|
| Status |
Public on Nov 23, 2008 |
| Title |
Trial1 Subject ID 1906 Day 3 |
| Sample type |
RNA |
| |
|
| Source name |
T1_1906_Day_3
|
| Organism |
Homo sapiens |
| Characteristics |
PBMC
T Cell Activation: 11.5
Neuralizing Antibody Titer: 160
Time: 3
Trial: 1
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Following PMBC isolation from CPT, 2 x 106 cells were lysed in 1 ml of TRIzol and stored at -80C (Cat# 15596-026; Invitrogen Life Technologies). After all time points were collected for a subject, the samples were thawed, and the RNA isolation proceeded according to the manufacturer’s protocol.
|
| Label |
Biotin
|
| Label protocol |
Total RNA sample quality was evaluated by spectrophotometer to determine quantity, protein contamination and organic solvent contamination, and an Agilent 2100 Bioanalyzer was used to check for RNA degradation. Two-round IVT amplification and labeling was performed starting with 50 ng intact, uncontaminated total RNA per sample, following the Affymetrix protocol (http://www.affymetrix.com/Auth/support/downloads/manuals/expression_print_manual.zip) (Affymetrix, CA).
|
| |
|
| Hybridization protocol |
After hybridization on Human U133 Plus 2.0 Arrays for 16 hours at 45 C and 60 rpm in a Hybridization Oven 640, slides were washed and stained with a Fluidics Station 450.
|
| Scan protocol |
Scanning was performed on a 7th generation GeneChip Scanner 3000, and the Affymetrix GCOS software was used to perform image analysis and generate raw intensity data.
|
| Description |
Gene expression from YF-17D Vaccinee
|
| Data processing |
For this analysis, we used Affymetrix Human Genome U133 Plus 2.0 Array, but instead of using Affymetrix’s sequence clusters to define genes, gene sequence clusters were RMA pre-processed and normalized with the UniGene (Build 199, January 16, 2007) Custom CDF Version 9 available from http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/CDF_download.asp to yield a list of 20,077 genes. Log2 fold changes versus day 0 (unvaccinated) of RMA pre-processed gene intensities for each subject are linked to the submission as a supplementary file.
|
| |
|
| Submission date |
Nov 05, 2008 |
| Last update date |
Nov 20, 2008 |
| Contact name |
Troy D Querec |
| Organization name |
Emory University
|
| Department |
Emory Vaccine Rearch Center
|
| Lab |
Pulendran
|
| Street address |
954 Gatewood Rd
|
| City |
Atlanta |
| State/province |
GA |
| ZIP/Postal code |
30329 |
| Country |
USA |
| |
|
| Platform ID |
GPL7567 |
| Series (2) |
| GSE13485 |
Profiling 20,077 genes in 25 vaccine recipients: U133 Plus 2.0, Custom CDF Version 9 |
| GSE13486 |
Time Course of Individuals Vaccinated with YF-17D |
|
