|
| Status |
Public on May 30, 2018 |
| Title |
Pam3csk4 acute, rep3 |
| Sample type |
RNA |
| |
|
| Source name |
Bone marrow derived macrophage, Pam3csk4 100ng/ml, 4hours, replicate 3
|
| Organism |
Mus musculus |
| Characteristics |
background strain: C57BL/6
gender: female
tissue: bone marrow
cell type: macrophages
strain: C57BL6
|
| Treatment protocol |
BMDMs were left untreated or stimulated with each ligand for 24 hours prior to wahing with phosphate buffered saline and the addition of fresh medium. Cells were then stimulted/re-stimulated with the appropriate TLR ligand for 4 hours prior to RNA extraction. Untreated cells were left untreated.
|
| Growth protocol |
Bone marrow derived macrophages were isolated from female 6 - 8 week C57BL/6 mice and differentiated for 7 days in L929 conditioned growth medium
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using Rneasy mini kit in combination with Qiashredders and a DNase step according to the manufacturers instructions (Qiagen).
|
| Label |
Cy3
|
| Label protocol |
Two hundred nanograms of total RNA was converted into labeled cRNA with nucleotides coupled to fluorescent dye Cy3 using the Low Input Quick Amp Kit (Agilent Technologies, Palo Alto, CA) following the manufacturer’s protocol.
|
| |
|
| Hybridization protocol |
Cy3-labeled cRNA (600 ng) from each sample was hybridized to an Agilent Mouse 8x60k Microarray. The hybridized array was then washed and scanned and data was extracted from the scanned image using Feature Extraction version 10.7 (Agilent Technologies).
|
| Scan protocol |
Cy3-labeled cRNA (600 ng) from each sample was hybridized to an Agilent Mouse 8x60k Microarray. The hybridized array was then washed and scanned and data was extracted from the scanned image using Feature Extraction version 10.7 (Agilent Technologies).
|
| Description |
Pam3csk4_3
Gene expression after toll-like receptor ligand stimulation of macrophages
|
| Data processing |
Data were pre-processed using limma R/Bioconductor package including RMA background correction, quantile normalisation and log2 transformation. Control probes were removed after normalisation. Detection threshold (log2) for Stemformatics graphing uses 95th percentile of negative control probe expression as per limma recommendation. Median expression is median (log2) of above-threshold expression of all non-control probes.
|
| |
|
| Submission date |
May 10, 2016 |
| Last update date |
Feb 27, 2019 |
| Contact name |
Othmar Korn |
| Organization name |
Australian Institute for Bioengineering and Nanotechnology
|
| Street address |
University of Queensland
|
| City |
St. Lucia |
| State/province |
Queensland |
| ZIP/Postal code |
4067 |
| Country |
Australia |
| |
|
| Platform ID |
GPL10787 |
| Series (1) |
| GSE81291 |
Comparison of gene expression in macrophages tolerised by different toll-like receptor ligands |
|
