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Sample GSM1198073 Query DataSets for GSM1198073
Status Public on Nov 04, 2013
Title WT Blood Ly6C monocyte, steady-state, replicate 1
Sample type RNA
 
Source name BMN_BA1_MoGene
Organism Mus musculus
Characteristics strain: C57BL/6
genotype/variation: WT
tissue origin: Blood
cell type: Monocyte
cell phenotype: CD11b+ Ly6Chigh
inflammation: None
gender: female
age: 6 weeks-old
Treatment protocol Inflammation was induced by application of 10µl of a 0.5% of DNFB diluted in acetone/olive oil (4:1). Ears and skin draining lymph nodes were harvested from untreated animals or 3 days post inflammation. Ear skin tissue was digested by dispase and collagenase 4 treatment, cells were enriched by percoll gradient and resuspended in PBS 2%FCS, EDTA 5mM before sorting by flow cytometry. Cutaneous lymph nodes were digested by collagenase 2 treatment, cells were enriched by optiprep gradient and resuspended in PBS 2%FCS, EDTA 5mM before sorting by flow cytometry.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from between 5x10E3 and 1x10E4 cells for each leukocyte subset with the Qiagen micro RNAeasy kit, according to the manufacturer protocol.
Label biotin
Label protocol Biotinylated double strand cDNA targets were prepared, from 5 ng to 20 ng of total RNA depending on the amount available per individual samples, using the NuGEN Ovation Pico WTA System V2 kit (Cat # 3302) and the NuGEN Encore Biotin Module kit (Cat # 4200) according to NuGEN recommendations.
 
Hybridization protocol Following fragmentation, 2 µg of cRNA were hybridized for 16 hr at 45°C on GeneChip Mouse Gene 1.0 ST . GeneChips were washed and stained in the Affymetrix Fluidics Station 450 .
Scan protocol GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.
Description WT Ly6Chi Blood monocyte from steady state B6 mice, FACS sorted as: live, Ly6Chi CD11b+
Data processing The data were RMA normalized in R and Bioconductor, using the affy package.
 
Submission date Jul 30, 2013
Last update date Oct 23, 2015
Contact name Marc DALOD
E-mail(s) dalod@ciml.univ-mrs.fr
Organization name Center of Immunology of Marseille Luminy (CIML)
Department Dendritic cells and antiviral defense
Lab dalod
Street address Parc scientifique de Luminy, Case 906
City Marseille
ZIP/Postal code 13288, Cedex 09
Country France
 
Platform ID GPL6246
Series (1)
GSE49358 Genome-wide expression study of the CD11b+ subsets of dermal myeloid cells and their migratory counterparts in the draining lymph node
Relations
Reanalyzed by GSE74316

Data table header descriptions
ID_REF
VALUE RMA normalized values

Data table
ID_REF VALUE
10338001 11.93161491
10338003 10.02733801
10338004 9.052882095
10338017 12.70907588
10338025 8.678783658
10338026 13.18606262
10338029 9.359806084
10338035 8.750924045
10338036 9.122767074
10338037 2.809635859
10338041 11.19992171
10338042 9.962728264
10338044 12.04356374
10338047 3.041103898
10338056 2.830529587
10338059 13.16212709
10338060 2.762700535
10338063 2.785866645
10338064 2.718583973
10338065 2.882168664

Total number of rows: 34760

Table truncated, full table size 709 Kbytes.




Supplementary file Size Download File type/resource
GSM1198073_BMN_BA1_MoGene.CEL.gz 4.0 Mb (ftp)(http) CEL
Processed data included within Sample table

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