Closed AHuffmyer closed 15 hours ago
Option 2
On Wed, Jul 31, 2024 at 4:57 PM Ariana S Huffmyer @.***> wrote:
Assigned #73 https://urldefense.com/v3/__https://github.com/urol-e5/timeseries/issues/73__;!!K-Hz7m0Vt54!kxLIdKiJxfzXbzt5B7PL9W8yhfty6VH0KfT-iVU_y_tJAjKYNXkaM-nUUw1MHhsw0ts9QnlX4AROxI1nFqjfxnE$ to @sr320 https://urldefense.com/v3/__https://github.com/sr320__;!!K-Hz7m0Vt54!kxLIdKiJxfzXbzt5B7PL9W8yhfty6VH0KfT-iVU_y_tJAjKYNXkaM-nUUw1MHhsw0ts9QnlX4AROxI1nqyheyHc$ .
— Reply to this email directly, view it on GitHub https://urldefense.com/v3/__https://github.com/urol-e5/timeseries/issues/73*event-13716251533__;Iw!!K-Hz7m0Vt54!kxLIdKiJxfzXbzt5B7PL9W8yhfty6VH0KfT-iVU_y_tJAjKYNXkaM-nUUw1MHhsw0ts9QnlX4AROxI1nETGg-pE$, or unsubscribe https://urldefense.com/v3/__https://github.com/notifications/unsubscribe-auth/ABB4PN4KLE7KOPWOJV6I3ZLZPFFSPAVCNFSM6AAAAABLZHTHH6VHI2DSMVQWIX3LMV45UABCJFZXG5LFIV3GK3TUJZXXI2LGNFRWC5DJN5XDWMJTG4YTMMRVGE2TGMY__;!!K-Hz7m0Vt54!kxLIdKiJxfzXbzt5B7PL9W8yhfty6VH0KfT-iVU_y_tJAjKYNXkaM-nUUw1MHhsw0ts9QnlX4AROxI1nzA-36-4$ . You are receiving this because you were assigned.Message ID: @.***>
Un targeted metabolite and lipid analyses at UW Northwest Metabolomics:
Assay Name | Assay Description | Platform | Metabolites | Comments |
---|---|---|---|---|
Global LC-MS | Aqueous Global Profiling | Agilent 6546 Q-TOF LC/MS | ~800 metabolite IDs + 4000+ unknown metabolites | Aqueous metabolites |
Lipid Global Profiling | Agilent 6546 Q-TOF LC/MS | >1000 lipids & >3000 unknown lipids species | Lipids |
Contact: nwmrc@uw.edu
@AHuffmyer submit request for quote
Estimate provided by UW previously including sample prep:
For untargeted and lipid analysis, you would need to provide two separate sample specimens (if possible) since these two assays require totally different sample prep. Our prices per sample are
Quantitative Lipidomics: $99 MS runs + $27 tissue sample prep + $15 BCA protein assay (needed for data normalization) = $141 TOTAL per sample
Global (untargeted) LC-MS profiling: $112 for LC-MS runs + $27 tissue sample prep + $15 BCA protein assay (needed for data normalization) = $154 TOTAL per sample
@AHuffmyer how much sample do we need compared to what Javi needs for the histone work and compared to the average size of nubbin we have?
@jarcasariego How much tissue do you require?
I'll inquire with UW for tissue input.
They recommend 5-10mg of tissue for each assay (will need 10-20 mg tissue for metabolomics and lipidomics). Some of the images of the frozen fragments are very small and I am worried we cannot get that much tissue.
We will need to first homogenize, separate host and symbiont, and lyophilize host fraction. The lyophilized host fraction is what we would submit.
Waiting to get more information from UW facility to ask a few more detailed questions and will chat with Javi about quantity needed for histone work.
If we are limited by tissue, we will need to decide if histone work or metabolomics/lipidomics is higher priority.
Here is an update on the analysis and information provided from UW:
Quoted sample prices are:
Total price per sample for lipidyzer is $129 (includes MS data acquisition + sample prep + BCA assay for data normalization) and for targeted LC-MS is $134 (includes MS data acquisition + sample prep + BCA assay for data normalization).
Total for both analyses per sample is $263.
Example data output from the targeted analysis of metabolites and lipids from UW.
2024-06-28_DataSample_Tissue.xlsx 2024-05-20_TargetedData-Tissue.xlsx
Test samples received at UW, will follow up with group when results are in hand to make decisions on next steps.
Decision that needs to be made at the bottom of this description
Request quote from UW Metabolomics for metabolomic and lipidomic analysis of time series samples:
Samples
Samples:
Species
Sites
Time points
Many samples were missing from time point 2 from Acropora (5 out of 10 colonies missing TP2) and Pocillopora (7 out of 10 colonies missing TP2). We do have all time point 2 samples for Porites (0 out of 10 colonies missing TP2).
Decision that needs to be made:
Option 1: Only process TP1, TP3, and TP4 samples for all species = 86 total samples (approx. $22,274).
Option 2: Process TP1, TP3, and TP4 for POC and ACR with all time points for POR = 96 total samples (approx. $24,864).
Are these options in the budget? If so, do we want to go with Option 1 or Option 2? If we have the budget, Option 2 would get us the most data, particularly for Porites.
@sr320 @hputnam do you have a preference for Option 1 or 2?