|
| Status |
Public on Jul 08, 2022 |
| Title |
DG-75 DMSO N1 |
| Sample type |
RNA |
| |
|
| Source name |
Burkitt Lymphoma cell line DG-75
|
| Organism |
Homo sapiens |
| Characteristics |
sample type: Peritoneal effusion
|
| Treatment protocol |
SU-DHL-4 and DG-75 cells were exposed to 1µM Entospletinib (Absource Diagnostics GmbH, München, Germany), 0.01µM AZD5153 (Absource Diagnostics GmbH, München, Germany), the combination (1µM Ento+ 0.01µM AZD) or DMSO as control for 72h.
|
| Growth protocol |
SU-DHL-4 und DG-75 cell lines were maintained in RPMI 1640 supplemented with 10% heat-inactivated fetal bovine serum (FBS) and and 100 µg/ml penicillin and streptomycin in a humidified atmosphere with 5% CO2 at 37C
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cell pellets were resuspended in QIAzol Lysis Reagent (QIAGEN, Venlo, Netherlands) and RNA Isolation was performed with miRNeasy Mini Kit (QIAGEN, Venlo, Netherlands) according to the manufacturer’s instructions
|
| Label |
biotin
|
| Label protocol |
200 ng total RNA was labeled using WT-labeling protocol (Affymetrix/Thermofisher).
|
| |
|
| Hybridization protocol |
Hybridization was performed for 16 hours at 45 degrees celsius using the GeneChip Hybridization Oven 645 (Affymetrix, St. Clara, USA).
|
| Scan protocol |
Scanning was done using the GeneChip Scanner 3000/7G (Affymetrix, St. Clara, USA) with 0.7 micron resolution.
|
| Description |
Gene expression data of treated DG-75 cell line
|
| Data processing |
Microarray data were RMA normalized using limma and probes were mapped to genes using affycoretools with probe mappings drawn from clariomhumantranscriptcluster.db. and a linear model was fitted of the form:
Where Yij is the intensity for gene j in sample i, Treatmenti is the treatment which sample i was subjected to, Linei is the cell line from which sample i was drawn and Batchi is the batch which sample i belongs to, while ij is the error term, with the coefficients β0, β1 and β2 estimated by least squares.
All contrasts were tested using the eBayes method of limma to perform a moderated t-test for each gene and the results were corrected for multiplicity using the Benjamini-Hochberg correction.
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| |
|
| Submission date |
Jul 01, 2022 |
| Last update date |
Aug 31, 2022 |
| Contact name |
Sina Sender |
| E-mail(s) |
sina.sender@med.uni-rostock.de
|
| Organization name |
Rostock University Medical Center
|
| Department |
Department of Medicine, Clinic III
|
| Lab |
Hematology/Oncology
|
| Street address |
Schillingallee 70
|
| City |
Rostock |
| State/province |
Mecklenburg Vorpommern |
| ZIP/Postal code |
18059 |
| Country |
Germany |
| |
|
| Platform ID |
GPL23126 |
| Series (2) |
| GSE207381 |
Evaluation of the synergistic potential of simultaneous pan- or isoform specific BET and SYK inhibition in B-cell lymphoma (microarray) |
| GSE207383 |
Evaluation of the synergistic potential of simultaneous pan- or isoform specific BET and SYK inhibition in B-cell lymphoma |
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