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Status |
Public on Mar 02, 2020 |
Title |
genomic DNA at diagnosis from BCP-ALL patient ALL_613 |
Sample type |
genomic |
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Source name |
ALL patient sample
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Organism |
Homo sapiens |
Characteristics |
disease state: ALL diagnosis immunophenotype: BCP-ALL cell type: primary acute lymphoblastic leukemia
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Extracted molecule |
genomic DNA |
Extraction protocol |
AllPrep DNA/RNA/miRNA Universal Kit
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Label |
Cy5 and Cy3
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Label protocol |
Standard Illumina Protocol
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Hybridization protocol |
bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450k Beadchip using standard Illumina protocol
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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.
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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)
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City |
Uppsala |
ZIP/Postal code |
75144 |
Country |
Sweden |
|
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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) |
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Relations |
Alternative to |
GSM1204016 |