Tissue culture of Xenopus cell lines S3, XTC (Stukenberg lab) and Small Molecules for Xenopus Research: Difference between pages

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Protocol submitted by VGP from Stukenberg lab protocols [http://www.xenbase.org/community/person.do?method=display&personId=1311&tabId=0]
==Notice to our users==
Please help us to improve this small molecules wiki and our other wikis by registering for a wiki account through our normal feedback email.


==Important small molecule references==
*[http://www.xenbase.org/literature/article.do?method=display&articleId=35021 Database of Small Molecules by Feldman and Hogue 2006] at [https://pubchem.ncbi.nlm.nih.gov/ PubChem]
*[http://www.xenbase.org/literature/article.do?method=display&articleId=47903 Wnt/Notch by Myers and Krieg 2014]
*[http://www.xenbase.org/literature/article.do?method=display&articleId=970 Ubiquitin-proteasome by Salic and King 2005]


link to protocol page [http://people.virginia.edu/~djb6t/LabWeb/frogs.htm]
==Alphabetical List of Small Molecules With Literature References==


Tissue Culture Care Instructions for Xenopus cell lines:  S3, XTC
*[[11-cis retinal]]
*[[18alpha-glycyrretinic acid]]
Media:  L-15 Medium (Leibovitz), Sigma-Aldrich product # L4386.  This comes in powder form, which we resuspend to a 66% solution (dissolve one 14.7g/L vial into 1.4L ddH2O and pH to 7.6)
*[[3,3,5-triiodothyronine (T3)]]
New media must be filter sterilized into sterile bottles. We usually use Nalgene 500mL receiver bottles and  Store media at 4˚C. 
*[[5HT (seratonin)]]
Before use with cells, you must add 10% FBS (fetal bovine serum),  1X Penn/Strep (antibiotic, comes as 100X stock), and 1X Sodium Pyruvate (also a 100X stock)
*[[activin]]
Notes: Antibiotics are good for about 1 month, so if you’re using your media for longer than that, re-supplement it accordingly.
*[[AG1296]]
*[[AG1879]]
Getting started:
*[[AGN193109]]
Keep everything sterile.  Don’t use non-autoclaved tips, coverslips, or pipets.  Make sure all dishes are sterile. 
*[[alpha-amanitin]]
Warm the media and trypsin (if using) to room temperature.  (I do this 30-60 minutes before I have hood time).
*[[anandamide]]
Make sure the UV light has been on in the hood you’re about to use.  Before use, turn off the UV and turn on the blower. Spray gloved hands with 70% EtOH. Wipe down the surface of the hood with 70% EtOH.  Spray down and wipe all bottles, (basically anything going into the hood) with 70% EtOH.
*[[apelin]]
*[[aphidicolin]]
Splitting/Passaging Cells:
*[[AZD1480]]
Remove media. Wash cells with 3-5mL of sterile Dulbecco’s Phosphate Buffered Saline (PBS).  Remove PBS and add 2mL 1XTrypsin (red color) per 100mm plate.  Swirl around and tap plates a few times.  Let sit a few minutes.  Add appropriate amount of fresh complete media to new plates for the dilution you’ve chosen.  S3 cells grow slowly, so don’t split them too dilute if you need to use them that same week.
*[[BAPTA-AM]]
*[[BMS-453]]
Growing cells on coverslips
*[[beta-xyloside]]
Coverslips should be at the very least autoclaved or baked at 250˚C.  You can also HCl-wash and poly-lysine coat coverslips.  Cells are often happier on poly-lysine coated coverslips, so if you’re not happy with how the cells look, you may want to try these.   You can transfer coverslips to tissue culture dishes in two ways, either by tweezer (make sure it’s been cleaned well with EtOH, or by using the suction on a sterile Pasteur pipette (of course if your coverslips are in solution, this won’t work). Rinse coverslips a few times in PBS, and then add an appropriate volume of fresh media to them. Then, split your cells as normal, adding a sufficient density of cells to each well. I’d advise splitting them pretty densely so that you can use them the next day if possible. Lab lore indicates that the cells are more mitotic if you use them the next day.
*[[bumetanide]]
*[[calcium ionophore]]
Finishing up
*[[CGP54626 ]]
Remove all your materials from the hood. Make sure you’ve turned off the aspirator, thrown away all pipettes, and plugged back in the pipetaid (if necessary). Wipe down the hood with 70% EtOH. Shut the hood, and turn on the UV light.
*[[Chelerythrine]]
*[[chymostatin ]]
*[[Colcemide]]
*[[concanamycin]]
*[[cycloheximide]]
*[[cyclopamine]]
*[[Cyclosporin A]]
*[[Cytochalasin B]]
*[[cytochalasin D]]
*[[Colcemide|Demecolcine]]
*[[deltamethrin]]
*[[dexamethosone]]
*[[DHT(dihydrotestosterone)]]
*[[diazepam]]
*[[Ex-527]]
*[[forskolin]]
*[[fusicoccin]]
*[[gentamycin]]
*[[GM6001]]
*[[heptanol]]
*[[herbimycin A]]
*[[IBMX]]
*[[jasplakinolide]]
*[[KT 5720]]
*[[lansoprazole]]
*[[LiCl]]
*[[Mg132]]
*[[MMP-2 inhibitor II]]
*[[nicorandil]]
*[[nifedipine]]
*[[nocodazole]]
*[[NSC-87877]]
*[[o-phenanthroline]]
*[[okadaic acid]]
*[[olomoucine]]
*[[ouabain]]
*[[PD-407824]]
*[[p-MPPI]]
*[[taxol|Paclitaxel]]
*[[phaclofen]]
*[[PMA]]
*[[PP2]]
*[[primaquine]]
*[[propylthiouracil]]
*[[quinpirole]]
*[[rapamycin]]
*[[retinoic acid]]
*[[RS67333]]
*[[RU486]]
*[[SB 203580]]
*[[SCH28080]]
*[[sodium nitroprusside]]
*[[SP600125 ]]
*[[SU5402]]
*[[SU6656]]
*[[Suramin]]
*[[tautomycin]]
*[[taxol]]
*[[thyroxine (T4)]]
*[[TTNPB]]
*[[tunicamycin]]
*[[Y27632]]
*[[ZM 447439]]
 
