http://wiki.docking.org/api.php?action=feedcontributions&user=Wendywilson&feedformat=atomDISI - User contributions [en]2024-03-29T15:58:05ZUser contributionsMediaWiki 1.39.1http://wiki.docking.org/index.php?title=File:Cas9_stable_cell_line.png&diff=10543File:Cas9 stable cell line.png2018-03-02T03:50:35Z<p>Wendywilson: CRISPR/Cas9 system used for genome engineering in molecular biology is composed of two components: sgRNA which is a combine of original trRNA and crRNA, and Cas9 endonuclease. By delivering Cas9 and sgRNA into a cell, Cas9 is targeted to a given locus ...</p>
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<div>CRISPR/Cas9 system used for genome engineering in molecular biology is composed of two components: sgRNA which is a combine of original trRNA and crRNA, and Cas9 endonuclease. By delivering Cas9 and sgRNA into a cell, Cas9 is targeted to a given locus based on sequence complementary between sgRNA and cell genome, and further induces a double strand break (DSB). In the presence of donor template, the DSB can be repaired by HDR (homology-directed repair) pathway enabling precise editing such as point mutation. When DNA repair template is not provided, the cell is forced to undergo NHEJ (non-homologous end joining) pathway resulting in indels (insertions or deletions). Apart from wild-type Cas9, a few variants have been developed for reducing off-target effects or for other applications. SpCas9-HF1 is a high-fidelity variant designed to reduce non-specific DNA contacts.<br />
https://www.creative-biogene.com/product/cas9-cell-line.html</div>Wendywilsonhttp://wiki.docking.org/index.php?title=File:RcAAV_Testing.png&diff=10542File:RcAAV Testing.png2018-03-02T03:48:15Z<p>Wendywilson: While AAV vectors are engineered to be replication defective, generation of replication-competent AAV (rcAAV) can still occur during vector manufacturing by means of recombination events within the producer cells. rcAAV may develop at any step during t...</p>
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<div>While AAV vectors are engineered to be replication defective, generation of replication-competent AAV (rcAAV) can still occur during vector manufacturing by means of recombination events within the producer cells. rcAAV may develop at any step during the manufacturing process of gene therapy products. Even though vector production systems have been specifically developed to reduce the risk of rcAAV generation, there is still a significant safety concern driving the recommendations for testing for rcAAV in cell banks, vector and final product release for AAV-based gene therapy products.<br />
https://www.creative-biogene.com/Services/Custom-Viral-Service/Replication-Competent-AAV-Testing.html</div>Wendywilsonhttp://wiki.docking.org/index.php?title=File:Limiting_dilution.png&diff=10541File:Limiting dilution.png2018-03-02T03:47:22Z<p>Wendywilson: Limiting dilution analysis attempts to determine the frequency of cells having a particular function that are present in a mixed population of cells. So limiting dilution analysis is an easy-operated method that used to measure the abundance of cells a...</p>
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<div>Limiting dilution analysis attempts to determine the frequency of cells having a particular function that are present in a mixed population of cells. So limiting dilution analysis is an easy-operated method that used to measure the abundance of cells able to perform a particular function.<br />
https://www.creative-biogene.com/support/limiting-dilution-protocol.html</div>Wendywilsonhttp://wiki.docking.org/index.php?title=File:Lentivirus_transduction.png&diff=10540File:Lentivirus transduction.png2018-03-02T03:46:15Z<p>Wendywilson: How can lentiviral vectors be used to make stable cell lines?
Many lentiviral vectors insert some selectable markers, such as the puromycin resistance gene, conferring resistance to antibiotics. If these antibiotics are added to the growth medium, they...</p>
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<div>How can lentiviral vectors be used to make stable cell lines?<br />
Many lentiviral vectors insert some selectable markers, such as the puromycin resistance gene, conferring resistance to antibiotics. If these antibiotics are added to the growth medium, they kill off any cells that have not incorporated the vector and those cells that survive can be expanded to create stable cell lines. Apart from that kind of lentiviral vectors, some lentiviral vectors have some other makers such as GFP. Cells which have incorporated the vector can be separated using FACS.<br />
https://www.creative-biogene.com/support/custom-lentivirus-service.html</div>Wendywilsonhttp://wiki.docking.org/index.php?title=File:Custom_Virus.png&diff=10539File:Custom Virus.png2018-03-02T03:45:29Z<p>Wendywilson: There are several viral gene delivery systems, including adenovirus, retrovirus and lentivirus. Which one should I use for my experiments?
