|
| Status |
Public on Dec 21, 2013 |
| Title |
Sca-1- PDC, replicate 3 |
| Sample type |
RNA |
| |
|
| Source name |
Sca-1- PDC collected from in vitro culture of differentiated bone marrow precursor cells using mFlt3-L
|
| Organism |
Mus musculus |
| Characteristics |
strain: BALB/c
gender: female
cell type: plasmacytoid dendritic cells (PDC)
genotype/variation: Sca-1-
|
| Treatment protocol |
Cells were directly lysed in RA1 buffer (Macherey-Nagel).
|
| Growth protocol |
Cells were directly isolated from indicated cell culture sources by magnetic and flow cytometric cell sorting.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was isolated using the NucleoSpin® RNA II kit (Macherey-Nagel) following manufacturer's instructions.
|
| Label |
Cy3
|
| Label protocol |
100 ng of each RNA was used as template to produce Cy3- labeled cRNA. The RNA samples were amplified and labeled using the Low Input Quick Amp Labeling Kit (Agilent Technologies) following the manufacturer’s protocol.
|
| |
|
| Hybridization protocol |
Cy3 labeled cRNAs were hybridized overnight (17 hours, 65°C) to an Agilent Whole Mouse Genome Oligo Microarrays (8x60K) using Agilent’s recommended hybridization chamber and oven.Finally, microarrays were washed once with wash buffer 1 for 1 min at RT followed by a second wash with wash buffer 2 for 1 min at 37°C and a final wash step with acetonitrile for 30 sec at RT.
|
| Scan protocol |
Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent’s Microarray Scanner System (G2505C, Agilent Technologies, Palo Alto, USA).
|
| Description |
1-_0h_3
gene expression analysis of SuperAmplified™ polyA RNA
|
| Data processing |
The Agilent Feature Extraction Software (FES 10.7.3.1 ) was used to read out and process the microarray image files.
FES derived output data files were further analyzed using the Rosetta Resolver gene expression data analysis system (Rosetta Biosoftware, Rosetta error model; Lee Weng et al 2006).
|
| |
|
| Submission date |
Dec 12, 2012 |
| Last update date |
Dec 22, 2013 |
| Contact name |
Stefan Tomiuk |
| E-mail(s) |
stefant@miltenyibiotec.de
|
| Organization name |
Miltenyi Biotec GmbH
|
| Department |
Bioinformatics
|
| Street address |
Friedrich-Ebert-Str. 68
|
| City |
Bergisch-Gladbach |
| ZIP/Postal code |
51429 |
| Country |
Germany |
| |
|
| Platform ID |
GPL10787 |
| Series (1) |
| GSE42860 |
Sca-1 expression defines different developmental stages of mouse PDC that show functional heterogeneity in the endosomal but not lysosomal TLR9 response |
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