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Sample GSM3307315 Query DataSets for GSM3307315
Status Public on Mar 02, 2020
Title genomic DNA at diagnosis from BCP-ALL patient ALL_613
Sample type genomic
 
Source name ALL patient sample
Organism Homo sapiens
Characteristics disease state: ALL diagnosis
immunophenotype: BCP-ALL
cell type: primary acute lymphoblastic leukemia
Extracted molecule genomic DNA
Extraction protocol AllPrep DNA/RNA/miRNA Universal Kit
Label Cy5 and Cy3
Label protocol Standard Illumina Protocol
 
Hybridization protocol bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450k Beadchip using standard Illumina protocol
Scan protocol not provided
Description copy number file (".cn") with LogR values for visualization in IGV
Data processing The raw signal intensities generated from the 450k array were normalized and transformed to “Log R ratio”, which corresponds to the observed intensity signal from the studied sample over the intensity signal obtained from a reference sample (baseline). To determine the reference baseline, 450k data from an in-house panel of CD19+ B-cells and CD3+ T-cells from healthy blood donors representing normal diploid genomes, was used. Log R ratios were analyzed using the CopyNumber450kCancer R package and with the Integrated Genome Viewer (IGV). LogR files with the extension ".cn" are submitted to GEO and can be visualized in IGV.
 
Submission date Jul 26, 2018
Last update date Mar 02, 2020
Contact name Yanara Marincevic-Zuniga
E-mail(s) yanara.marincevic_zuniga@medsci.uu.se
Organization name Uppsala University
Department Medical Sciences
Lab Molecular Medicine
Street address Husargatan 3, BOX 1432, Biomedicinskt Centrum (BMC)
City Uppsala
ZIP/Postal code 75144
Country Sweden
 
Platform ID GPL13534
Series (2)
GSE116057 Refined detection and phasing of structural aberrations in pediatric acute lymphoblastic leukemia by linked-read whole genome sequencing
GSE117692 Refined detection and phasing of structural aberrations in pediatric acute lymphoblastic leukemia by linked-read whole genome sequencing (ALL_450k)
Relations
Alternative to GSM1204016

Supplementary file Size Download File type/resource
GSM3307315_450kLogR_ALL_613.cn.gz 8.1 Mb (ftp)(http) CN
GSM3307315_5854945015_R05C01_Grn.idat.gz 4.2 Mb (ftp)(http) IDAT
GSM3307315_5854945015_R05C01_Red.idat.gz 4.2 Mb (ftp)(http) IDAT
Processed data provided as supplementary file

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