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Sample GSM4887230 Query DataSets for GSM4887230
Status Public on Jan 19, 2021
Title acute_myeloid_leukemia [101_SNP6.0]
Sample type genomic
 
Source name mononuclear cells
Organism Homo sapiens
Characteristics disease: acute myeloid leukemia
gender: male
Treatment protocol None
Growth protocol None
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was extracted using the AllPrep DNA/RNA Mini Kit or the DNA Blood Mini Kit (Qiagen). DNA quality and quantity was assessed using a Nanodrop Spectrophotometer, PicoGreen and agarose gel electrophoresis.
Label biotin
Label protocol As per manufacturer (Affymetrix, Thermo Fisher Scientific)
 
Hybridization protocol DNA was processed through the following steps: digestion, ligation, amplification and purification, fragmentation, labeling, hybridization in each array according to the manufacturer's instructions. The volume of 10x Fragmentation Buffer and Fragmentation Reagent has been increased compared to the standard protocol in order to improve the quality of the fragmented DNA, according to the Affymetrix Technical Support’s suggestion.
Scan protocol The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.
Description Genomic data from bone marrow cells of AML patients at diagnosis
Data processing CEL files (SNP 6.0 and Cytoscan HD Array) were processed with Genotyping console (GTC) 4.1 and Chromosome Analysis Suite (ChAS) v. 4.1 to obtain CN5.CNCHP and cyhd.cychp files, respectively. CN5.CNCHP and cyhd.cychp were used to check QC, thresholds and MAPD. CEL files were used to produce raw segments files for the analysis as described in the correspective papers.
CEL, CN5.CNCHP and cyhd.cychp files obtained from SNP 6.0 and Cytoscan HD were uploaded.
 
Submission date Nov 06, 2020
Last update date Jan 19, 2021
Contact name Giorgia Simonetti
E-mail(s) giorgia.simonetti@irst.emr.it
Organization name IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori"
Lab Giorgia Simonetti
Street address Via Piero Maroncelli, 40
City Meldola
State/province FC
ZIP/Postal code 47014
Country Italy
 
Platform ID GPL6801
Series (1)
GSE160982 SNP array of 121 AML patients at diagnosis

Supplementary file Size Download File type/resource
GSM4887230_101_SNP6.0_GenomeWideSNP_6_.CEL.gz 28.7 Mb (ftp)(http) CEL
GSM4887230_101_SNP6.0_GenomeWideSNP_6_.CN5.CNCHP.gz 35.0 Mb (ftp)(http) CNCHP
Processed data provided as supplementary file

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