1) Retrovirus: requires active cell division. In addition, there is a significant risk of integration into the h...</p>
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<div>There are several viral gene delivery systems, including adenovirus, retrovirus and lentivirus. Which one should I use for my experiments?<br />
<br />
1) Retrovirus: requires active cell division. In addition, there is a significant risk of integration into the host genome, leading to mutation of genes or activation of onco-genes in the host system, which is a concern for scientists. <br />
2) Lentivirus: can infect both dividing and non-dividing cells. Like retrovirus, there is a significant risk of integration into the host genome, leading to mutation of genes or activation of oncogenes in the host system. <br />
3) Adenovirus: 100% gene delivery efficiency in most cell types including dividing and non-dividing or primary cells. There is no integration with the host system. <br />
4) AAV: has the capacity to produce high titer virus with broad spectrum of tropism in dividing and non-dividing cells and potential for long-term gene transfer with minimum immnunogenicity.<br />
https://www.creative-biogene.com/Support/Virus.html</div>Wendywilsonhttp://wiki.docking.org/index.php?title=File:Synthesize_gene.png&diff=10538File:Synthesize gene.png2018-03-02T03:43:37Z<p>Wendywilson: What is the difference between a long oligo and a synthetic gene?
Answer: Due to limitations in oligo synthesis chemistry and other practical considerations, oligos are produced as mixture of single-stranded DNA strands and are limited in length to ~20...</p>
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<div>What is the difference between a long oligo and a synthetic gene?<br />
Answer: Due to limitations in oligo synthesis chemistry and other practical considerations, oligos are produced as mixture of single-stranded DNA strands and are limited in length to ~200 bases. However, synthetic genes can extend to several thousand, double-stranded base pairs.<br />
https://www.creative-biogene.com/Support/Gene-Synthesis.html</div>Wendywilsonhttp://wiki.docking.org/index.php?title=File:Gene_service.png&diff=10537File:Gene service.png2018-03-02T03:42:49Z<p>Wendywilson: How do you deliver synthetic genes?
Answer: Creative Biogene will deliver 5.0ug plasmid DNA containing gene of interest in the vector and its bacterial stock.
https://www.creative-biogene.com/Support/Gene-Synthesis.html</p>
<hr />
<div>How do you deliver synthetic genes?<br />
Answer: Creative Biogene will deliver 5.0ug plasmid DNA containing gene of interest in the vector and its bacterial stock.<br />
https://www.creative-biogene.com/Support/Gene-Synthesis.html</div>Wendywilsonhttp://wiki.docking.org/index.php?title=File:3_UTR_Cloning.png&diff=10536File:3 UTR Cloning.png2018-03-02T03:41:52Z<p>Wendywilson: Creative Biogene has developed an advanced vector-based miRNA expression plasmids, which can help to ease the difficulty in your research. These purified and ready to transfect miRNA expression plasmids can be used for a variety of applications to down...</p>
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<div>Creative Biogene has developed an advanced vector-based miRNA expression plasmids, which can help to ease the difficulty in your research. These purified and ready to transfect miRNA expression plasmids can be used for a variety of applications to down-regulate gene expression. Besides, we can also provide miRNA mimics and inhibitors which enhance or block miRNA regulation of target gene expression. Especially miRNA inhibitors, they are designed and optimized for miRNA loss of function study.<br />
