|
| Status |
Public on Sep 05, 2021 |
| Title |
Case18_SNParray |
| Sample type |
genomic |
| |
|
| Source name |
Unsorted Bone Marrow Cells
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: bone marrow
cytogenetics: 46,XY,t(7;14)(q22;q32)
age: 50
disease state: acute leukemia
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA were extracted from bone marrow cells or periferichal blood cells of patients using All Prep DNA/RNA Mini Kit (Qiagen). DNA quality and quantity was assessed using a Nanodrop Spectrophotometer, Bioanalyzer and/or Tapestation visualization (Agilent 2100 Bioanalyzer) 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 7G.
|
| Description |
Case_18 (UPN#147)
|
| Data processing |
Protocol was supported by Affymetrix GeneChip Command Console (AGCC) software. Analysis was performed through Affymetrix Chromosome Analysis (ChAS) software with filters set at 200 Kb dimension for Copy Number Alterations (CNAs) and 10 Mb dimensions for copy neutral loss of heterozygosity (cnLOH). Our data refer to NetAffx Build 32.3 (hg19) database.
Genotype Call (SNP call): AA, AB, BB, NC, and NoCall; 'Signal' = Summarized signal
|
| |
|
| Submission date |
Nov 23, 2020 |
| Last update date |
Sep 05, 2021 |
| Contact name |
Danika Di Giacomo |
| E-mail(s) |
danika.digiacomo@unipg.it
|
| Phone |
00390755782624
|
| Organization name |
University of Perugia
|
| Department |
Medicine
|
| Lab |
Molecolare Medicine
|
| Street address |
Piazzale Menghini 0
|
| City |
Perugia |
| ZIP/Postal code |
06132 |
| Country |
Italy |
| |
|
| Platform ID |
GPL16131 |
| Series (2) |
| GSE162000 |
Affymetrix SNP array data for acute leukemias with a 14q32/BCL11B rearrangement |
| GSE162283 |
14q32 recombinations deregulating BCL11B mark a distinct Mixed Phenotype Leukemia |
|
