|
| Status |
Public on Dec 06, 2011 |
| Title |
Basal 6h replicate 1 |
| Sample type |
RNA |
| |
|
| Source name |
peritoneal macrophages isolated from C57/BL6 mice
|
| Organism |
Mus musculus |
| Characteristics |
sample type: peritoneal macrophages isolated from wt C57/Bl6 mice by peritoneal lavage
cell type: peritoneal macrophage
genetic background: C57/Bl6
treatment: untreated
time: 6 h
|
| Treatment protocol |
Treatment of peritoneal macrophages with 1 ug/ml of recombinant histidine-rich glycoprotein during 6 and 24 hours.
|
| Growth protocol |
isolated peritoneal macrophages incubated overnight in RPMI/5% FCS
|
| Extracted molecule |
total RNA |
| Extraction protocol |
total RNA from macrophages was extracted using an Rneasy Mini kit from Qiagen
|
| Label |
biotin
|
| Label protocol |
250 nanograms of total RNA/sample were used to generate amplified and biotinylated sense-strand cDNA from the entire expressed genome according to the Ambion WT Expression Kit
|
| |
|
| Hybridization protocol |
GeneChip ST Arrays (GeneChip Mouse Gene 1.0 ST Array) were hybridized for 16 hours in a 45°C incubator, rotated at 60 rpm.
|
| Scan protocol |
The arrays were scanned using the GeneChip Scanner 3000 7G.
|
| Description |
gene expression data from peritoneal macrophages cultured for 6 h. In RPMI/5%FCS
|
| Data processing |
Subsequent analysis of the gene expression data was carried out in the freely available statistical computing language R (http://www.r-project.org) using packages available from the Bioconductor project (www.bioconductor.org). The raw data was normalized in the Affymetrix provided software Expression Console using the robust multi-array average (RMA) method. In order to search for the differentially expressed genes between the hrg-/- samples and the wt samples group an empirical Bayes moderated t-test was then applied, using the ‘limma’ package. To address the problem with multiple testing, the p-values were adjusted using the method of Benjamini and Hochberg
|
| |
|
| Submission date |
Dec 05, 2011 |
| Last update date |
Dec 06, 2011 |
| Contact name |
Sonia Tugues |
| E-mail(s) |
[email protected]
|
| Organization name |
Uppsala University
|
| Department |
Genetics and pathology
|
| Street address |
dag hammarsjöldsväg 20
|
| City |
Uppsala |
| ZIP/Postal code |
75185 |
| Country |
Sweden |
| |
|
| Platform ID |
GPL6246 |
| Series (1) |
| GSE34164 |
Expression data from isolated peritoneal macrophages treated with Histidine-rich glycoprotein |
|
