|
| Status |
Public on Dec 10, 2009 |
| Title |
U937 cells with knock-down of Pirin - Replica 2 |
| Sample type |
RNA |
| |
|
| Source name |
U937 myelomonocytic cell line, PIR knock-down
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: U937
pir knock-down: yes
|
| Growth protocol |
U937 cell lines were maintained in RPMI-1640 supplemented with 10% FCS and 2mM glutamine at 37°C in a humidified atmosphere containing 5% CO2.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using TRIzol Reagent (Gibco), followed by clean up on RNeasy mini/midi columns (RNeasy Mini/Midi Kit, Qiagen). For each sample, an RNA pool was obtained by mixing equal quantities of total RNA from each of the three independent RNA extractions.
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA The size and the accuracy of quantitation of targets were checked by agarose gel electrophoresis of 2ug aliquots, prior to and after fragmentation. After fragmentation, targets were diluted in hybridisation buffer at a concentration of 150ug/ml.
|
| |
|
| Hybridization protocol |
Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip GeneChip HG-U133 Plus v.2 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station. Two copies of the GeneChip HG-U133 Plus v.2 were hybridized with each biotin-labeled target.
|
| Scan protocol |
Images were scanned using an Affymetrix GeneArray Scanner, using default parameters.
|
| Description |
U937 is a human cell line established from a diffuse histiocytic lymphoma and displaying monocytic characteristics.
|
| Data processing |
The data were analyzed with GeneChip operating system (GCOS) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.
|
| |
|
| Submission date |
Jun 24, 2009 |
| Last update date |
Aug 28, 2018 |
| Contact name |
Myriam Alcalay |
| E-mail(s) |
myriam.alcalay@ieo.eu
|
| Organization name |
European Institute of Oncology
|
| Department |
Experimental Oncology
|
| Lab |
Functional Genomics
|
| Street address |
Via Adamello 16
|
| City |
Milan |
| ZIP/Postal code |
20139 |
| Country |
Italy |
| |
|
| Platform ID |
GPL570 |
| Series (1) |
| GSE16798 |
Genes regulated after knock-down of Pirin in U937 cells |
|
| Relations |
| Reanalyzed by |
GSE119087 |
