|
| Status |
Public on Jul 03, 2020 |
| Title |
PD-TALL28_XENO28 |
| Sample type |
RNA |
| |
|
| Source name |
T-ALL xenografts in NOD/SCID mouse
|
| Organism |
Homo sapiens |
| Characteristics |
subject status: pediatric T-cell Acute Lymphoblastic Leukemia (T-ALL) patient_28
tissue: Spleen
gant-61 sensitivity: GANT-61:Sensitive
|
| Treatment protocol |
No treatment was performed on cells which were subjected to RNA extraction.
|
| Growth protocol |
Frozen Leukemia cells (from xenografted mice) were injected into NOD/SCID mice. When mice became sick, cells from the spleens were harvested and processed for RNA extraction.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol extraction of total RNA was performed according to the manufacturer's instructions.
|
| Label |
Cy3
|
| Label protocol |
RNA was amplified and labeled using the Low Input Quick Amp Labeling Kit, One Color (5190-2305; Agilent Technologies, Santa Clara, CA, USA)
|
| |
|
| Hybridization protocol |
600ng cy3-labeled, linearly amplified cRNA (specific activity > 6 pmol cy3 per µg cRNA) was hybridised with the Gene Expression Hybridization Kit (Cat nr. 5188-5242, Agilent Technologies) to the SurePrint G3 Human Gene Expression Microarray G4851A (design ID 028004). After hybridization, microarrays were washed at room temperature with GE Wash Buffer 1 (Agilent), 1 minute with GE Wash Buffer 2 (Agilent) at room temperature and 1 minute with GE Wash Buffer 3 (Agilent) at 37°C.
|
| Scan protocol |
Slides were scanned on the Agilent G2564CA Microarray Scanner. Data was extracted using Agilent Feature Extraction Software.
|
| Data processing |
The data were normalized using R software [www.r-ptoject.org] with BioConductor package [www.bioconductor.org] using limma. normalizeVSN function was used to normalize samples from GPL13607 Platform and removed duplicated probes by limma function avereps.
|
| |
|
| Submission date |
Jul 02, 2020 |
| Last update date |
Jul 03, 2020 |
| Contact name |
Erich Piovan |
| E-mail(s) |
erich.piovan@unipd.it
|
| Organization name |
University of Padua
|
| Department |
Dep. Surgery, Oncology and Gastroenterology
|
| Street address |
via Gattamelata 64
|
| City |
Padua |
| ZIP/Postal code |
35128 |
| Country |
USA |
| |
|
| Platform ID |
GPL14550 |
| Series (2) |
| GSE153717 |
T-cell acute lymphobalstic leukemia xenografts in NOD/SCID mouse |
| GSE153750 |
Cross-talk between GLI transcription factors and FOXC1 promotes T-cell acute lymphoblastic leukemia dissemination |
|
