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Sample GSM833305 Query DataSets for GSM833305
Status Public on May 03, 2012
Title wild type unstimulated replicate 1
Sample type RNA
 
Source name WT 1 medium
Organism Mus musculus
Characteristics treatment: unstimulated
cell type: bone-marrow derived dendritic cells
genetic background: C57Bl/6
genotype: Wild type
Treatment protocol Bone marrow-derived dendritic cells (BM-DCs) were transferred to new culture dishes at a density of 1 million BM-DC per 2 ml medium. The BM-DCs were incubated with either medium (unstimulated) or preformed Ag-Ab complexes (IC) containing 1 µg/ml OVA (Worthington) and 50 µg/ml rabbit anti-OVA IgG (ICN biomedicals) at 37 degrees for 4 hours.
Growth protocol Bone marrow was harvested from the femurs and tibia derived from two female and two male mice of each mouse strain. The cells of all 12 mice were cultured separately in IMDM supplemented with GM-CSF containing supernatant in petri dishes. Non-adherent and semi-adherent cells were transferred to new dishes and fresh medium on days 4 and 7. On day 10, the cells were harvested and the % of immature CD11c+ DCs was determined by flow cytometry, which was typically above 85%.
Extracted molecule total RNA
Extraction protocol Total RNA was isolated from cells by Qiagen RNA Easy kit. RNA was amplified by using the Illumina RNA Amplification kit.
Label Biotin
Label protocol Illumina RNA amplfication kit includes incorporation of biotin.
 
Hybridization protocol Samples were hybridised on Illumina mouse WG-6 V1.1 expression BeadChips.
Scan protocol BeadChips were scanned on the Illumina BeadArray 500GX Scanner.
Description 04_A
Data processing Raw data was exported by Illumina BeadStudio V3.0 software and imported and stored in Rosetta Resolver software.
Not Normalized data sheet contains intensities corrected for background by Rosetta's default error model; Normalized data sheet contains intensities normalized with Rosetta's default error model for Illumina arrays on a back-transformed linear scale and where different probes for the same gene are averaged and thus get the same value
 
Submission date Nov 15, 2011
Last update date May 03, 2012
Contact name Peter A.C. 't Hoen
E-mail(s) p.a.c.hoen@lumc.nl
Phone +31 71 5269421
Fax +31 71 5268285
URL http://www.humgen.nl
Organization name Leiden University Medical Center
Department Center for Human and Clinical Genetics
Street address PO Box 9600
City Leiden
ZIP/Postal code 2300 RC
Country Netherlands
 
Platform ID GPL6481
Series (1)
GSE33718 Genome-wide analysis of Fcγ receptor ligation on dendritic cells from wild-type, FcγRIIb KO or FcR γ chain KO mice

Data table header descriptions
ID_REF
VALUE intensities normalized with Rosetta's default error model for Illumina arrays on a back-transformed linear scale and where different probes for the same gene are averaged and thus get the same value

Data table
ID_REF VALUE
10243 0.31174
10280 0.06736
10575 0.10888
20048 0.11236
20296 40.44036
20343 0.70427
20373 0.08689
20431 55.29459
50014 0.04293
50017 0.77596
50019 0.97076
50020 0.2132
50022 0.03796
50025 0.03206
50026 0.35701
50035 0.1575
50037 0.19648
50039 2.68755
50040 0.54043
50041 0.64306

Total number of rows: 46643

Table truncated, full table size 763 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
Processed data are available on Series record

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