|
| Status |
Public on Dec 08, 2012 |
| Title |
Human iDC control no stimulation, replicate 1 |
| Sample type |
RNA |
| |
|
| Source name |
Human iDC control_no stimulation
|
| Organism |
Homo sapiens |
| Characteristics |
tissue source: peripheral blood mononuclear cells
responder cells: immature dendritic cells (iDCs)
|
| Treatment protocol |
On day 7 iDCs were either left without stimulation (2 control samples) or stimulated with 1 mg/l human recombinant IL-8 (2 IL-8 samples) or with recombinant Brugia malayi AsnRS (2 samples rBmAsnRS). After 48 hours, cells were harvested, pelleted and frozen at -86*C (in TRIzol) for RNA extraction.
|
| Growth protocol |
Human immature dendritic cells (iDCs) were generated from CD14+ cells isolated from human peripheral blood mononuclear cells, cultured in 6 well plates for 5 days with 50 ng/ml of IL-4 and GM-CSF (1000 IU/ml).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted and amplified using an Affymetrix two-cycle cDNA synthesis kit (Affymetrix, Santa Clara, CA).
|
| Label |
biotin
|
| Label protocol |
cRNA was synthesized, labeled, fragmented, and hybridized to an array in accordance to the Affymetrix GeneChip expression analysis technical manual.
|
| |
|
| Hybridization protocol |
The GeneChip human genome U133 plus 2.0 array was selected for these studies for its overall comprehensive coverage.
|
| Scan protocol |
After hybridization, arrays were washed and stained with Affymetrix fluidics protocol FS450_0001 and scanned with a 7G Affymetrix GeneChip Scanner
|
| Description |
Ctrl KRON14
|
| Data processing |
Image data were analyzed with Affymetrix Expression Console™ software and normalized with Robust Multichip Analysis (RMA; www.bioconductor.org/) to determine signal log ratios. The mean fold change was calculated from the 2 independent biological replicates for each of the 3 experimental conditions (6 arrays total). The statistical significance of differential gene expression and false discovery rates (FDR) were derived through a Rank Product algorithm available as an analysis package in BioConductor (RankProd, www.bioconductor.org/).
|
| |
|
| Submission date |
Aug 08, 2012 |
| Last update date |
Dec 08, 2012 |
| Contact name |
Michael Andrew Kron |
| E-mail(s) |
[email protected]
|
| Phone |
414 955 5613
|
| Fax |
414 955 6568
|
| Organization name |
Medical College of Wisconsin
|
| Department |
Medicine
|
| Lab |
BIotechnology and Bioengineering
|
| Street address |
8701 Watertown Plank Road
|
| City |
Milwaukee |
| State/province |
Wisconsin |
| ZIP/Postal code |
53206 |
| Country |
USA |
| |
|
| Platform ID |
GPL570 |
| Series (1) |
| GSE39999 |
Filarial nematode AsnRS interacts with interleukin 8 receptors in iDCs but causes different gene expression patterns compared to iDCs stimulated by interleukin 8. |
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