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Sample GSM7511293 Query DataSets for GSM7511293
Status Public on Jun 30, 2024
Title UPD sample 3 [patient C; CMA2022216]
Sample type genomic
 
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
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)
 
Hybridization protocol DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.
Scan protocol The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.
Description Hybridized to 750K
[CytoScan750K_Array] Affymetrix CytoScan 750K 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 DNAcopy package for R Bioconductor on raw data.
Genotype Call (SNP call): AA, AB, BB, NC, and NoCall; 'Signal' = Summarized signal
 
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

Supplementary file Size Download File type/resource
GSM7511293_20220816_173947_015_CMA2022216.CEL.gz 19.7 Mb (ftp)(http) CEL
GSM7511293_20220816_173947_015_CMA2022216.cy750K.cychp.gz 26.1 Mb (ftp)(http) CYCHP
Processed data provided as supplementary file

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