Difference between revisions of "Physco growth conditions mapped to EO"
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| + | Go back to: [[Cosmoss-_Physcomitrella]] page | ||
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| + | Also see [http://www.cosmoss.org/ Cosmoss], the ''Physcomitrella patens'' resource site. | ||
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| + | [https://docs.google.com/spreadsheet/ccc?key=0Ar1O1Y7eIKhsdGx4SUh6cTV0bmJxSWRyTmQ1Z3FEV0E Phsyco_mapping] | ||
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| + | Go to:[[Background info on Physco biology and culture]] | ||
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'''List from MH (08/25/2011, by email)''' | '''List from MH (08/25/2011, by email)''' | ||
We did: | We did: | ||
| − | + | * germinating spores PO:0025017 | |
| − | + | * protonema PO:0030003, here we have the protonema in liquid culture (minmal medium and full medium) and on agar (solid) | |
| − | + | * gametophore (early stage) PO:0030018 | |
| − | + | * gametophores (later stage, gametangia visible) PO:0030018, here we also have data for a strain collected here in Germany from Freiburg Reute (I hope this ill find a place in the PO) | |
| − | + | * non-vascular leaf PO:0025075 | |
| − | + | * protoplasts PO:0000006 | |
At the moment all the experiments are assigned to a specific plant anatomy but they could also be added at the corresponding growth stage. As for the protonema I'm not sure if the different growth conditions can somehow be included. If not we would prefer to add the protonema in minimal medium liquid culture. | At the moment all the experiments are assigned to a specific plant anatomy but they could also be added at the corresponding growth stage. As for the protonema I'm not sure if the different growth conditions can somehow be included. If not we would prefer to add the protonema in minimal medium liquid culture. | ||
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Here follows the list of stress treatments that we have done so far: | Here follows the list of stress treatments that we have done so far: | ||
| − | + | * leaflet time series (different time points after detaching the leaflet) | |
| − | + | * sun light | |
| − | + | * strong light | |
| − | + | * dark (2 and 3 weeks) | |
| − | + | * dehydration | |
| − | + | * rehydration | |
| − | + | * UV light | |
| − | + | * Abscisic acid | |
| − | + | * botrytis infection | |
Please contact me again if the format isn't as you expected or if you have any questions. | Please contact me again if the format isn't as you expected or if you have any questions. | ||
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Manuel | Manuel | ||
| + | =Mappings to the [http://www.gramene.org/plant_ontology/ontology_browse.html#eo EO]= | ||
| − | + | * leaflet time series (different time points after detaching the leaflet) – no EO mapping. Leaflet in this case means non-vascular leaf. | |
| − | + | * sun light - EO:0007193 day light intensity | |
| − | + | * strong light - EO:0007075 high light intensity regimen | |
| − | leaflet time series (different time points after detaching the leaflet) – no EO mapping. Leaflet in this case means non-vascular leaf. | ||
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| − | sun light - EO:0007193 day light intensity | ||
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| − | strong light - EO:0007075 high light intensity regimen | ||
''LC: I would suggest reversing these two as we now have additional info about the actual light intensities. Also, these EO terms are not actually defined.'' | ''LC: I would suggest reversing these two as we now have additional info about the actual light intensities. Also, these EO terms are not actually defined.'' | ||
| − | sun light (up to 1000µmol) | + | * sun light (up to 1000µmol) |
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| − | + | * strong light (800µmol) | |
| + | * dark (2 and 3 weeks) - EO:0007270 continuous dark (no light) regimen | ||
| + | * dehydration - EO:0007404 drought environment or EO:0007383 watering regimen | ||
| + | * rehydration - EO:0007383 watering regimen | ||
| + | * UV light - EO:0007222 UV light regimen (has subtypes for UV A, B, and C) | ||
| + | * abscisic acid - EO:0007105 abscisic acid regimen | ||
| + | * Botrytis infection - EO:0007233 fungi (should request new subtype for Boytrytis) | ||
| − | Solid media: tissue culture growth media EO:0007266 | + | * Solid media: tissue culture growth media EO:0007266 |
Def'n: The treatment involving use of solid growth media for growing the plants or tissue cultured samples | Def'n: The treatment involving use of solid growth media for growing the plants or tissue cultured samples | ||
| − | liquid growth media (EO:0007265) | + | * liquid growth media (EO:0007265) |
Latest revision as of 14:52, 15 November 2011
Go back to: Cosmoss-_Physcomitrella page
Also see Cosmoss, the Physcomitrella patens resource site.
Go to:Background info on Physco biology and culture
List from MH (08/25/2011, by email)
We did:
- germinating spores PO:0025017
- protonema PO:0030003, here we have the protonema in liquid culture (minmal medium and full medium) and on agar (solid)
- gametophore (early stage) PO:0030018
- gametophores (later stage, gametangia visible) PO:0030018, here we also have data for a strain collected here in Germany from Freiburg Reute (I hope this ill find a place in the PO)
- non-vascular leaf PO:0025075
- protoplasts PO:0000006
At the moment all the experiments are assigned to a specific plant anatomy but they could also be added at the corresponding growth stage. As for the protonema I'm not sure if the different growth conditions can somehow be included. If not we would prefer to add the protonema in minimal medium liquid culture. In the files are listed all the genes that are expressed, with an normalized microarray signal higher than RPS21 (where we know from other evidences that it is expressed). We did this as we don't have confirmation by RealTime PCR for all the microarrays.
Here follows the list of stress treatments that we have done so far:
- leaflet time series (different time points after detaching the leaflet)
- sun light
- strong light
- dark (2 and 3 weeks)
- dehydration
- rehydration
- UV light
- Abscisic acid
- botrytis infection
Please contact me again if the format isn't as you expected or if you have any questions.
Best, Manuel
Mappings to the EO
- leaflet time series (different time points after detaching the leaflet) – no EO mapping. Leaflet in this case means non-vascular leaf.
- sun light - EO:0007193 day light intensity
- strong light - EO:0007075 high light intensity regimen
LC: I would suggest reversing these two as we now have additional info about the actual light intensities. Also, these EO terms are not actually defined.
- sun light (up to 1000µmol)
- strong light (800µmol)
- dark (2 and 3 weeks) - EO:0007270 continuous dark (no light) regimen
- dehydration - EO:0007404 drought environment or EO:0007383 watering regimen
- rehydration - EO:0007383 watering regimen
- UV light - EO:0007222 UV light regimen (has subtypes for UV A, B, and C)
- abscisic acid - EO:0007105 abscisic acid regimen
- Botrytis infection - EO:0007233 fungi (should request new subtype for Boytrytis)
- Solid media: tissue culture growth media EO:0007266
Def'n: The treatment involving use of solid growth media for growing the plants or tissue cultured samples
- liquid growth media (EO:0007265)
