|
| Status |
Public on Dec 31, 2009 |
| Title |
LPS 1d (Rag-1 null) A |
| Sample type |
RNA |
| |
|
| Source name |
mouse lung
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
genotype/variation: Rag-1 null
age: 6-8 wks old
gender: male
tissue: whole lung
treatment: LPS
time: 1d
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted with Trizol reagent followed by purification and DNase I treatment using QIAGEN RNeasy mini kit according to manufacturer's protocol. Quality control was performed with an Agilent Bioanalyzer.
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA was prepared using the Ambion MessageAmp kit for Illumina arrays.
|
| |
|
| Hybridization protocol |
Standard Illumina hybridization protocol
|
| Scan protocol |
Standard Illumina scanning protocol
|
| Description |
replicate 1
|
| Data processing |
The data were normalized using in-house software described in Grigoryev et, Identification of candidate genes in scleroderma-related pulmonary arterial hypertension. Transl Res 151(4):197-207. Briefly, the significance (P>0.95) of hybridization signals were tested and “Present” and “Absent” transcripts identified. The chip background and brightness were computed using high quartile and whole set of “Absent” hybridization signals, respectively. The expression data was stratified by experimental conditions (n=3) and hybridization of each transcript was evaluated. The transcripts that had P>0.95 and produced signal at least twice as high as that of background in at least 75% of hybridizations in any given group of mice were considered Present. The signal intensity values of these transcripts from each chip were background adjusted and divided by a chip brightness coefficient for normalization. Only Present values are reported and used for Significance Analysis of Microarrays (SAM) analysis.
|
| |
|
| Submission date |
Jul 27, 2009 |
| Last update date |
Oct 19, 2010 |
| Contact name |
Dmitry N Grigoryev |
| E-mail(s) |
[email protected]
|
| Phone |
410 550 1557
|
| Organization name |
JHU
|
| Lab |
HopGene
|
| Street address |
|
| City |
Baltimore |
| State/province |
MD |
| ZIP/Postal code |
21224 |
| Country |
USA |
| |
|
| Platform ID |
GPL4865 |
| Series (1) |
| GSE17355 |
Regulatory T cell-mediated resolution of lung injury: Identification of potential target genes via expression profiling |
|
