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Sample GSM8282660 Query DataSets for GSM8282660
Status Public on May 26, 2024
Title acute lymphoblastic leukemia M18
Sample type genomic
 
Source name blast cells, bone marrow
Organism Homo sapiens
Characteristics disease: acute lymphoblastic leukemia
age: 17.8y
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was extracted from mononuclear cell preparations of leukemic blasts obtained from peripheral blood or bone marrow at diagnosis using the Qiagen DNA Blood Mini 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.
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.
 
Submission date May 21, 2024
Last update date May 26, 2024
Contact name Borys Styka
E-mail(s) borys.styka@wp.pl
Phone 605577272
Organization name University Children's Hospital in Lublin
Department Genetic diagnostics department
Lab Laboratory of molecular genetics
Street address ul. Prof. Antoniego Gębali 6
City Lublin
State/province Lubelskie
ZIP/Postal code 20-093
Country Poland
 
Platform ID GPL16131
Series (1)
GSE267970 Affymetrix SNP array data for T-cell acute lymphoblastic leukemia samples

Supplementary file Size Download File type/resource
GSM8282660_Y05698.CEL.gz 29.7 Mb (ftp)(http) CEL
GSM8282660_Y05698.cyhd.cychp.gz 95.5 Mb (ftp)(http) CYCHP

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