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Sample GSM371672 Query DataSets for GSM371672
Status Public on Aug 03, 2009
Title Monocyte_Ly6Chi_Spleen_01
Sample type RNA
Source name Monocyte Ly-6Chi, Spleen
Organism Mus musculus
Characteristics strain: C57BL/6
gender: female
age: 8-12 weeks
tissue: Spleen
cell type: monocyte
monocyte subset: Ly6Chi
cell signature: Ly-6Chi monocytes were identified as CD11bhi (CD90/B220/CD49b/NK1.1/Ly-6G)lo (F4/80/I-Ab/CD11c)lo
Biomaterial provider C57BL/6 mice were purchased from The Jackson Laboratory, Bar Harbor, Maine 04609 USA
Treatment protocol healthy mice, no treatment
Growth protocol CHOW
Extracted molecule total RNA
Extraction protocol Monocyte subsets from blood and spleen of a group of four mice were isolated by fluorescence activated cell sorting (FACS) as CD11bhi (CD90/B220/CD49b/NK1.1/Ly-6G)lo (F4/80/I-Ab/CD11c)lo Ly-6Chi cells.
Samples of 1,000 Ly-6Chi blood and Ly-6Chi splenic monocytes were collected directly into 20 µl lysis buffer of the PicoPure RNA isolation kit (Arcturus). RNA extraction was subsequently performed according to the manufacturer’s instructions (Arcturus).
Total RNA quality was assessed using RNA pico lab chips on the Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA). RIN (RNA integrity number) >= 8.
Label Cy3
Label protocol RNA was amplified using the NuGen WT-Ovation Pico System, and the amplified cDNA was labeled using the FL-Ovation cDNA Fluorescent Module (NuGen Technologies, San Carlos, Ca). 5ng of input total RNA was reverse–transcribed into cDNA and then amplified using a linear isothermal amplification process (SPIA). The amplified products were CY-3 labeled and fragmented according to manufacturer’s guidelines.
Hybridization protocol Labeled cDNA was assessed using the Nanodrop ND-100 (Nanodrop Technologies, Inc., Wilmington DE) and the Agilent 2100 Bioanalyzer; equal amounts of Cy3-labeled target were hybridized to Agilent whole mouse genome 4x44K Ink-jet arrays. Hybridizations were performed for 14 h according to the manufacturers protocol.
Scan protocol Arrays were scanned using the Agilent microarray scanner. Raw signal intensities were extracted with their Feature Extraction v9.1 software.
Description Sample preparation, labeling, and array hybridizations were performed according to standard protocols from the UCSF Shared Microarray Core Facilities and Agilent Technologies ( and
Data processing The dataset was normalized using the quantile normalization method. No background subtraction was performed, and the median feature pixel intensity was used as the raw signal before normalization. All procedures were carried out using functions in the R package limma in Bioconductor.
Submission date Feb 16, 2009
Last update date Sep 26, 2011
Contact name Martin Etzrodt
Phone (617) 643-0500
Fax (617) 643-6133
Organization name Massachusetts General Hospital
Department Center for Systems Biology
Lab Pittet Lab
Street address 185 Cambridge Street
City Boston
State/province MA
ZIP/Postal code 02114
Country USA
Platform ID GPL7202
Series (1)
GSE14850 Microarray analysis of splenic reservoir monocytes and their blood counterparts

Data table header descriptions
VALUE normalized signal

Data table
A_52_P616356 6.997291768
A_52_P580582 7.701198147
A_52_P403405 6.610102063
A_52_P819156 8.120738818
A_51_P331831 7.046128301
A_51_P430630 7.006676715
A_52_P502357 6.119589621
A_52_P299964 6.886839706
A_51_P356389 7.434259441
A_52_P684402 10.435739
A_51_P414208 6.252074043
A_51_P280918 6.802920199
A_52_P613688 9.857346258
A_52_P258194 7.62342429
A_52_P229271 9.183578336
A_52_P214630 6.120576629
A_52_P579519 6.222191138
A_52_P979997 6.174925683
A_52_P453864 7.376939322
A_52_P655842 6.756973226

Total number of rows: 41174

Table truncated, full table size 983 Kbytes.

Supplementary file Size Download File type/resource
GSM371672.txt.gz 9.2 Mb (ftp)(http) TXT
Processed data included within Sample table

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