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Sample GSM371664 Query DataSets for GSM371664
Status Public on Aug 03, 2009
Title Monocyte_Ly6Chi_Blood_01
Sample type RNA
Source name Monocyte Ly-6Chi, Blood
Organism Mus musculus
Characteristics strain: C57BL/6
gender: female
age: 8-12 weeks
tissue: Blood
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 (3)
GSE14850 Microarray analysis of splenic reservoir monocytes and their blood counterparts
GSE32364 Murine blood monocyte subsets
GSE32392 Regulation of Monocyte Functional Heterogeneity by miR-146a

Data table header descriptions
VALUE normalized signal

Data table
A_52_P616356 6.752798758
A_52_P580582 7.053586544
A_52_P403405 6.648357582
A_52_P819156 7.036924888
A_51_P331831 7.678363218
A_51_P430630 7.113073491
A_52_P502357 6.174301544
A_52_P299964 6.919608239
A_51_P356389 8.818410891
A_52_P684402 10.63079958
A_51_P414208 6.337064339
A_51_P280918 7.02306125
A_52_P613688 8.82792134
A_52_P258194 7.623918607
A_52_P229271 9.586369855
A_52_P214630 6.112765282
A_52_P579519 6.168045268
A_52_P979997 6.174301544
A_52_P453864 6.010528106
A_52_P655842 6.777666281

Total number of rows: 41174

Table truncated, full table size 987 Kbytes.

Supplementary file Size Download File type/resource
GSM371664.txt.gz 9.1 Mb (ftp)(http) TXT
Processed data included within Sample table

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