|
| Status |
Public on Aug 01, 2010 |
| Title |
RH_rep3 |
| Sample type |
RNA |
| |
|
| Source name |
Human Foreskin fibroblasts, infected with different strains of Toxoplasma gondii
|
| Organism |
Homo sapiens |
| Characteristics |
infection: RH
|
| Growth protocol |
Veg, RH, RH-ROP21 and RH-ROP38 parasites were cultivated using standard methods (Roos, Donald et al. 1994) harvested by syringe passage and inoculated at a 20:1 multiplicity of infection (MOI) into HFF cells. 24hs incubation was allowed before harvest and RNA isolation.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested from HFF cellsusing the RNeasy kit (Qiagen) according to the manufacturer’s instructions. RNA quality was ascertained using a spectrophotometer (NanoDrop), and confirmed with an Agilent Bioanalyzer. Only samples with comparable ratios of parasite:host RNA (deter¬mined by Agilent Bioanalyzer) were used for hybridization.
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared with the Ovation Aminoallyl RNA Amplification and Labeling System
|
| |
|
| Hybridization protocol |
Standard Illumina hybridization protocol
|
| Scan protocol |
Standard Illumina scanning protocol
|
| Description |
replicate 3
4247668011_F
Sentrix Barcode: 4247668011
Sample Section: F
|
| Data processing |
Data was average normalized, no background substraction, and differential expression determined using Illumina Bead Studio Gene expression module v 3.3 with uninfected HFF cells used as reference group. Normalization was performed across all samples. Non-compatible probes between platforms Human Ref8 V2 and V3 were automatically eliminated during normalization leaving only 15,555 human genes for analysis across all samples.
|
| |
|
| Submission date |
Jun 17, 2010 |
| Last update date |
Jun 17, 2010 |
| Contact name |
Lucia Peixoto |
| E-mail(s) |
[email protected]
|
| Phone |
5093686764
|
| Organization name |
Washington State University, Spokane
|
| Department |
College of Medicine
|
| Street address |
PO Box 1495
|
| City |
Spokane |
| State/province |
WA |
| ZIP/Postal code |
99224 |
| Country |
USA |
| |
|
| Platform ID |
GPL6104 |
| Series (1) |
| GSE22402 |
Genome-wide analysis of gene expression response upon infection with Toxoplasma gondii |
|