The Following are in need of standardization and curation
*[[AP1510]]
*[[AR-A014418]]
*[[BHQ]]
*[[b-aminoproprionitrile]]
*[[beclomethasone]]
*[[Butyrate]]
*[[celastrol]]
*[[celecoxib]]
*[[chromanol 293B]]
*[[cytochalasin D]]
*[[colchicine]]
*[[diclofenac]]
*[[etoposide]]
*[[GW843682X]]
*[[latrunculin B]]
*[[methimazole]]
*[[MBCD or MBetaCD]]
*[[MS222]]
*[[nicardipine]]
*[[Nu6102]]
*[[PTU|propylthiouracil(PTU) inhibits thyroxine]]
*[[PTU|phenylthiouracil(PTU inhibits melanophore formation]]
*[[purmorphamine]]
*[[Pyrazoleanthrone]]
*[[R(+)BayK 8644]]
*[[RHC80267]]
*[[RL-3]]
*[[SB-431542]]
*[[SB505124]]
*[[TG003]]
*[[Thapsigargin]]
*[[Trichostain A]]
*[[U0126]]
*[[U73122]]
*[[Echinomycin]]
*[[Gö 6983]]
*[[phenylhydrazine]]
 
==List of Molecules Affecting Specific Pathways==
===cAMP===
*[[IBMX]]
*[[RU486]]
 
===CDK/Cyclins===
*[[olomoucine]]
 
===ERK/MAPK===
*[[U0126]]
 
===JAK/STAT===
*[[AZD1480]]
 
===JNK===
*[[SP600125]]
*[[Pyrazoleanthrone]]
 
===Nitric Oxide===
*[[sodium nitroprusside]]
 
===PDGF===
*[[AG1296]]
*[[AP1510]]
 
===Retinoic Acid===
*[[AGN193109]]
*[[retinoic acid]]
*[[TTNPB]]
*[[BMS-453]]
 
===Shh===
*[[cyclopamine]]
*[[purmorphamine]]
 
===TGF-beta/BMP===
*[[SB-431542]]
*[[SB505124]]
 
===Thyroid Signaling===
*[[PTU]]
 
===Wnt===
*[[LiCl]]
 
===Epigenetics===
*[[Ex-527]]
 
===Protease Inhibitors===
*[[chymostatin]]
*[[GM6001|GM6001 (MMP inhibitor)]]
*[[o-phenanthroline|o-phenanthroline(MMP inhibitor)]]
*[[BB-94|BB-94 MMP inhibitor]]
*[[GI254023X| GI254023X MMP10 inhibitor]]
 