https://www.creative-biogene.com/Product/MicroRNA-3UTR-Target-Cloning</div>Wendywilsonhttp://wiki.docking.org/index.php?title=File:Ion_Channel_Function.png&diff=10489File:Ion Channel Function.png2018-01-02T04:26:14Z<p>Wendywilson: Manual patch clamp is considered the ‘gold standard’ for assessing [https://www.creative-biogene.com/Services/Drug-Discovery-Services/Ion-Channel-Screening-and-profiling-with-Functional-Assays.html ion channel function]. It measures biophysical and...</p>
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<div>Manual patch clamp is considered the ‘gold standard’ for assessing [https://www.creative-biogene.com/Services/Drug-Discovery-Services/Ion-Channel-Screening-and-profiling-with-Functional-Assays.html ion channel function]. It measures biophysical and pharmacological properties of voltage-gated and ligandgated ion channels present in cells or membrane patch or tissues with unmatched temporal resolution. It provides sufficient information to assess compound effects and distinguish various modes of action, for instance, state-dependent modulation.</div>Wendywilsonhttp://wiki.docking.org/index.php?title=File:Synthesis_gene.png&diff=10488File:Synthesis gene.png2018-01-02T04:23:40Z<p>Wendywilson: Artificial [https://www.creative-biogene.com/Services/Gene-Service/Gene-Synthesis-and-cloning-service.html gene synthesis], sometimes known as DNA printing is a method in synthetic biology that is used to create artificial genes in the laboratory.</p>
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<div>Artificial [https://www.creative-biogene.com/Services/Gene-Service/Gene-Synthesis-and-cloning-service.html gene synthesis], sometimes known as DNA printing is a method in synthetic biology that is used to create artificial genes in the laboratory.</div>Wendywilsonhttp://wiki.docking.org/index.php?title=File:Cell_line_knockout.png&diff=10487File:Cell line knockout.png2018-01-02T04:22:23Z<p>Wendywilson: Only 1 sgRNA is used to achieve [https://www.creative-biogene.com/Services/Stable-cell-line-generation/Custom-Genome-Editing-Cell-Lines.html cell line knockout]. In the case that the first sgRNA does not allow for success, we would try another from the...</p>
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<div>Only 1 sgRNA is used to achieve [https://www.creative-biogene.com/Services/Stable-cell-line-generation/Custom-Genome-Editing-Cell-Lines.html cell line knockout]. In the case that the first sgRNA does not allow for success, we would try another from the set of 3 synthesized sgRNAs.</div>Wendywilsonhttp://wiki.docking.org/index.php?title=File:GMP_virus.png&diff=10486File:GMP virus.png2018-01-02T04:20:52Z<p>Wendywilson: During a period of development, Creative Biogene has already possessed sophisticated equipments, advanced technologies and highly experienced staffs which are available to provide you with [https://www.creative-biogene.com/Services/Custom-Viral-Service...</p>
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<div>During a period of development, Creative Biogene has already possessed sophisticated equipments, advanced technologies and highly experienced staffs which are available to provide you with [https://www.creative-biogene.com/Services/Custom-Viral-Service/GMP-grade-viral-service.html GMP virus]es.</div>Wendywilsonhttp://wiki.docking.org/index.php?title=Contract_Research_Organizations&diff=9729Contract Research Organizations2016-11-18T06:00:35Z<p>Wendywilson: /* Other CROs */</p>
<hr />
<div>Contract research organizations are companies that will perform specific in vitro and in vivo assays to testing the activity of compounds or therapies. Listed here are companies that the Shoichet lab has either worked with or considered working with in the past.<br />
<br />
==[http://pdsp.med.unc.edu PDSP]==<br />
The NIMH Psychoactive Drug Screening Program run by the Roth lab at UNC Chapel Hill, has been a close collaborator in performing in vitro binding and functional assays for almost all GPCR targets and and several transporters. If the PDSP has the assay, they are typically our first choice.<br />
<br />
To submit compounds for screening:<br />
