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Sample GSM1888375 Query DataSets for GSM1888375
Status Public on Oct 01, 2015
Title AF [12ZS032519]
Sample type genomic
 
Source name Prenatal diagnosis_AF
Organism Homo sapiens
Characteristics sample origin: Prenatal diagnosis
clinical indication: adv mat age
tissue: Amniotic fluid
Treatment protocol Samples were untreated
Growth protocol Uncultured samples of chorionic villus sampling, amniotic fluid, placental tissue and blood were used for direct DNA extraction
Extracted molecule genomic DNA
Extraction protocol Genomic DNA extraction done by Qiagen DNeasy® Blood & Tissue Kit following manufacturer's instructions
Label C-Bio and A-DNP
Label protocol Illumina standard protocol for CytoSNP 12 chips (GPL16483), using automation with the Tecan Evo robot.
 
Hybridization protocol Illumina standard protocol for CytoSNP 12 chips (GPL16483), using automation with the Tecan Evo robot.
Scan protocol Illumina standard protocol for CytoSNP 12 chips (GPL16483), using automation with the Tecan Evo robot.
Data processing Genomic DNA was genotyped using KaryoStudio V 1.3.11 and GenomeStudio V2011.1 (Illumina) based on hg19.
 
Submission date Sep 18, 2015
Last update date Oct 01, 2015
Contact name Zirui DONG
E-mail(s) elvisdong@link.cuhk.edu.hk
Organization name The Chinese University of Hong Kong
Department Dept. of Obstetrics and Gynaecology
Street address Shatin, N.T.
City Hong Kong
ZIP/Postal code 999077
Country China
 
Platform ID GPL8855
Series (2)
GSE73190 Chromosomal microarray analysis for validation of the NGS-based CNV detection results in clinical samples
GSE73191 Chromosomal microarray data for validation of copy-number variants detection from a low-coverage whole-genome sequencing approach in clinical samples

Data table header descriptions
ID_REF
VALUE Genotype: AA,AB,BB,or NC (no call)
GC_SCORE
Theta
R
B_Allele_Freq
Log_R_Ratio

Data table
ID_REF VALUE GC_SCORE Theta R B_Allele_Freq Log_R_Ratio
rs3817595 AB 0.8525 0.460 2.392 0.5055 0.0730
rs734560 AA 0.8232 0.012 1.599 0.0000 0.1291
rs1153651 AA 0.4832 0.036 1.125 0.0000 0.0984
rs7659192 AA 0.7318 0.047 1.101 0.0007 NC0.1275
rs10806671 AA 0.5071 0.028 0.769 0.0073 0.1242
rs4721548 BB 0.6256 0.969 1.294 1.0000 0.0773
rs2088629 BB 0.9201 0.981 0.625 0.9986 NC0.4105
rs17809603 AA 0.9312 0.006 1.190 0.0000 NC0.0427
rs2066705 AA 0.7149 0.070 0.924 0.0018 0.1158
rs7173425 BB 0.9532 0.987 0.959 1.0000 NC0.1369
rs6546985 AA 0.7981 0.014 0.816 0.0000 0.0125
rs1072517 AB 0.8417 0.572 0.552 0.5541 0.1402
rs1934003 AB 0.8736 0.677 0.637 0.5547 NC0.2166
rs13060855 BB 0.9126 0.975 1.056 1.0000 0.0852
rs7251178 BB 0.9058 0.974 0.980 0.9992 NC0.0441
rs6058234 BB 0.1952 0.739 0.809 1.0000 NC0.0556
rs7690085 AB 0.9183 0.583 0.894 0.4861 NC0.0455
rs2783425 AA 0.8999 0.062 0.977 0.0045 NC0.1101
rs250416 AB 0.8636 0.548 1.360 0.4859 0.0189
rs1903961 AA 0.3982 0.013 1.874 0.0000 0.0706

Total number of rows: 299436

Table truncated, full table size 13676 Kbytes.




Supplementary file Size Download File type/resource
GSM1888375_12ZS032519_Grn.idat.gz 2.0 Mb (ftp)(http) IDAT
GSM1888375_12ZS032519_Red.idat.gz 2.0 Mb (ftp)(http) IDAT
Processed data included within Sample table

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