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Status |
Public on Jun 30, 2024 |
Title |
UPD sample 3 [patient C; CMA2022216] |
Sample type |
genomic |
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Source name |
Amniotic fluid 3
|
Organism |
Homo sapiens |
Characteristics |
patient id: patient C genotype: chromosome 14 UPD phenotype: Hypotonia, ARDS outcome: death tissue: Amniotic fluid
|
Treatment protocol |
None
|
Growth protocol |
Amniotic fluid and peripheral blood were collected without growth
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Extracted molecule |
genomic DNA |
Extraction protocol |
Genomic DNA was extracted from amnoitic fluid obtained from preganant women using the Qiagen DNAiso Kit. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer, PicoGreen and agarose gel electrophoresis.
|
Label |
Biotin
|
Label protocol |
As per manufacturer (Affymetrix)
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Hybridization protocol |
DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.
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Scan protocol |
The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.
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Description |
Hybridized to 750K [CytoScan750K_Array] Affymetrix CytoScan 750K Array
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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 DNAcopy package for R Bioconductor on raw data. Genotype Call (SNP call): AA, AB, BB, NC, and NoCall; 'Signal' = Summarized signal
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Submission date |
Jun 27, 2023 |
Last update date |
Jun 30, 2024 |
Contact name |
Qi Chen |
E-mail(s) |
xwl0806@yeah.net
|
Phone |
+8618252586936
|
Organization name |
Fourth affiliated hospital of Jiangsu University
|
Street address |
20 ZHENDONG ROAD
|
City |
Zhenjiang |
ZIP/Postal code |
212001 |
Country |
China |
|
|
Platform ID |
GPL18637 |
Series (1) |
GSE235878 |
Uniparental disomy: expanding the clinical and molecular phenotypes of whole chromosomes |
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