|
| Status |
Public on Jan 14, 2014 |
| Title |
BMDM_0.1ng_4hr_2nd |
| Sample type |
RNA |
| |
|
| Source name |
BMDM cells, low LPS
|
| Organism |
Mus musculus |
| Characteristics |
strain/background: C57BL/6
cell_type: bone-marrow-derived macrophages
lps_concentration: 0.1ng/ml
incubation_time: 4hr
experimental_replicate: 2
|
| Treatment protocol |
BMDM cells were preincubated in Hanks' balanced salt solution containing 2% FBS (v/v) at 37°C and 5% CO2 for at least 2 hours before the application of LPS (Alexis Biochemicals; Salmonella minnesota R595 TLRgrade, ALX-581-008-L002).
|
| Growth protocol |
Bone-marrow-derived macrophages (BMDMs) were differentiated from bone marrow precursors with M-CSF by standard protocols.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was purified by Qiagen RNeasy kit.
|
| Label |
biotin
|
| Label protocol |
Illumina TotalPrep RNA Amplification Kit (Ambion).
|
| |
|
| Hybridization protocol |
Standard Illumina hybridization protocol.
|
| Scan protocol |
Standard Illumina scanning protocol with Illumina HiScan-SQ.
|
| Description |
7604659025_H
Primary cultured BMDM cells.
|
| Data processing |
Signal data was extracted from the image files with the Gene Expression module (v. 1.9.0) of the GenomeStudio software (v. 2011.1) from Illumina, Inc. Signal intensities were converted to log2 scale. Probes that didn't show detection p-value < 0.1 in at least 2 arrays were removed from the dataset. After filtering probes, quantile normalization was applied across all arrays. ANOVA was performed on the normalized log2 expression estimates to test for mRNA expression differences. A p-value of 0.05 was used for the statistical significance cutoff, after adjusting for the familywise error rate (FWER) using Benjamini-Hochberg method to account for multiple testing. Statistical analysis was performed using JMP/Genomics software version 6.0.
|
| |
|
| Submission date |
Jan 03, 2014 |
| Last update date |
Jan 14, 2014 |
| Contact name |
Timothy G Myers |
| E-mail(s) |
[email protected]
|
| Organization name |
National Institute of Allergy and Infectious Diseases
|
| Department |
Research Technologies Branch
|
| Lab |
Genomic Technologies Section
|
| Street address |
50 South Drive, Room 5509
|
| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892-8005 |
| Country |
USA |
| |
|
| Platform ID |
GPL6885 |
| Series (1) |
| GSE53810 |
Switching of the Relative Dominance Between Feedback Mechanisms in Lipopolysaccharide-Induced NF-kB Signaling |
|
