|
| Status |
Public on Mar 02, 2020 |
| Title |
genomic DNA at diagnosis from BCP-ALL patient ALL_604 |
| 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 |
GSM1204007 |
