|
| Status |
Public on Jul 30, 2023 |
| Title |
miRNA_DMSO_control_replicate_2 |
| Sample type |
RNA |
| |
|
| Source name |
BE(2)-C cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: BE(2)-C cells
treatment: DMSO
time point: 24 h
tumor entity: neuroblastoma
|
| Treatment protocol |
BE(2)-C cells were treated with 5 nM, 10 nM and 15 nM for 24h with the clinically approved histone deacetylase inhibitor, panobinostat in two independent duplicates.
|
| Growth protocol |
Neuroblastoma BE(2)-C cell line was maintained in DMEM (Lonza, Basel, Switzerland), supplemented with 10% FCS (Sigma-Aldrich, Hamburg, Germany) and 1% non-essential amino acids (NEAA; Lonza) at 37° C and 5% CO2. Cell lines were monitored for infections using the PlasmoTest™ Kit (Invivo-Gen, according to the manufacturer’s instructions).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the RNeasy Mini Columns (Qiagen, Hilden, Germany) in accordance with manufacturer’s instructions including a purification step with DNase I.
|
| Label |
Cy3
|
| Label protocol |
Fluorescently-labeled miRNA were prepared according to Agilent protocol miRNA Complete Labeling and Hyb Kit.
|
| |
|
| Hybridization protocol |
100ng of Cy3 labeled miRNA sample were hybridized for at least 20 hr at 55°C on Agilent human miRNA Microarray V21.0, 8x60k according to manufacturer's instructions.
|
| Scan protocol |
Gene Expression Microarrays were scanned using the Agilent Scanner G2505C. The scanned images were analyzed with Feature Extraction Software (Agilent technologies) using default settings.
|
| Description |
257015612085_1_1
replicate 2
|
| Data processing |
Data extraction was done for all beads individually, and outliers are removed when the absolute difference to the median is greater than 2.5 times MAD(2.5 Hampel’s method). All remaining bead level data points are than quantile normalized. As test for significance the student’s t-test is used on the bead expression values of the two groups of interest. In the case of significance of expression against background we tested for greater than all negative beads for this sample and in the case of comparing separate groups we tested for inequality of the means of the groups. In both cases Benjamini-Hochberg correction was applied to the complete set of p-values of all ProbeIDs on the chip.
|
| |
|
| Submission date |
Apr 30, 2019 |
| Last update date |
Jul 30, 2023 |
| Contact name |
Hedwig Elisabeth Deubzer |
| E-mail(s) |
[email protected]
|
| Organization name |
Charite - University Hospital Berlin
|
| Department |
Department of Pediatrics, Division of Oncology and Hematology
|
| Lab |
Deubzer
|
| Street address |
Augustenburger Platz 1
|
| City |
Berlin |
| State/province |
Berlin |
| ZIP/Postal code |
13353 |
| Country |
Germany |
| |
|
| Platform ID |
GPL21576 |
| Series (2) |
| GSE130523 |
AVEN is an indirectly druggable mediator of neuroblastoma cell tumorigenicity and chemotherapy resistance [microarray] |
| GSE130524 |
AVEN is an indirectly druggable mediator of neuroblastoma cell tumorigenicity and chemotherapy resistance |
|
