|
| Status |
Public on Sep 28, 2014 |
| Title |
preAM WT d2 biological rep2 |
| Sample type |
RNA |
| |
|
| Source name |
AM from lungs of 2 PPARg fl/fl mice at d2 after birth
|
| Organism |
Mus musculus |
| Characteristics |
background strain: C57BL/6
|
| Treatment protocol |
Organs were minced and digested with 2 mg/ml of type IV collagenase (Worthington) and 0.02 mg/ml DNaseI (Sigma) at 37°C for 45 minutes and subsequently passed through a 70 μm cell strainer. Cells were stained with eF780, anti-mouse CD45, CD11c, CD11b and Siglec-F. Mature AM were sorted as eF780-CD45+CD11chighautofluorescencehighSiglec-F+ and CD11blow or CD11bhigh from 11 days old or adult Ppargfl/fl and CD11c-Cre/Ppargfl/fl mice, respectively (BD FACSAria IIIu) and pre-AM (eF780-CD45+F4/80+CD11chigh and Siglec-FintCD11bint or Siglec-FlowCD11bhigh) were sorted from 2 days old mice.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was prepared from sorted populations using Trizol extraction and PureLink RNA Mini Kit (ambion, Life Technologies Co.) according to the manufacturer's instructions.
|
| Label |
biotin
|
| Label protocol |
Sense-stranded cDNA (5 µg) was fragmented and biotin-labeled according to the standard Affymetrix protocol (GeneChip® WT Terminal Labeling and Hybridization User Manual, 2011, Affymetrix)
|
| |
|
| Hybridization protocol |
Samples were further hybridized for 20 hr at 48ºC on Affymetrix® Mouse Gene 1.1 ST Array Strip in the Affymetrix GeneAtlas Hybridization Station. Arrays were then washed and stained using Affymetrix GeneAtlas Fluidics Station.
|
| Scan protocol |
An Affymetrix GeneAtlas Imaging Station was used to measure the fluorescent intensity emitted by the labeled target.
|
| Description |
preAM
|
| Data processing |
R (version 2.15.2)/Bioconductor (version 2.11) was used to perform RMA with package "affy".
|
| |
|
| Submission date |
Aug 08, 2014 |
| Last update date |
Sep 28, 2014 |
| Contact name |
Christoph Schneider |
| Organization name |
ETH Zurich
|
| Department |
Department of Biology, Institute of Molecular Health Sciences
|
| Lab |
Molecular Biomedicine
|
| Street address |
Otto-Stern-Weg 7
|
| City |
Zurich |
| ZIP/Postal code |
8093 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL11533 |
| Series (2) |
| GSE60247 |
PPARγ controls alveolar macrophage identity [part1] |
| GSE60249 |
PPARγ controls alveolar macrophage identity |
|