# Login to the [https://pdspdb.unc.edu/html/pdspV2/web/index.php PDSP].<br />
# Create a new request<br />
** Provide the grant number, name name, known activity and rational<br />
** Add the compounds and requested assays<br />
<br />
Here is the address to send compounds vis FedEx (good as of 11/2014)<br />
<br />
PDSP<br />
Attn: Xi-Ping Huang<br />
120 Mason Farm Rd<br />
2113 Genetic Medicine Bldg<br />
Chapel Hill, NC 27514<br />
TEL: (919)-966-8777<br />
<br />
When sending compounds provide:<br />
* Shoichet Lab<br />
* project name<br />
* compound id, amount submitted, molecular weight (they usually would like at least 10 mg)<br />
* label the vials with the ID/name and the PDSP# assigned (they will send you labels)<br />
<br />
==[https://www.eurofinspanlabs.com/Panlabs Eurofins Panlabs]==<br />
Located in Taiwan, they have 1,350 assays covering the following target classes<br />
*Cytokine/Chemokine (41)<br />
*GPCR (270)<br />
*Ion Channel (41)<br />
*Kinase (154)<br />
*Nuclear Receptor (16)<br />
*Other (15)<br />
*Phosphatase (31)<br />
*Phosphodiesterase (19)<br />
*Protease (51)<br />
*Transporter (19)<br />
They were used by both Henry Lin and Matthew O'Meara (2013-2014) and they gave reasonable results at reasonable prices.<br />
<br />
The shoichet lab contact there has been (10/14):<br />
Judy Winslow, phone #: 425-785-3736, email: JudyWinslow@eurofins.com.<br />
<br />
==[http://www.reactionbiology.com Reaction Biology]==<br />
Located in Pennsylvania, Reaction Biology specializes in Kinase assays and have a few epigenetic and other assays:<br />
*HMT/DNMT Assays<br />
*HDAC/HAT Assays<br />
*Bromodomain Assays<br />
*DUB Assays<br />
*Protease Assays<br />
*PDE Assays<br />
*CYP/hERG/Bcl/HSP90 Assays<br />
*Cell Assays<br />
*Phosphatase Assays<br />
<br />
Their tag line is ''With the largest functional kinase activity assay panel in the industry, RBC provides kinase, epigenetic, and other profiling services to over 590 companies worldwide. RBC specializes in custom assay conditions, high quality reproducible data, and outstanding service.''<br />
<br />
* ~104.00USD for 10 dose IC50 singlet curve (with 20% academic discount)<br />
*They have a minimum order of 300USD order<br />
<br />
==[http://www.carnabio.com/english CarnaBio]==<br />
Located in Japan, CarnBio has an extensive Kinase pannel of 311 targets and a 2-week turn around. Christian Laggner used them for the kinase assays in [http://www.nature.com/nchembio/journal/v8/n2/abs/nchembio.732.html (Laggner NatChemBio 2012)].<br />
<br />
==[http://www.multispaninc.com Multispan]==<br />
In Hayward CA, Multispan 230 validated GPCR assays. 320 human GPCR and 180 murine GPCR cDNAs are cloned for custom assays. Apparently Mike Keiser has used them, though if PDSP has the target/assay that is the way to go.<br />
<br />
==[http://www.chantest.com ChanTest - Now part of Charles River]==<br />
In Cleveland OH, they have a range of Ion Channel assays. Brian says we've used them before and they were reasonable.<br />
They've now been acquired by Charles River.<br />
<br />
''ChanTest has developed the world’s most complete library of validated human ion channel-expressing cell lines to serve all the ion channel needs of its pharmaceutical and biotech customers.''<br />
<br />
==[http://www.aurorabiomed.com/ion-channel-screening-assays/ Aurora Biomed]==<br />
Aurora’s product range includes automated liquid-handling equipment, atomic absorption spectrometers, atomic fluorescence spectrometers, ion channel screening technology and microwave digestion systems, increasing the efficiency of sample management in a wide range of research applications. We are headquartered in Vancouver, BC, Canada.<br />
<br />
Matt worked with Andy Hegel (andrew.hegle@aurorabiomed.com) to test compounds with patch-clamp assays for the Systems SEA project in 2014. They gave us a discount of 200$ per datapoint.<br />
