Public study designs in the metabolomic repository SetupX

Rice infection transcript vs metabolome study

Tue, 28 Jul 2009 00:00:00 -0700

A resistant rice genotype Xa21 was compared to its susceptible control background line without Xa21 under infection with Xanthomonas Oryzae pv. Oryzae strains which differ in avrXa21 activity.
Pxo99 carries avrXa21 activity, and Raxst lacks this activity

FSA Potato 2003

Fri, 30 Nov 2007 00:00:00 -0800

Selection and refinement of metabolomics tools for the assessment of 'substantial equivalence' in traditional potato cultivars and genetically modified lines.

Mitochondrial lipid oxidation Adams & Harper

Sat, 21 Feb 2009 00:00:00 -0800

-please type here your own abstract-

Fatb Induction Experiment (FatBIE)

Thu, 20 Sep 2007 00:00:00 -0700

This experiment tests the consequence of a mutation at the FatB gene (At1g08510) in the wound-response of Arabidopsis. The FatB mutant allele (fatb KD J. Ohlrogge (Plant Cell 2003, Vol 15, 1020-1033)) was obtained from Dr. Katayonn Dehesh, University of California, Davis, Davis, CA. This allele is in the Ws background.

The standardized growth conditions are as follows:

1. Seeds (between 14 and 16) are sown on media in 100 x 100 x 15mm square Falcon Petri Dishes (Fisher Scientific, catalogue #08-757-11A). Seeds were arranged on the plates in a single horizontal line at the 1-cm mark from the top of the plate.

2. Each plate contains between 20 and 25-ml of sterile MS media containing 0.1% (w/v) sucrose.

3. Prior to sowing, seeds were sterilized by treating for 1-minute at room temperature with a 300-µl solution of 50% (v/v) ethanol, this solution was removed and replaced with a 300-µl solution consisting of 1% (v/v) Tween 20 (Fischer BioReagents, catalogue #BP33750), and 50% (v/v) bleach solution (Clorox), and incubated at room temperature for 10-minutes. The seeds were then washed with three changes of 0.3-ml of sterile water.

4. Upon sowing with seeds, the plates were wrapped with Micro-pore tape (3M Health Care, catalogue #1530-0), and then stored horizontally for 4-days at 4 oC, with illumination of 1 µmol/m2.

5. On the 5th day, plates were moved to the growth room, and held in a vertical position in Plexi-glass holders for 12-days this growth room condition is explained in Table I.

6. On the 13th day, at 11:30 am local time, plates were uncovered in the growth room and leaves were wounded by piercing with an 18 gauge sterile needle (Stephanie state approximately how many piercings per leaf). Plates were then recovered with their lids and wrapped with Micro-pore tape (3M Health Care, catalogue #1530-0). Uncovering, wounding and resealing the plates took 3 minutes for each plate. All plants, including the non-wounded plants, were exposed to the air for this amount of time. Plates were then placed vertically in Plexi-glass holders at normal conditions.

7. On 13th day, at 1:30 pm (2 hours after induction) petri plates were opened and the aerial portions of these plants were harvested immediately upon plate opening.

8. Upon harvesting, plant material was quenched by immersion in liquid nitrogen and stored at 70 0C.
Dates of time line:

Event Date
Sowing of seeds 09/25/06
Move into growth room 09/29/06
Induction 10/11/06
Harvest 10/11/06
Shipment to analytical labs 11/07/06

Extraction Optimization

Sat, 12 Jan 2008 00:00:00 -0800

Steel Ball/ Glass bead + Chloroform/ Isopropanol

Mutant Experiment #3 (ME#3)

Sun, 26 Aug 2007 00:00:00 -0700

Mutant Experiment #3 (ME#3)

This experiment tests the effect of individual mutations on the metabolome of Arabidopsis.

The standardized growth conditions are as follows:

1. Seeds (between 14 and 16) are sown on media in 100 x 100 x 15mm square Falcon Petri Dishes (Fisher Scientific, catalogue #08-757-11A). Seeds were arranged on the plates in a single horizontal line at the 1-cm mark from the top of the plate.

