|
| Status |
Public on Jan 19, 2021 |
| Title |
acute_myeloid_leukemia [102_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 |
|
