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Sample GSM678298 Query DataSets for GSM678298
Status Public on Apr 01, 2011
Title CD11b+ F4/80+ FOXP3+ rep3
Sample type RNA
 
Source name spleen of C57 FOXP3 GFP mice
Organism Mus musculus
Characteristics cell type: CD11b+ F4/80+ FOXP3+
strain: C57 FOXP3/GFP
Treatment protocol none
Growth protocol Freshly isolated Macrophages and MacRegs were derived from 4-6 month old C57 FOXP3/GFP mice through two consecutive rounds of fluorescent cell sorting using CD11b and F4/80 and GFP FOXP3. Freshly isolated CD4+Foxp3- and CD4+Foxp3+ cells were obtained from C57 FOXP3/GFP mice of the same age, through two consecutive rounds of fluorescent cell sorting. Three independent isolations were executed on separate days to obtain biological replicates.
Extracted molecule total RNA
Extraction protocol RNA was extracted according to manufacturers instructionsusing the Rneasy MiniKit (Qiagen) , RNA was measured with the NanoDrop 1000 (Thermo Scientific) and integrity verified through Agilent Bioanalyzer 2100 using the nano chip.
Label cy3
Label protocol Agilent Low RNA Input Linear Amplification Kit PLUS was used incorporating cy3, according to manufacturers instructions
 
Hybridization protocol Agilent In Situ Hybridization Kit Plus was used according to manufacturers instructions, and labeled samples were hybridized to the Mouse whole genome 4X44k chip.
Scan protocol GE2-v5_95_Feb07 (Read Only), using Agilent Technologies Scanner G2505B US45102967
Description MacReg
Data processing Images were quantified using Agilent Feature Extraction Software (version A.9.5.1.1). Using Genespring GX11, the data was normalized to the 75th percentile and a baseline transformation to median of all samples was performed. Probes were filtered by percentile, removing those that fall beneath the 20th %. Probes were then filtered by flags removing those that did not have passing or marginal in 3 of the 6 samples. The two treatment populations (Mac Foxp3 neg and Mac Foxp3 pos were averaged and a t-test was performed to select genes that were significantly differentialy expressed between both populations. This list was further screened for a minimum of 2 fold change between the populations.
 
Submission date Feb 22, 2011
Last update date Apr 01, 2011
Contact name Cheryl E Myers
E-mail(s) myers.cheryl@mayo.edu
Phone 480-301-4056
Organization name Mayo Clinic College of Medicine
Department Immunology
Lab Cohen
Street address 13400 E Shea Blvd
City Scottsdale
State/province AZ
ZIP/Postal code 85259
Country USA
 
Platform ID GPL7202
Series (1)
GSE23793 Gene expression profile of Foxp3 expressing naturally ocurring regulatory macrophages from mice

Data table header descriptions
ID_REF
VALUE log 2 of normalized signal intensity

Data table
ID_REF VALUE
GE_BrightCorner -1.0270281
DarkCorner -0.025574207
A_52_P616356 3.6487656
A_52_P580582 -0.59097385
A_52_P403405 -0.48642254
A_52_P819156 3.756688
A_51_P331831 -0.24854374
A_51_P430630 0.10236311
A_52_P502357 0.020445824
A_52_P299964 -0.6659007
A_51_P356389 -0.46792173
A_52_P684402 0.15092158
A_51_P414208 0.41465855
A_51_P280918 0.57177305
A_52_P613688 -1.1761532
A_52_P258194 1.1689153
A_52_P229271 -0.09443331
A_52_P214630 -0.011295319
A_52_P579519 1.1905808
A_52_P979997 -0.02985859

Total number of rows: 41252

Table truncated, full table size 975 Kbytes.




Supplementary file Size Download File type/resource
GSM678298.txt.gz 2.2 Mb (ftp)(http) TXT
Processed data included within Sample table

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