|
| Status |
Public on Jan 02, 2009 |
| Title |
skin_IFNgKO_Ystraininfected_24hrs_rep1 |
| Sample type |
RNA |
| |
|
| Source Name |
skin, IFNgKO, Y strain infected, 24 hours
|
| Organism(s) |
Mus musculus |
| Characteristics |
C.129S7(B6)-Ifngtm1Ts/J, female, 16-18g, tissue:skin, Y strain infected
|
| Treatment protocol |
mice were shaved an injected intradermally on the side flank with 100uL of saline vehicle or 10^6 T. cruzi split between 2 adjacent sites
|
| Growth protocol |
Trypomastigotes harvested from culture supernatants were washed twice in sterile 0.9 % saline prior to injection
|
| Extracted molecule |
total RNA |
| Extraction protocol |
24 hours post-injection skin surrounding the injection site was excised and snap frozen in liquid nitrogen. Frozen tissue was mixed with Trizol reagent and homogenized using the OMNI tissue homogenizer or Lysing Martrix D (QBiogene) and the FP120 machine (Savant). RNA was extracted from homogenized tissue using Trizol reagent (Invitrogen) according to manufacturer’s RNA isolation protocol. The RNA was then purified using the RNAeasy Kit (Qiagen) according to the RNA cleanup protocol.
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5ug of total RNA (Expression Analysis Technical Manual, 2001, Affymetrix)
|
| |
|
| Hybridization protocol |
Following fragmentation of 20ug of cRNA, 15 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
|
| Scan protocol |
GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 with Autoloader
|
| Description |
Gene expression data for Y strain infected IFNg-/- mice
|
| Data processing |
Genepattern Software v2.0 (43) and normalized using ExpressionFileCreator under default settings to do RMA with quartile normalization, background correction and median scaling.
|
| |
|
| Submission date |
Nov 07, 2008 |
| Contact name |
Barbara Burleigh |
| E-mail(s) |
bburleig@hsph.harvard.edu
|
| Phone |
617-432-2495
|
| Organization name |
Harvard School of Public Health
|
| Department |
Immunology and Infectious Diseases
|
| Street address |
665 Huntington Ave
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
|
| Platform ID |
GPL1261 |
| Series (1) |
| GSE13522 |
Transcriptional response in skin of mouse 24 hours after intradermal infection with Trypanosoma cruzi |
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