<br />
<br />
==[http://www.perkinelmer.com/ PerkinElmer]==<br />
AS OF JAN 1 2015 THEY ARE DISCONTINUING THEIR ASSAY SERVICES DIVISION<br />
<br />
Large collection of in vitro services including:<br />
* Cytochrome P450<br />
* Cytokine/Chemokine Secretion<br />
* GPCRs<br />
* Ion Channels (Ligand- & Voltage-Gated)<br />
* Kinases<br />
* Nuclear Receptors<br />
* Other - Enzymes<br />
* Other - Receptors<br />
* Phosphodiesterases (PDEs)<br />
* Transporters<br />
and some in vivo services<br />
<br />
[http://www.perkinelmer.com/Catalog/Category/ID/Complete-Services-Assay-List Complete Assay Services List]<br />
<br />
==[http://optiviabio.com/ Optivia]==<br />
Specialized in transporters, based in the Bay Area.<br />
<br />
==[http://www.solvobiotech.com/ Solvo]==<br />
Specialized in transporters, based in the Bay Area.<br />
<br />
==[http://www.genscript.com/bio-assay_center.html GenScript]==<br />
They have few assays for different classes of targets<br />
<br />
In particular they have a protease panel covering over 70 proteases and can possibly develop further targets<br />
<br />
==[http://bpsbioscience.com/ BPS Biosciences]==<br />
Mostly enzymes<br />
<br />
==[http://www.invivogen.com/innate-immunity InvivoGen]==<br />
Located in San Diego, focusing on immune response<br />
<br />
Assays for Pattern Recognition Receptor activity<br />
* Toll-Like Receptors<br />
* NOD-Like Receptors<br />
* RIG-I-Like Receptors<br />
* C-type Lectin Receptors<br />
* Cytosolic dsDNA Sensors<br />
* Inflammasome<br />
* Autophagy & Innate Immunity<br />
* PRR & PAMPs Detection<br />
<br />
==[http://indigobiosciences.com/screening-services/nuclear-receptor-assays/ INDIGO Biosciences]==<br />
Located in Pennsylvania, they can do nuclear hormone assay.<br />
<br />
3,500 minimum order size e.g. 1 compound at 5 receptors at 10 doses each<br />
<br />
==[http://www.soralabs.com/services/ Sora Labs]==<br />
It looks like they have some enzyme assays that they can run.<br />
<br />
==[http://www.fluofarma.com/ FlouFarma]==<br />
Located in France, high content screening of live cells<br />
<br />
==[http://www.cytoskeleton.com/custom-services/compound-screening Cytoskeleton]==<br />
Compound screening against tubulin, microtubule, myosin, sarcomere, kinesin and small G-proteins.<br />
<br />
==[https://www.caymanchem.com/app/template/services%2CHome.vm Cayman Chemical]==<br />
* Assay Services<br />
Biochemists with experience in the areas of eicosanoids, steroids, oxidative stress, and inhibitor screening<br />
Use Cayman’s extensive line of well-characterized biochemical kits<br />
Enzyme immunoassay, colorimetric, and fluorometric assays available<br />
* Screening Services<br />
Comprehensive screening laboratory focused on epigenetics<br />
Backed by our core strengths in protein production, assay development, chemical synthesis, and medicinal chemistry<br />
Capacity to test compounds at a rate of up to 100,000 compounds per week<br />
Ability to profile compounds against a broad epigenetic enzyme panel<br />
Includes assays for methyltransferases, demethylases, acetyltransferases, deacetylases (HDACs and SIRTS), and histone code readers (ex. bromodomain proteins)<br />
<br />
==[http://www.discoverx.com/ DiscoveRx]==<br />
GPCR, Kinases, Nuclear Receptors, Epigenetic Targets and Signaling Pathways<br />
<br />
==[http://www.hdbiosciences.com/EngHTS.htm HD Biosciences]==<br />
HD Biosciences Co., Ltd. is a Shanghai-based, biology-focused preclinical drug discovery contract research organization (CRO). They do hit identification, hit-to-lead, assay development in major target classes, such as GPCRs, kinases, ion channels and transporters, and in a high-throughput screening format using plate-based platforms. Our screening capabilities span from cell line generation, biochemical, and cell-based functional assays for receptors, enzymes and ion channels in a variety of techniques, including:<br />
