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Sample GSM1874152 Query DataSets for GSM1874152
Status Public on Oct 01, 2015
Title CVS [14S0593155]
Sample type genomic
 
Channel 1
Source name Miscarriage_CVS
Organism Homo sapiens
Characteristics sample origin: Miscarriage
clinical indication: Miscarriage
tissue: Chorionic villus sampling (CVS)
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 Cy5
Label protocol Three costumized aCGH approach have different procedure for DNA fragmentation and labelling; Agilent-022023:1 µg of Genomic DNA samples were fragmented. The fragmented DNA sample were labeled with Cy5 and the corresponding fragmented reference controls were labeled Cy3 using Agilent SureTag DNA Labeling Kit. Agilent-068656:300 ng of Genomic DNA samples were heat fragmented. The fragmented DNA samples were labeled with Cy5 and the corresponding fragmented reference controls were labeled Cy3 using Agilent SureTag DNA Labeling Kit. Agilent-035130:300 ng of Genomic DNA samples were enzyme digested. The digested DNA samples were labeled with Cy5 and the corresponding fragmented reference controls were labeled Cy3 using Agilent SureTag DNA Labeling Kit.
 
Channel 2
Source name control_blood
Organism Homo sapiens
Characteristics sample origin: Healthy Chinese adult control
tissue: blood
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 Cy3
Label protocol Three costumized aCGH approach have different procedure for DNA fragmentation and labelling; Agilent-022023:1 µg of Genomic DNA samples were fragmented. The fragmented DNA sample were labeled with Cy5 and the corresponding fragmented reference controls were labeled Cy3 using Agilent SureTag DNA Labeling Kit. Agilent-068656:300 ng of Genomic DNA samples were heat fragmented. The fragmented DNA samples were labeled with Cy5 and the corresponding fragmented reference controls were labeled Cy3 using Agilent SureTag DNA Labeling Kit. Agilent-035130:300 ng of Genomic DNA samples were enzyme digested. The digested DNA samples were labeled with Cy5 and the corresponding fragmented reference controls were labeled Cy3 using Agilent SureTag DNA Labeling Kit.
 
 
Hybridization protocol After clean up and QC check, Cy3 and Cy5 labeled DNA samples were mixed together with Cot-1 DNA, blocking agent and hybridization buffer using Agilent Oligo aCGH/ChIP-on-Chip Hybridization kit according to manufacturer's protocol. Samples were hybridized on array for 24 hours at 65oC. After hybridization, slides were washed sequential
Scan protocol Scanned on an Agilent G2505C scanner.
Data processing Agilent Feature Extraction Software (v 11.5.1.1) was used for background subtraction
Dye was normalized automatically according to the dye norm list in eArray generating the normalized log10 ratio (Cy5/Cy3), representing test/reference
 
Submission date Sep 10, 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 GPL20899
Series (2)
GSE72891 aCGH for CNV detection 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 normalized log10 ratio (Cy5/Cy3) representing test/reference

Data table
ID_REF VALUE
A_16_P01445300 -1.03E-01
A_14_P118521 -2.58E-02
A_16_P16685532 2.31E-02
A_16_P20918307 2.67E-02
A_16_P38382650 7.76E-02
CUHK_P118879 2.29E-02
A_16_P00158896 7.87E-02
A_16_P20235323 -7.58E-03
A_16_P20304748 -9.71E-03
A_16_P19030974 -2.85E-02
A_16_P39316284 5.01E-02
A_16_P37551776 3.47E-02
A_16_P20368573 -1.02E-02
A_16_P39258589 -2.47E-02
A_16_P16004212 -4.24E-02
A_16_P20812434 -1.62E-02
A_14_P110933 -8.88E-02
A_16_P15992034 1.38E-02
A_16_P00190456 6.75E-03
A_16_P03170257 1.62E-01

Total number of rows: 43004

Table truncated, full table size 1014 Kbytes.




Supplementary file Size Download File type/resource
GSM1874152_14S0593155.txt.gz 5.6 Mb (ftp)(http) TXT
Processed data included within Sample table

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