|
| Status |
Public on Jun 20, 2014 |
| Title |
RajiNB 1 |
| Sample type |
RNA |
| |
|
| Source name |
cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: Raji
treatment: Treated for 24 hours with NaB
|
| Treatment protocol |
Burkitt's lymphoma cell line Raji was treated with NaB isolated or combined with VP-16 for 24 hours. Cells were collected by centrifugation and total RNA was extracted using Trizol. DNA microarrays were used to access global gene expression modulation upon treatment of Raji cell line with VP-16 and a combination of NaB and VP-16. Gene expression of treated cells was compared with controls consisting of untreated cells. Microarray analysis was performed using Agilent Whole Human Genome Microarray 4_44K arrays and labeled using the One Color Quick Amp Labeling Kit (Agilent Technologies). Two biological replicates were included for each experimental condition.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using Trizol (Invitrogen), following the manufacturer's protocol.
|
| Label |
Cy3
|
| Label protocol |
Microarray analysis was performed using Agilent Whole Human Genome Microarray 4x44K arrays and the One Color Quick Amp Labeling Kit (Agilent Technologies, Santa Clara, USA). Target cDNA was generated from 800ng of total RNA, which was reverse-transcribed and labeled with Cy3.
|
| |
|
| Hybridization protocol |
1.5 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 250 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed for 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.
|
| Scan protocol |
Slides were scanned immediately after washing on theGenePix Scanner using settings suggested by Agilent
|
| Description |
Gene Expression
|
| Data processing |
The scanned images were analyzed with Feature Extraction Software v 9.5.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
|
| |
|
| Submission date |
Jun 28, 2013 |
| Last update date |
Oct 04, 2023 |
| Contact name |
Patricia Severino |
| E-mail(s) |
[email protected]
|
| Phone |
5511984661282
|
| Organization name |
Hospital Israelita Albert Einstein
|
| Department |
Albert Einstein Research and Education Institute
|
| Street address |
Rua Comendador Elias Jafet, 755
|
| City |
Sao Paulo |
| State/province |
Sao Paulo |
| ZIP/Postal code |
05653-000 |
| Country |
Brazil |
| |
|
| Platform ID |
GPL4133 |
| Series (1) |
| GSE48399 |
Histone Deacetylase Inhibitor prevents cell growth in Burkitt's lymphoma by regulating PI3K/Akt pathways and leading to up regulation of micro RNA-143, -145 and -101 |
|
