
AFFX-5Q-123 No Call 0 0 0 0 0 0 0
AFFX-5Q-456 No Call 0 0 0 0 0 0 0
AFFX-5Q-789 No Call 0 0 0 0 0 0 0
AFFX-5Q-ABC No Call 0 0 0 0 0 0 0
AFFX-barcodeA No Call 0 0 0 0 0 0 0
AFFX-barcodeB No Call 0 0 0 0 0 0 0
AFFX-barcodeC No Call 0 0 0 0 0 0 0
AFFX-barcodeD No Call 0 0 0 0 0 0 0
AFFX-barcodeE No Call 0 0 0 0 0 0 0
AFFX-barcodeF No Call 0 0 0 0 0 0 0
AFFX-barcodeG No Call 0 0 0 0 0 0 0
AFFX-barcodeH No Call 0 0 0 0 0 0 0
AFFX-barcodeI No Call 0 0 0 0 0 0 0
AFFX-barcodeJ No Call 0 0 0 0 0 0 0
AFFX-barcodeK No Call 0 0 0 0 0 0 0
AFFX-barcodeL No Call 0 0 0 0 0 0 0
AFFX-barcodeM No Call 0 0 0 0 0 0 0
AFFX-barcodeN No Call 0 0 0 0 0 0 0
AFFX-barcodeO No Call 0 0 0 0 0 0 0
AFFX-barcodeP No Call 0 0 0 0 0 0 0

Total number of rows: 262338

Table truncated, full table size 18856 Kbytes.




Supplementary file Size Download File type/resource
GSM1103275_SNP067CY2.CEL.gz 21.2 Mb (ftp)(http) CEL
GSM1103275_SNP067CY2.CHP.gz 773.3 Kb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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