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Status |
Public on Jul 01, 2012 |
Title |
ODN1612 for 9 hours (K Control)- repeat 2 - mAdbID:105011 |
Sample type |
RNA |
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Channel 1 |
Source name |
ODN1612 for 9 hours (K control)
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Organism |
Homo sapiens |
Characteristics |
cell line: CAL-1 cell type: plasmacytoid dendritic cells (pDC) disease state: Leukemia treatment type: small molecule agent: TLR9 ligand ODN1612 treatment dose: 3 uM treatment time: 9 hours
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Treatment protocol |
Treatment type: small molecule Agent: TLR9 ligand ODN1612 Treatment dose: 3 uM Treatment time: 9 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 (ODN1612 for 9 h).
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Extracted molecule |
total RNA |
Extraction protocol |
TRIzol Extraction Protocol Other: Total RNA was extracted using TRIzol Reagent (Invitrogen) as specified by the manufacturer.
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Label |
cy5
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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.
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Channel 2 |
Source name |
Universal Human Reference RNA
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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.
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Biomaterial provider |
Stratagene (La Jolla, CA)
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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.
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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.
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Scan protocol |
Creator: GenePix Pro 6.0.1.25 Scanner: GenePix 4000B [136824] ScanPower: 10;; 10 LaserPower: 3.47606;; 4.43129 Temperature: 27.7001 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/.
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Description |
mAdb experiment ID: 105011
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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.
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Submission date |
Jul 21, 2011 |
Last update date |
Jul 01, 2012 |
Contact name |
Folkert Steinhagen |
E-mail(s) |
Folkert.Steinhagen@ukb.uni-bonn.de
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Phone |
+491788315703
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Organization name |
National Cancer Institute
|
Street address |
Breddert 37
|
City |
Hilden |
ZIP/Postal code |
40723 |
Country |
Germany |
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Platform ID |
GPL3779 |
Series (1) |
GSE30849 |
Type I Interferon Dependent Anti-viral Activity |
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