|
| Status |
Public on Aug 17, 2022 |
| Title |
CTH+10 fibroblasts |
| Sample type |
genomic |
| |
|
| Source name |
Bone Marrow Fibroblasts
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: T-ALL
chromothripsis status: positive
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA were extracted from bone marrow 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, ligated, 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
|
| Data processing |
Protocol was supported by Affymetrix GeneChip Command Console (AGCC) software. Analysis was performed through Affymetrix Chromosome Analysis 4.0 (ChAS) software with filters set at 200 Kb for Copy Number Alterations (CNAs) and 10 Mb 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 |
Jun 01, 2022 |
| Last update date |
Aug 17, 2022 |
| Contact name |
Cristina Mecucci |
| E-mail(s) |
cristina.mecucci@unipg.it
|
| Phone |
+39 075 5783808
|
| Organization name |
University of Perugia
|
| Department |
Department of Medicine, Hematology and Bone Marrow Transplantation Unit
|
| Lab |
Laboratory of Cytogenetics and Molecular Genetics
|
| Street address |
Piazzale Menghini n.9
|
| City |
Perugia |
| ZIP/Postal code |
06132 |
| Country |
Italy |
| |
|
| Platform ID |
GPL16131 |
| Series (2) |
| GSE205269 |
Chromothripsis is a frequent event and underlies typical genetic changes in early T-cell precursor lymphoblastic leukemia in adults [SNP] |
| GSE205270 |
Chromothripsis is a frequent event and underlies typical genetic changes in early T-cell precursor lymphoblastic leukemia in adults |
|
