|
| Status |
Public on Jan 01, 2022 |
| Title |
KO_u_rep2 |
| Sample type |
RNA |
| |
|
| Source name |
LPS unstimulated miR-155 KO DC cells replicate2
|
| Organism |
Mus musculus |
| Characteristics |
cell type: Cultured bone marrow cells
gender: male
strain: C57BL/6Jax
genotype/variation: miR-155 KO
|
| Treatment protocol |
On day 7, cells were stimulated in 100 ng/mL LPS and after 16 h, DC from both unstimulated samples and stimulated samples were sorted by FACS also verifying their inflammatory status by CD86 expression. RNA from WT- and miR-155 KO DC, either unstimulated (CD86-) or LPS-stimulated (CD86+) was isolated and used for agilent microarray analysis.
|
| Growth protocol |
Bone marrow cells were cultured in 40 ng/mL GM-CSF enriched media for 7 days.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted by using the miRMeasy kit (Qiagen, 217004), following the manufacturer’s protocol. Additional on-column DNase digestion was performed. The total RNA was quatified by a NanoDrop-1000 spectrophotometer and RNA quality was established by an Agilent 2100 Bioanalyzer (Agilent Technologies).
|
| Label |
Cy3
|
| Label protocol |
Cyanine-3 (Cy3) labeled cRNA was prepared using Low Input Quick Amp Labeling Kit, One-Color (Agilent, 5190-2305) according to manufacturer’s instructions (One-Color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labeling v6.5, May 2012), followed by RNAeasy column purification (Qiagen, 4106).
|
| |
|
| Hybridization protocol |
Hybridization and washing were done using Agilent Gene Expression Hybridization Kit (Agilent, 5188-5242) and Agilent Wash Buffer Kit (Agilent, 5188-5327) according to manufacturer’s protocols (One-Color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labeling v6.5, May 2012).
|
| Scan protocol |
Slides were scanned (after washing) on the Agilent Microarray Scanner (G2565CA) using one color scan setting for 4x 44k array slides (Profile: AgilentHD_GX1col, resolution: 5 μm).
|
| Description |
Gene expression of GM-CSF cultured and LPS treated DC cells
|
| Data processing |
The scanned images were analyzed with Feature Extraction Software using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. Further data processing was done using GeneSpring GX Software v12.0
|
| |
|
| Submission date |
Aug 10, 2012 |
| Last update date |
Jan 01, 2022 |
| Contact name |
Yoko Fukuda Yuzawa |
| Organization name |
Max-Planck Institute of Immunobiology
|
| Street address |
Stübeweg 51
|
| City |
Freiburg |
| ZIP/Postal code |
79108 |
| Country |
Germany |
| |
|
| Platform ID |
GPL7202 |
| Series (1) |
| GSE40027 |
GM-CSF cultured and LPS stimulated WT and miR-155 KO DC |
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