Transcript ASU_TVDC_ tech_call_Minutes_05-26-2009 final

ASU TVDC Progress Report
5/26/09
Kathryn F. Sykes and Stephen A. Johnston
Completed Milestones: 25, 26, 28 and 32, 33, 34
Active Milestones: 35, 36
Currently Inactive Milestones: 30, 37, 38
Slide 1
MILESTONE 35
Array hybridations with mouse RNAs
from virulent Schu 4 infection
& RT PCR confirmation of candidates
Gray: (sub )milestone title
Red: completed
Green: in progress
Virulent Schu 4 Samples
RT-PCR Confirmations
Initial samples
Dose-Response of Infection
Ongoing
Slide 2
Current Status
• Based on the decisions to process slides using the Agilent
hybridization chambers we have re-run duplicate LAPT
amplifications from the first rat experiment and one mouse
experiment.
• The data generated from these experiments were compared to
previous data.
Slide 3
Raw Signal Intensity
Histogram of Microarray Signals from Rat
Experiments
0
1
3
5
7
24
Slide 4
MILESTONE 36
Final integration of expression data
and informatics analysis
Gray: (sub )milestone title
Red: completed
Green: in progress
Ongoing
Slide 5
Data Acquisition from Agilent-Processed Arrays
Up-regulated
Rat
Down-regulated
Mouse
176
36
163
Rat
Mouse
202
15
188
Slide 6
Cross Comparison of Lists Between Hybridization Systems
Down-regulated
Up-regulated
Agilent
35
Static
1
19
Agilent
14
Static
1
41
Slide 7
Cross Comparison of Lists Between Hybridization Systems
Unchanged
Static
28
Agilent
5
197
Slide 8
Gene Lists from Cross Comparison Studies
Up Over Time
FTT1346
hypothetical protein
Constant
FTT1352
hypothetical protein
FTT0928c
beta-glucosidase-related glycosidase
purN phosphoribosylglycinamide
formyltransferase
hypothetical protein
lpnB (Lipoprotein)
FTT0895
FTT0612
FTT0904
Down Over Time
FTT1727c
multidrug resistance protein, membrane located
Slide 9
Upcoming Transcriptome Goals
• LAPT
• 2 New Mouse Experiments (> 1-2000 CFU at T1)
• 1 New Rat Experiment
• Gene Selection and qPCR verification
• Final 10 candidates selected
Slide 10
Action Items
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ASU will look at compilation of all microarray data, but with higher
confidence with Agilent generated data.
UNM will send mouse and rat RNAs to ASU during week of 6/01/09. The
SCHU S4 titers will be higher in the lung RNAs, than prior kinetic series of
lung RNAs
UNM can make more SCHU S4 genomic DNA as ASU requests it.
Within 2 weeks of receiving the new RNAs from UNM, ASU anticipates
being done with all arrays and will start picking genes in June.
Mitch: is working on edits to MS 33 MSCR and the SOP
Mitch: is working on the MS 34 MSCR and has all that he needs from Terry
Wu for MSCR 34.
Mitch: is working on the MS 35 MSCR in advance.
Barbara: On 5/28/09, emailed to Freyja and Malu, Phillip Stafford’s reanalysis of the Ft polypeptide screening data in the NHP ELIspot with notes
on the data organization in the presentation.
Slide 11