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Sample GSM371676 Query DataSets for GSM371676
Status Public on Aug 03, 2009
Title Monocyte_Ly6Chi_Spleen_04
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 (http://www.arrays.ucsf.edu and http://www.agilent.com).
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
E-mail(s) ETZRODT.MARTIN@MGH.HARVARD.EDU
Phone (617) 643-0500
Fax (617) 643-6133
URL http://csb.mgh.harvard.edu/pittet
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
ID_REF
VALUE normalized signal

Data table
ID_REF VALUE
A_52_P616356 7.232514627
A_52_P580582 7.164278438
A_52_P403405 6.49285462
A_52_P819156 7.127079032
A_51_P331831 8.558183023
A_51_P430630 6.721099189
A_52_P502357 6.145295335
A_52_P299964 7.318367245
A_51_P356389 8.52585393
A_52_P684402 9.594515807
A_51_P414208 6.281350515
A_51_P280918 6.860699033
A_52_P613688 9.168727015
A_52_P258194 7.272046524
A_52_P229271 8.895725636
A_52_P214630 6.084926515
A_52_P579519 6.183635381
A_52_P979997 6.104598754
A_52_P453864 7.524044492
A_52_P655842 6.656424863

Total number of rows: 41174

Table truncated, full table size 991 Kbytes.




Supplementary file Size Download File type/resource
GSM371676.txt.gz 9.1 Mb (ftp)(http) TXT
Processed data included within Sample table

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