|
| Status |
Public on Apr 06, 2012 |
| Title |
Monocyte_Ly6Clo_Blood_03 |
| Sample type |
RNA |
| |
|
| Source name |
Monocyte Ly-6Clo, Blood
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
gender: female
age: 8-12 weeks
tissue: Blood
cell type: monocyte
monocyte subset: Ly6Clo
cell signature: Ly-6Clo monocytes were identified as CD11b hi (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-6Clo blood 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.
|
| 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 |
Sep 24, 2011 |
| Last update date |
Apr 06, 2012 |
| 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 (2) |
| GSE32364 |
Murine blood monocyte subsets |
| GSE32392 |
Regulation of Monocyte Functional Heterogeneity by miR-146a |
|
