|
| Status |
Public on May 27, 2011 |
| Title |
SL29-mock-1 |
| Sample type |
RNA |
| |
|
| Source name |
SL-29 chicken embryonic fibroblasts, mock-infected
|
| Organism |
Gallus gallus |
| Characteristics |
cell line: SL-29 (chicken embryonic fibroblasts)
parasite strain: none (mock-infected)
time point: 24hr post-infection
|
| Treatment protocol |
SL-29 cells were infected with Toxoplasma gondii tachyzoites (prepared by syringe-lysis from infected HFFs and extensive washing in PBS) of the indicated strain at multiplicity of infection ~3; mock-infection was carried out by syringe-lysing HFFs instead of HFFs and adding equivalent volume of resuspension to SL-29 cells; 24 hours post-infection, the supernatant was removed and cells were lysed in Trizol for RNA extraction.
|
| Growth protocol |
SL-29 (ATCC CRL-1590) chicken embryonic fibroblast cells were grown to confluence in Dulbecco’s modified Eagle’s medium (30-2002; ATCC, Manassas, VA) supplemented with 5% FCS (Hyclone, Logan, UT) and 5% tryptose phosphate broth (Sigma, St. Louis, MO). Passage #<10 for all experiments performed.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol extraction of total RNA was performed according to the manufacturer's instructions.
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol for one-cycle amplification from 5 ug total RNA (GeneChip Expression Analysis Technical Manual, P/N 702232 Rev. 3, Affymetrix).
|
| |
|
| Hybridization protocol |
Following fragmentation, 10 ug of cRNA were hybridizedl on GeneChip Chicken Genome Array in Affymetrix GeneChip Hybridization Oven 640, for 16 hours at 45C, 60rpm. Arrays were washed and stained in Affymetrix Fluidics Station 450 according to manufacturer's protocol.
|
| Scan protocol |
GeneChips were scanned using the Affymetrix GeneChip Scanner 7G.
|
| Description |
Gene expression data from mock-infected SL-29s,24 hpi
|
| Data processing |
The data were normalized using Robust Multichip Average normalization and analyzed using MeV v. 4.6.1 from the TM4 software suite
|
| |
|
| Submission date |
May 26, 2011 |
| Last update date |
May 27, 2011 |
| Contact name |
Yi-Ching Ong |
| E-mail(s) |
ongyc@stanford.edu
|
| Phone |
650-723-7884
|
| Organization name |
Stanford University
|
| Department |
Microbiology & Immunology
|
| Street address |
299 W. Campus Dr.
|
| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94305 |
| Country |
USA |
| |
|
| Platform ID |
GPL3213 |
| Series (2) |
| GSE29562 |
Strain-dependent host responses in chicken embryonic fibroblasts infected with Toxoplasma gondii [ME49, CEP, and Mock] |
| GSE29565 |
Expression data from chicken embryonic fibroblasts infected with Toxoplasma gondii |
|