==Small Molecules by Biological Function==
===Angiogenesis===
*[[herbimycin A]]
*[[Suramin]]
 
===Apoptosis===
*[[cycloheximide]]
*[[alpha-amanitin]]
*[[Cyclosporin A]]
*[[2,2ʹ-Methylenebis(1,3-cyclohexanedione)]]
*[[NS3694]]
 
===Autophagy===
*[[LY-294002]]
 
===Calcium Signaling===
*[[nifedipine]]
*[[R(+)BayK 8644]]
*[[nicardipine]]
*[[deltamethrin]]
*[[BHQ]]
*[[Thapsigargin]]
 
===Circadian Rhythm===
*[[quinpirole]]
 
===Cytoskeletal Inhibitors===
*[[Cytochalasin B]]
*[[cytochalasin D]]
*[[Colcemide]]
*[[jasplakinolide]] is an activator
*[[taxol]]
*[[taxol|Paclitaxel]]
 
===Cell Cycle, including mitosis===
*[[Colcemide]]
*[[olomoucine]]
*[[PD-407824]]
 
===DNA Damage/Repair===
*[[etoposide]]
 
===Growth Cone, Filopodia, and other Cytoskeletal projections===
*[[PP2]]
*[[SU6656]]
*[[cytochalasin D]] 0.1 uM Sigma
*[[latrunculin B]] 30nM Sigma
*[[colchicine]] 12.5uM Sigma
*[[nocodazole]] 0.1uM Sigma
*[[RHC80267]]
 
===Hatching===
*[[ouabain]]
 
===Metamorphosis===
*[[3,3,5-triiodothyronine (T3)]]
*[[methimazole]]
*[[propylthiouracil]]
*[[thyroxine (T4)]]
 
===Neurotransmission===
*[[diazepam]]
*[[p-MPPI]]
*[[phaclofen]]
*[[RS67333]]
*[[deltamethrin]]
 
===Protein Recycling===
*[[primaquine]]
 
==Drugs by Gene Class==
 
===Channels, including ATPases===
*[[ouabain]]
===G Protein Receptors===
*[[purmorphamine]]
===Kinases===
*[[KT 5720]]
*[[olomoucine]]
*[[PD-407824]]
*[[SB 203580]]
*[[Y27632]]
*[[ZM 447439]]
 
===Phosphatases===
*[[Cyclosporin A]]
*[[deltamethrin]]
*[[okadaic acid]]
*[[tautomycin]]
 
===Small GTPases===
 
 
===Protein Synthesis===
*[[anisomycin]] 40uM Sigma
*[[cycloheximide]] 40uM
 
==Textpresso Small Molecules to Research==
*[http://www.xenbase.org/literature/article.do?method=display&articleId=43038 importazole inhibits importin]
*[http://www.xenbase.org/literature/article.do?method=display&articleId=42068 M119]
*[http://www.xenbase.org/literature/article.do?method=display&articleId=42068 GBG or GBetaGamma or G Protein Beta Gamma]
*[[LY-294002| LY-294002 inhibits PI3K and autophagy]]
 
==Models of Anemia==
*[phenylhydrazine]

Revision as of 12:56, 8 August 2016

Notice to our users

Please help us to improve this small molecules wiki and our other wikis by registering for a wiki account through our normal feedback email.

Important small molecule references

Alphabetical List of Small Molecules With Literature References

The Following are in need of standardization and curation

List of Molecules Affecting Specific Pathways

cAMP

CDK/Cyclins

ERK/MAPK

JAK/STAT

JNK

Nitric Oxide

PDGF

Retinoic Acid

Shh

TGF-beta/BMP

Thyroid Signaling

Wnt

Epigenetics

Protease Inhibitors

Small Molecules by Biological Function

Angiogenesis

Apoptosis

Autophagy

Calcium Signaling

Circadian Rhythm

Cytoskeletal Inhibitors

Cell Cycle, including mitosis

DNA Damage/Repair

Growth Cone, Filopodia, and other Cytoskeletal projections

Hatching

Metamorphosis

Neurotransmission

Protein Recycling

Drugs by Gene Class

Channels, including ATPases

G Protein Receptors

Kinases

Phosphatases

Small GTPases

Protein Synthesis

Textpresso Small Molecules to Research

Models of Anemia

  • [phenylhydrazine]