|
| Status |
Public on Jul 01, 2014 |
| Title |
Kidney_LPS+vehicle_rep.3 |
| Sample type |
RNA |
| |
|
| Source name |
Kidney tissue, LPS
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6J
tissue: kidney
gender: male
treatment: LPS
|
| Treatment protocol |
LPS
Mice subjected to LPS and (mod)IVIg or vehicle controls.
|
| Growth protocol |
Animal experiments were carried out after approval of the local ethics committee.
Animal experiments were carried out after approval of the local ethics committee. Male 20 to 30 weeks old C57BL/6 Jackson mice were used.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Standard
Liver and kidney homogenates were obtained by standard protocols. Blood was processed with the RNeasy® Mini Kit from Qiagen in accordance to the Purification of Total RNA from Animal Cells Using Spin Technology protocol and the Purification of Total RNA from Animal Tissues protocol, respectively. RNA concentration and purity were determined and quality control was performed with the automated electrophoresis system ExperionTM (Bio-Rad Laboratories) according to the manufacturer’s specifications.
|
| Label |
biotin
|
| Label protocol |
Amplification and biotinylation of RNA were carried out using the TargetAmp™-Nano Labeling Kit for Illumina® Expression BeadChip® (Epicentre).
|
| |
|
| Hybridization protocol |
Hybridization was in agreement with the Whole-Genome Gene Expression protocol from Illumina.
|
| Scan protocol |
Illumina mouseRef8 V2 chips were scanned using the BeadArray Reader 500 X from Illumina.
|
| Description |
in vivo
|
| Data processing |
Raw data were obtained using GenomeStudio (v 1.9.0) and annotation by MouseRef-8_V2_0_R3_11278551_A.bgx.xml. Robust spline normalization (rsn) and detection filtering were performed via the lumi package within Bioconductor and R. Each organ was processed separately. One sample from kidney and one samples from blood did not pass quality control and were removed. Filtering of differentially expressed genes was conducted by linear model approaches with LIMMA and its moderated t-statistics (empirical Bayes).
|
| |
|
| Submission date |
Mar 07, 2014 |
| Last update date |
Oct 01, 2015 |
| Contact name |
S. Lambeck |
| Organization name |
JUH
|
| Street address |
Erlanger Allee 101
|
| City |
Jena |
| ZIP/Postal code |
07743 |
| Country |
Germany |
| |
|
| Platform ID |
GPL6885 |
| Series (1) |
| GSE55694 |
Murine study of combined LPS and modified immunoglobulins associated gene expression changes in vivo |
|
