|
| Status |
Public on May 14, 2015 |
| Title |
MAM with control Ab rep1 [MC3] |
| Sample type |
RNA |
| |
|
| Source name |
MAM with control Ab
|
| Organism |
Mus musculus |
| Characteristics |
strain background: FVB
genotype/variation: wild-type
treated with: control antibody
phenotype: pro-metastatic, control antibody
cell type: metastasis-associated macrophages (MAM)
|
| Growth protocol |
Metastasis associated macrophage were FACS sorted from mice bearing pulmonary metastasis of breast tumor cells treated with Ctrl and MF1 antibody
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the RNeasy Mini kit (Qiagen Inc., Valencia, CA, USA) and DNA was removed by on-column DNase digestion with the RNase-Free DNase set (Qiagen). RNA was amplified with Ambion MessageAmp II aRNA kit (Invitrogen, Grand Island, NY, USA). RNA quality and concentration was determined by analysis with an Agilent 2100 bioanalyzer at the Einstein Genomic Core Facility
|
| Label |
Cy3
|
| Label protocol |
Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.
|
| |
|
| Hybridization protocol |
Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.
|
| Scan protocol |
Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.
|
| Description |
SAMPLE 1
This sample is of FACS sorted macrophages associated with pulmonary metastasis of breast tumor from mouse treated with control antibody. It is the first of three biological replicates used in this experiment, each from separate mouse.
|
| Data processing |
The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).
|
| |
|
| Submission date |
May 13, 2015 |
| Last update date |
May 14, 2015 |
| Contact name |
Bin-Zhi Qian |
| E-mail(s) |
binzhi.qian@ed.ac.uk
|
| Organization name |
University of Edinburgh
|
| Department |
MRC Centre for Reproductive Health
|
| Street address |
47 Little France Crescent
|
| City |
Edinburgh |
| ZIP/Postal code |
EH16 4TJ |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL13179 |
| Series (1) |
| GSE68843 |
Transcriptom analysis of FLT1 regulated genes in metastasis associated macrophages |
|
