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Sample GSM765445 Query DataSets for GSM765445
Status Public on Jul 01, 2012
Title 'K' ODN for 27 hours - repeat 2 - mAdbID:102880
Sample type RNA
 
Channel 1
Source name 'K' ODN for 27 hours
Organism Homo sapiens
Characteristics cell line: CAL-1
cell type: plasmacytoid dendritic cells (pDC)
disease state: Leukemia
treatment type: small molecule
agent: TLR9 ligand 'K' (CpG-B) ODN
treatment dose: 3 uM
treatment time: 27 hours
Treatment protocol Treatment type: small molecule
Agent: TLR9 ligand 'K' (CpG-B) ODN
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 'K' ODN for 1-27 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: 3.47301;; 3.7965
Temperature: 25.6554
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: 102880
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

Data table header descriptions
ID_REF mAdb well id plus replicate number
VALUE normalized log ratio (log2 of CY5 channel/CY3 channel) representing test/reference

Data table
ID_REF VALUE
1718855_1 -0.234
1718857_1 -0.280
1718858_1 -0.198
1718860_1 -0.376
1718861_1 -0.383
1718862_1 0.556
1718863_1 0.230
1718864_1 -0.535
1718878_1 -1.329
1718879_1 -1.023
1718880_1 1.087
1718883_1 0.803
1718884_1 -0.162
1718885_1 -0.416
1718886_1 -0.656
1718887_1 -0.690
1718888_1 -0.048
1718901_1 0.647
1718926_1 0.403
1718928_1 1.012

Total number of rows: 29039

Table truncated, full table size 455 Kbytes.




Supplementary file Size Download File type/resource
GSM765445_102880.gpr.gz 3.7 Mb (ftp)(http) GPR
Raw data provided as supplementary file
Processed data included within Sample table

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