|
| Status |
Public on Feb 25, 2010 |
| Title |
C. albicans Signature Validation Cohort_1394_3120_15446_1424 |
| Sample type |
RNA |
| |
|
| Source name |
BALB/c male mice, C.albicans Signature Validation Cohort
|
| Organism |
Mus musculus |
| Characteristics |
cohort: C.albicans Signature Validation Cohort
tissue: Whole Blood
genotype: BALB/c
age: 8 wk old
infection status: candida
infection duration (days): 1
|
| Treatment protocol |
Infection protocol: Mice were injected using a standard tail vein injection. Daily weights and twice-daily activity levels were noted to assess the clinical status of the mice. Mice were then sacrificed by CO2 asphyxiation at pre-determined time intervals of 24 (n=8 mice), 48 (n = 6 mice), 72 (n = 7 mice), and 96-hours (n = 7 mice) post injection. Control mice were also sacrificed on day 1 and day 4 and processed identically to their experimental counterparts.
|
| Growth protocol |
For C.albicans: C. albicans was grown in YPD broth for 12-17 hours at 25 °C and 225 rpm. The fungal broth was washed with sterile phosphate buffered saline (PBS) and adjusted to a dose of 2×105cfu per 200µl of inoculum.
For S.aureus: S. aureus was grown in trypticase soy broth (TSB) at 30°C and 225rpm with aeration overnight. 1-2 mL of overnight broth was suspended in 100mL of fresh TSB and shaken at 150rpm for 1-2 hours at 30°C. Once in log phase, the bacterial broth was then harvested by centrifugation, washed with sterile PBS and re-suspended in it to an OD600 of 0.20.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Whole blood RNA isolation and beta-globin reduction was carried out using the manufacturer’s protocol (Mouse Ribopure and GlobinClear, Ambion Inc).
|
| Label |
biotin
|
| Label protocol |
RNA from samples that met quality checks [260/280 ratio >1.8, 260/230 ration > 1.8 and RNA Integrity Number (RIN) > 7] was amplified and biotin-labeled using MessageAmp Premier RNA Amplification Kit (Ambion, Valencia, CA) according to standard protocols at the Duke University Microarray Core facility.
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| |
|
| Hybridization protocol |
Amplification and hybridization onto Affymetrix murine 430A2.0 microarrays were performed by Duke University Microarray Core.
|
| Scan protocol |
Probe intensities were detected using Axon Genepix 4000B Scanner (Molecular Devices, Union City, CA). Image files were generated using Affymetrix® GeneChip® Command Console® Software (AGCC).
|
| Description |
C. albicans Signature Validation Cohort
|
| Data processing |
Expression Console (Affymetrix, Santa Clara, CA) was used to ensure that microarray data intensity files met quality control parameters. Next, expression data from samples that met the quality standards were used in MATLAB to develop predictive models.
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| |
|
| Submission date |
Feb 25, 2010 |
| Last update date |
Feb 25, 2010 |
| Contact name |
Hamza Aziz |
| E-mail(s) |
ha2@duke.edu
|
| Organization name |
Duke University
|
| Department |
Institute of Genomic Science and Policy
|
| Lab |
Geoffrey Ginsburg
|
| Street address |
101 Science Drive
|
| City |
Durham |
| State/province |
NC |
| ZIP/Postal code |
27708 |
| Country |
USA |
| |
|
| Platform ID |
GPL8321 |
| Series (1) |
| GSE20524 |
Blood Gene Expression Signatures Predict Invasive Candidiasis |
|