2. Each plate contains between 20 and 25-ml of sterile MS media containing 0.1% (w/v) sucrose.

3. Prior to sowing, seeds were sterilized by treating for 1-minute at room temperature with a 300-µl solution of 50% (v/v) ethanol, this solution was removed and replaced with a 300-µl solution consisting of 1% (v/v) Tween 20 (Fischer BioReagents, catalogue #BP33750), and 50% (v/v) bleach solution (Clorox), and incubated at room temperature for 10-minutes. The seeds were then washed with three changes of 0.3-ml of sterile water.

4. Upon sowing with seeds, the plates were wrapped with Micropore tape (3M Health Care, catalogue #1530-0), and then stored horizontally for 4-days at 4 oC, with illumination of 1 µmol/m2.

5. On the 5th day, plates were moved to the growth room, and held in a vertical position in Plexi-glass holders for 17-days this growth room condition is labeled in Table I.

6. On 18th day Petri plates were opened and the aerial portions of these plants were harvested immediately upon plate opening.

7. Upon harvesting, plant material was quenched by immersion in liquid nitrogen and stored at 70 0C.
Dates of time line:

Event Date
Sowing of seeds 02/22/2007
Move into growth room 02/26/2007
Harvest 03/14/2007
Shipment to analytical labs 04/18/2007

Canada Samples

Tue, 24 Feb 2009 00:00:00 -0800

University of Ottawa

Mutant Experiment #4 (ME#4)

Thu, 20 Sep 2007 00:00:00 -0700

This experiment tests the effect of individual mutations on the metabolome of Arabidopsis.

The standardized growth conditions are as follows:

1. Seeds (between 14 and 16) are sown on media in 100 x 100 x 15mm square Falcon Petri Dishes (Fisher Scientific, catalogue #08-757-11A). Seeds were arranged on the plates in a single horizontal line at the 1-cm mark from the top of the plate.

2. Each plate contains between 20 and 25-ml of sterile MS media containing 0.1% (w/v) sucrose.

3. Prior to sowing, seeds were sterilized by treating for 1-minute at room temperature with a 300-µl solution of 50% (v/v) ethanol, this solution was removed and replaced with a 300-µl solution consisting of 1% (v/v) Tween 20 (Fischer BioReagents, catalogue #BP33750), and 50% (v/v) bleach solution (Clorox), and incubated at room temperature for 10-minutes. The seeds were then washed with three changes of 0.3-ml of sterile water.

4. Upon sowing with seeds, the plates were wrapped with Micropore tape (3M Health Care, catalogue #1530-0), and then stored horizontally for 4-days at 4 oC, with illumination of 1 µmol/m2.

5. On the 5th day, plates were moved to the growth room, and held in a vertical position in Plexi-glass holders for 17-days this growth room condition is labeled in Table I.

6. On 18th day Petri plates were opened and the aerial portions of these plants were harvested immediately upon plate opening.

7. Upon harvesting, plant material was quenched by immersion in liquid nitrogen and stored at 70 0C.

White Wine Study: 1H-NMR / GC-TOF Comparison

Tue, 07 Jul 2009 00:00:00 -0700

In this study, seventeen white wines including Chardonnays, Viogniers, Pinot gris, Rieslings and Sauvignon blancs (which were part of a M.S. study in the Viticulture & Enology Department on white wine mouthfeel properties-- see comments below), were analyzed by both 1H-NMR and GC-TOF. Samples were prepared by solvent exchange (D2O) to get rid of the ethanol and reduce the water signal. Information obtained from the two analytical methods will be compared. Additionally, chemical data obtained will be mined with the sensory data collected to further investigate the chemical basis for mouthfeel properties in wine.

NOTE: Winery names have been removed from study design, as requested by donors.

Intestinal Samples II pre/post transplantaion

Fri, 10 Apr 2009 00:00:00 -0700

-please type here your own abstract-