|
| Status |
Public on Jul 01, 2012 |
| Title |
D122 for 27 hours (D control) - repeat 1 - mAdbID:105010 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
D122 for 27 hours (D control)
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: CAL-1
cell type: plasmacytoid dendritic cells (pDC)
disease state: Leukemia
treatment type: small molecule
agent: D122
treatment dose: 3 uM
treatment time: 27 hours
|
| Treatment protocol |
Treatment type: small molecule
Agent: D122
Treatment dose: 3 uM
Treatment time: 27 hours
In-vitro treatment: The pDC cell line CAL-1 was grown in complete medium (RPMI 1640; Lonza) supplemented with 2mM L-Glutamin, 1mM sodium pyruvate, 10mM HEPES, 1x MEM NEAA (all Gibco) to which 10% heat-inactivated fetal bovine serum (Lonza) was added. Typically cells were maintained in a 150cm2 flask with a density of 1-2.4 x 106 cells / ml and washed every 3 days. Before stimulation of cells for microarray analysis, cells were cultured for 3 days at 37 C in a 5% CO2 air incubator. Cells were then washed and plated in a 75cm2 flask (30 x 106/ 15 ml (80% confluence)), and rested over night before being stimulated with 3uM respective control ODNs for the duration of maximal gene expression (D122 for 27 h).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
TRIzol Extraction Protocol
Other: Total RNA was extracted using TRIzol Reagent (Invitrogen) as specified by the manufacturer.
|
| Label |
cy5
|
| Label protocol |
Cy5 Sample Labeling
Other: Ten microliters of cDNA was labeled with Cy5 reactive dyes (Amersham Biosciences, UK) diluted in 5 ul of DMSO plus 1.7 ul of 1 M NaHCO3 for 90 min in the dark.
|
| |
|
| Channel 2 |
| Source name |
Universal Human Reference RNA
|
| Organism |
Homo sapiens |
| Characteristics |
sample type: Equal quantities of total RNA from each cell line (brain, breast, B-lymphocyte, cervix, liver, liposarcoma, macrophages, skin, testis, Y-lymphocyte) were pooled together.
|
| Biomaterial provider |
Stratagene (La Jolla, CA)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
TRIzol Extraction Protocol
Other: Total RNA was extracted using TRIzol Reagent (Invitrogen) as specified by the manufacturer.
|
| Label |
cy3
|
| Label protocol |
Cy3 Sample Labeling
Other: Ten microliters of cDNA was labeled with Cy3 reactive dyes (Amersham Biosciences, UK) diluted in 5 ul of DMSO plus 1.7 ul of 1 M NaHCO3 for 90 min in the dark.
|
| |
|
| |
| Hybridization protocol |
Hybridization Protocol
Other: The probes were mixed, diluted in 5 ul DMSO plus 1.7 ul of 1 M NaHCO3 and hybridized to 36K human 60-mer oligonucleotide array slides (NCI Human Array Set Hs-OperonV3.0) at 42 C for 18 h in a MAUI hybridization system (BioMicro Systems) followed by washing, centrifugation and air drying.
|
| Scan protocol |
Creator: GenePix Pro 6.0.1.25
Scanner: GenePix 4000B [136824]
ScanPower: 10;; 10
LaserPower: 3.44554;; 4.29395
Temperature: 26.0216
Scanning Protocol
Other: Arrays were scanned using a GenePix 4000B Scanner (Axon Instruments) and analyzed using the GenePix Pro 6.0 Software Tool (Axon Instruments) using GAL files provided by the manufacturer at http://madb.nci.nih.gov/.
|
| Description |
mAdb experiment ID: 105010
|
| Data processing |
BRB Array Tools Data Processing Protocol
Calculation Method: Gene expression analysis was performed using BRB Array Tools Version 3.8.1 developed by the NCI Biometric Research Branch (Bethesda, MD). Data were background-corrected, flagged values were removed, spots in which both signals were <100 were filtered, ratios were log base 2 transformed, and lowest intensity-dependant normalization was used to adjust for differences in labeling intensities of the Cy3 and Cy5 dyes. Analysis was restricted to genes present in >60% of the arrays after filtering. In toto, 29,039 features were reproducibly tracked in all microarrays.
|
| |
|
| Submission date |
Jul 21, 2011 |
| Last update date |
Jul 01, 2012 |
| Contact name |
Folkert Steinhagen |
| E-mail(s) |
Folkert.Steinhagen@ukb.uni-bonn.de
|
| Phone |
+491788315703
|
| Organization name |
National Cancer Institute
|
| Street address |
Breddert 37
|
| City |
Hilden |
| ZIP/Postal code |
40723 |
| Country |
Germany |
| |
|
| Platform ID |
GPL3779 |
| Series (1) |
| GSE30849 |
Type I Interferon Dependent Anti-viral Activity |
|
