|
| Status |
Public on May 19, 2014 |
| Title |
BMDM(KO)_3h LPS_rep1 |
| Sample type |
RNA |
| |
|
| Source name |
BMDM(KO)_3h LPS
|
| Organism |
Mus musculus |
| Characteristics |
individual: mouse#3
genotype: Commd1 knockout
treatment: 3hr LPS
cell type: Bone marrow derived macrophages
|
| Treatment protocol |
Cells were treated with LPS (10ng/mL, Escherichia coli 026:B6, Sigma).
|
| Growth protocol |
BMDMs were generated by isolation of bone marrow cells from long bones, which were cultured in RPMI supplemented with 10% FCS, antibiotics (penicillin G 100μg/mL and streptomycin 100μg/mL) and Fungizone (Fisher), in the presence of GM-CSF (20ng/ml, Peprotech). Myeloid differentiation was allowed to proceed for 10 days.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was prepared by use of RNeasy Mini Kit (Qiagen).
|
| Label |
Cy3
|
| Label protocol |
Synthesis of Cy3-labeled cRNA was performed with the “Quick Amp Labeling kit, one color” (#5190-0442, Agilent Technologies) according to the manufacturer’s recommendations.
|
| |
|
| Hybridization protocol |
cRNA fragmentation, hybridization and washing steps were also carried-out exactly as recommended: “One-Color Microarray-Based Gene Expression Analysis Protocol V5.7”.
|
| Scan protocol |
Slides were scanned on the Agilent Micro Array Scanner G2565CA (pixel resolution 5 µm, bit depth 20).
|
| Data processing |
Data extraction was performed with the “Feature Extraction Software V10.7.3.1” by using the recommended default extraction protocol file: GE1_107_Sep09.xml. The single channel data generated by the Feature Extraction software were normalized and analyzed in Genespring GX software, version 12.0 (Agilent Technologies). Low expression values were raised to the constant value 15 (defined as threshold) to minimize false positive ratios. Data were log2 transformed, normalized to 75th percentile of each array according to the standard procedure in Genespring GX.
|
| |
|
| Submission date |
Dec 16, 2013 |
| Last update date |
May 20, 2014 |
| Contact name |
Oliver Dittrich-Breiholz |
| E-mail(s) |
dittrich.oliver@mh-hannover.de
|
| Organization name |
Medical School Hannover
|
| Department |
Research Core Unit Genomics
|
| Street address |
Carl-Neuberg-Str. 1
|
| City |
Hannover |
| ZIP/Postal code |
30625 |
| Country |
Germany |
| |
|
| Platform ID |
GPL11202 |
| Series (1) |
| GSE53368 |
Copper Metabolism Domain-Containing 1 Represses Genes That Promote Inflammation and Protects Mice From Colitis and Colitis-Associated Cancer |
|
