|
| Status |
Public on May 26, 2024 |
| Title |
acute lymphoblastic leukemia M3 |
| Sample type |
genomic |
| |
|
| Source name |
blast cells, bone marrow
|
| Organism |
Homo sapiens |
| Characteristics |
disease: acute lymphoblastic leukemia
age: 12.2
|
| 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 |
|
