|
| Status |
Public on Aug 17, 2022 |
| Title |
CTH-21 |
| Sample type |
RNA |
| |
|
| Source name |
Unsorted Bone Marrow Cells
|
| Organism |
Homo sapiens |
| Characteristics |
disease state: T-ALL
cell type: Unsorted Bone Marrow Cells
chromothripsis status: negative
phenotype: immature
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from bone marrow or peripheral blood samples using a QIAamp RNA Blood Mini Kit (Qiagen) at a QIAcube automated station
|
| Label |
biotin
|
| Label protocol |
GeneChip® WT PLUS Reagent Kit (Affymetrix Applied Biosystem Microarray, Thermo Fisher, Milan, Italy) was used to generates amplified and biotinylated sense-strand DNA targets from total RNA; it uses a reverse transcription priming method that primes the entire length of RNA. Amplified cDNA was quantified, fragmented, marked, and prepared for hybridization from the GeneChip® Clariom S Human Array (Thermo Fisher Scientific) for expression level measurement
|
| |
|
| Hybridization protocol |
Hybridization of the microarrays was performed in a GeneChip® Hybridization Oven 645 (Affymetrix/Thermo Fisher Scientific). GeneChips were washed and stained
|
| Scan protocol |
Arrays were scanned using the GeneChip Scanner 3000 (Affymetrix Applied Biosystem Microarray, Thermo Fisher, Milan, Italy)
|
| Data processing |
Primary data analysis was performed with Transcriptome Analysis Console software version 4.0 (TAC 4.0.2.15). Differentially expressed RNA were estimated by fold-change filtering combined with Student’s t-test. Transcripts with fold change in expression ≥ ±2.0 and FDR<0.05 were considered significantly differentially expressed. Hierarchical clustering was performed to show the distinguishing genes expression pattern among samples
|
| |
|
| 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 |
GPL23159 |
| Series (2) |
| GSE205265 |
Chromothripsis is a frequent event and underlies typical genetic changes in early T-cell precursor lymphoblastic leukemia in adults [gene expression] |
| GSE205270 |
Chromothripsis is a frequent event and underlies typical genetic changes in early T-cell precursor lymphoblastic leukemia in adults |
|
