NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM765465 Query DataSets for GSM765465
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

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 -0.215
1718857_1 -0.617
1718858_1 0.076
1718860_1
1718861_1 -0.007
1718862_1
1718863_1 0.426
1718864_1 0.128
1718878_1 -1.231
1718879_1 -1.291
1718880_1 0.117
1718883_1
1718884_1
1718885_1 -0.249
1718886_1
1718887_1 -0.318
1718888_1 -0.115
1718901_1 0.421
1718926_1 0.103
1718928_1 -0.086

Total number of rows: 29039

Table truncated, full table size 466 Kbytes.




Supplementary file Size Download File type/resource
GSM765465_105010.gpr.gz 3.9 Mb (ftp)(http) GPR
Raw data provided as supplementary file
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap