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Sample GSM1916136 Query DataSets for GSM1916136
Status Public on Feb 14, 2017
Title pDC.CLN_3
Sample type RNA
 
Source name Plasmacytoid dendritic cells_cutaneous lymph node
Organism Mus musculus
Characteristics strain: C57BL/6
tissue: cutaneous lymph nodes
cell markers: CD45(+)Lin(-)CD117(-)CD11b(-)CD11c(low)MHC-II(- to low)PDCA-1(+)B220(+)Ly6C(+)
cell type: plasmacytoid dendritic cells
Extracted molecule total RNA
Extraction protocol Plasmacytoid dendritic cells were purified by flow cytometry and total RNA was extracted with the Qiagen micro RNAeasy kit, with on column DNase digestion, according to the manufacturer protocol.
Label biotin
Label protocol 1 to 20 ng of RNA from each sample was used to synthesize biotinylated probes, using 2 successive rounds of cRNA amplification (using the NuGEN Ovation Pico WTA System V2 Kit and the NuGEN Encore Biotin Module Kit according to NuGEN recommendations) with appropriate quality control to ensure full length synthesis.
 
Hybridization protocol Following fragmentation and end-labeling, 2.07 μg of cDNAs were hybridized for 16 hours at 45°C on Affymetrix GeneChip Mouse Gene 1.0 ST arrays. The chips were washed and stained in the GeneChip Fluidics Station 450.
Scan protocol GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G (Affymetrix) at a resolution of 0.7 µm.
Description Untreated
Data processing The data were RMA normalized in R and Bioconductor, using the oligo package.
 
Submission date Oct 22, 2015
Last update date Feb 14, 2017
Contact name Marc DALOD
E-mail(s) dalod@ciml.univ-mrs.fr
Organization name CIML
Street address Parc Scientifique et Technologique de Luminy, 163 avenue de Luminy, Case 906, 13288 Marseille cedex 9
City MARSEILLE
ZIP/Postal code 13009
Country France
 
Platform ID GPL6246
Series (1)
GSE74276 Gene expression profiling of plasmacytoid dendritic cells from cutaneous lymph nodes
Relations
Reanalyzed by GSE74316

Data table header descriptions
ID_REF
VALUE RMA normalized log2 values

Data table
ID_REF VALUE
10338001 12.00132156564
10338002 4.36337874292056
10338003 10.6027082047285
10338004 9.4414041191081
10338005 2.31643909292559
10338006 2.51095922505523
10338007 2.842805713578
10338008 2.96866647608155
10338009 6.53084002530125
10338010 2.41965075312333
10338011 4.04779756747931
10338012 2.46487777591007
10338013 2.17125800496232
10338014 2.27394312213364
10338015 2.27394312213364
10338016 5.91408732766928
10338017 12.6426366900391
10338018 5.04838355008984
10338019 3.61436549238623
10338020 6.71836131065262

Total number of rows: 35556

Table truncated, full table size 898 Kbytes.




Supplementary file Size Download File type/resource
GSM1916136_BMN_FR3_MoGene.CEL.gz 3.7 Mb (ftp)(http) CEL
Processed data included within Sample table

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