|
| Status |
Public on Oct 31, 2016 |
| Title |
LLC4_2cPE |
| Sample type |
RNA |
| |
|
| Source name |
CLL cells - treated with 2cPE, patient LLC4
|
| Organism |
Homo sapiens |
| Characteristics |
patient id: LLC4
cell type: chronic lymphocytic leukemia (CLL)
|
| Treatment protocol |
Leukemia CD19+ B-cells from 10 different patients were treated or not for 6 hours with 6nM of bortezomib or with 4µM of 2cPE
|
| Growth protocol |
Purified peripheral blood cells were cultured in RPMI-1640 medium supplemented with 10% heated inactivated fetal calf serum. Mediums were supplied with penicillin (100 U/mL), glutamine (2 mmol/L), and streptomycin (100 μg/mL).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using RNeasy Mini kit (Qiagen). RNA samples concentration and purity (assessed as 260/280 nm and 260/230 nm ratios) were evaluated by NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies; Wilmington, DE), while RNA integrity was assessed by using the Agilent 2100 Bioanalyzer (Agilent Technologies; Waldbrunn, Germany).
|
| Label |
biotin
|
| Label protocol |
cDNA synthesis and biotin-labeled target synthesis were performed using the GeneAtlas 3´ IVT Express Kit according to the protocol supplied by Affymetrix.
|
| |
|
| Hybridization protocol |
Labeled cRNA was hybridized on Affymetrix Human Genome U219 Array.
|
| Scan protocol |
The HG-U219 Array Strips (Affymetrix; Santa Clara, CA) hybridization, staining, and scanning were performed by using the GeneAtlas Platform.
|
| Description |
Human Chronic lymphocytic leukemia cells treated with 2cPE
|
| Data processing |
Data processing was performed with BioConductor packages (http://www.bioconductor.org/), using Brainarray HGU219_Hs_ENTREZG version 18 custom chip definition file. Robust Multi-Array Average (RMA) normalization was applied.Normalized intensity values for all probes on the Affymetrix chip are presented in the Matrix table. Data analysis was performed using the paired t-test as implemented in the R statistical package. P values were adjusted for multiple testing using the False Discovery Rate method. Differentially expressed genes (DEGs) were selected based on fold change >1.5 and <-1.5 fold and P values <0.05.
|
| |
|
| Submission date |
Oct 30, 2015 |
| Last update date |
Oct 31, 2016 |
| Contact name |
raffaella picco |
| E-mail(s) |
raf.picco@uniud.it
|
| Organization name |
university of Udine
|
| Department |
department of medical and biological sciences
|
| Lab |
bioinformatics
|
| Street address |
piazzale kolbe 4
|
| City |
udine |
| ZIP/Postal code |
33100 |
| Country |
Italy |
| |
|
| Platform ID |
GPL20650 |
| Series (1) |
| GSE74514 |
The isopeptidase inhibitor 2cPE triggers proteotoxic stress and ATM activation in chronic lymphocytic leukemia cells. |
|
