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Sample GSM765453 Query DataSets for GSM765453
Status Public on Jul 01, 2012
Title Untreated Control - repeat 1 - mAdbID:103509
Sample type RNA
 
Channel 1
Source name Untreated Control
Organism Homo sapiens
Characteristics cell line: CAL-1
cell type: plasmacytoid dendritic cells (pDC)
disease state: Leukemia
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: 3.50963;; 4.4557
Temperature: 27.9138
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: 103509
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 -0.191
1718857_1 -0.296
1718858_1 0.056
1718860_1 -0.191
1718861_1 0.197
1718862_1 0.680
1718863_1 0.401
1718864_1 -0.032
1718878_1 -0.077
1718879_1 -0.166
1718880_1 0.151
1718883_1 0.030
1718884_1 -0.193
1718885_1 -0.187
1718886_1 -0.502
1718887_1 -0.589
1718888_1 -0.361
1718901_1 0.836
1718926_1 0.706
1718928_1 0.078

Total number of rows: 29039

Table truncated, full table size 465 Kbytes.




Supplementary file Size Download File type/resource
GSM765453_103509.gpr.gz 3.9 Mb (ftp)(http) GPR
Raw data provided as supplementary file
Processed data included within Sample table

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