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Sample GSM1198078 Query DataSets for GSM1198078
Status Public on Nov 04, 2013
Title WT Dermis P1, steady-state, replicate 3
Sample type RNA
 
Source name BMN_BC4_MoGene
Organism Mus musculus
Characteristics strain: C57BL/6
genotype/variation: WT
tissue origin: Dermis
cell type: Monocyte
cell phenotype: CD11b+ CD64low Ly6Chigh CCR2+ MHCII-
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 Dermal P1 from steady state B6 mice, FACS sorted as: live, CD11b+ CD24-CD64low Ly6Chigh CCR2+ MHCII-
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 12.08253694
10338003 10.36120368
10338004 9.161427629
10338017 12.49086916
10338025 8.91522655
10338026 13.0630257
10338029 9.378905399
10338035 9.054930537
10338036 9.021975396
10338037 2.908811299
10338041 10.98097476
10338042 10.08013454
10338044 12.05827533
10338047 3.180908283
10338056 2.923027327
10338059 13.18139871
10338060 2.857568086
10338063 2.805281567
10338064 2.780334129
10338065 2.985276003

Total number of rows: 34760

Table truncated, full table size 709 Kbytes.




Supplementary file Size Download File type/resource
GSM1198078_BMN_BC4_MoGene.CEL.gz 3.8 Mb (ftp)(http) CEL
Processed data included within Sample table

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