<br />
* Fluorescence (e.g. HTRF, FP, FRET, FLIPR, Flexstation) <br />
* Absorbance <br />
* Luminescence (e.g. luciferase, b-lactamase, deGFP, reporter gene)<br />
* Radiometrics (e.g. SPA, MicroBeta, Filtration) <br />
* Electrophysiology (e.g. patch clamps) <br />
* ImageXpress (e.g. live cell image HCA/HCS)<br />
<br />
<br />
==[http://www.absorption.com/resources/assay-data-sheets/ Absorption Systems]==<br />
Absorption Systems is a preclinical CRO. They have locations in Exton, PA, San Diego, CA, and Panama City, Panama. They work with a wide variety of customers in the pharmaceutical and biotech industry, including small virtual pharma companies, large pharma companies with weekly programs, and specialty CROs looking for services that complement their own offerings. In vitro and in vivo areas of speciality include:<br />
<br />
* BCS + Biowaivers<br />
* Wound healing and psoriasis disease models<br />
* Formulation<br />
* Metabolism<br />
* Permeability<br />
* Pharmacokinetics<br />
* Protein binding (e.g. fraction bound in plasma)<br />
* Toxicology<br />
* Transporters<br />
<br />
==[http://www.cyprotex.com/toxicology Cyprotex]==<br />
Cyprotex is a contract research organization specializing in preclinical ADME-Tox with offices in the UK and US.<br />
<br />
Permeability & Transporters<br />
* Caco-2 permeability<br />
* Transporter interactions<br />
* PAMPA-GI and PAMPA-BBB<br />
* MDCK and MDR1-MDCK<br />
* Transdermal absorption<br />
* Intranasal absorption<br />
<br />
Distribution - reversible/time dependent<br />
* Plasma protein binding<br />
* Whole blood binding<br />
* Blood to plasma ratio<br />
* Brain tissue binding<br />
* Microsomal binding<br />
<br />
Metabolism<br />
* Metabolic stability microsomes, hepatocytes, S9, plasma/blood<br />
* Metabolite profiling and identification<br />
* Reaction phenotyping<br />
* CYP inhibition<br />
* UGT inhibition<br />
* MAO inhibition<br />
* CYP induction<br />
* PXR and AhR nuclear <br />
<br />
receptor activation<br />
* 3D microtissues<br />
<br />
==[http://www.brunswicklabs.com/biological-analysis Brunswick Labs]==<br />
Brunswick Laboratories is an independent, full-service bioanalytical laboratory specializing in the science of Antioxidants, Oxidative Stress, Anti-inflammatory, Synthetic and Natural Compound Bioanalysis.<br />
<br />
+1-508-281-6660<br />
blservices@brunswicklabs.com<br />
200 Turnpike Road, Southborough, MA 01772, USA<br />
<br />
* Bioavailability, BioAbsorption, and BioUptake study via Caco-2 human intestinal cells<br />
* Anti-inflammatory: LOX, COX, TNF-alpha, NFkB, Interleukins (ILs), and PGE2 as biomarkers<br />
* Oxidative Stress Analysis for biological samples<br />
* Antioxidation effect in a biological system: Nrf2, Cellular Antioxidant Assay (CAA) <br />
* Diabetes and Weight Management: insulin secretion, insulin receptor activity, glucose uptake, glucose metabolism, and carbohydrate digestion as biomarkers<br />
* Detoxification and Liver Function: Phase I and Phase II liver enzymes, liver function biomakers in serum<br />
* Energy metabolism investigation via human cells <br />
* Anti-cancer Function evaluation: cancer cell viability, proliferation, apoptosis, and invasion as biomarkers <br />
* Anti-aging Assays: SIRT-1, telomerase activity as biomarkers<br />
* Preclinical Investigations for Skin Care Products: UV protection, melanin (age spot) inhibition, anti-aging, anti-inflammatory<br />
<br />
==[http://biotoxsciences.com/In_Vitro_Services BioToxSciences]==<br />
http://biotoxsciences.com/In_Vitro_Services<br />
<br />
Based in San Diego, they have a range of in-vitro functional assays<br />
<br />
==Other CROs==<br />
* [http://www.ricerca.com Ricerca]<br />
* [http://www.amsbio.com/ amsbio] not really a CRO but apparently they can do assays<br />
* [http://stores.arraybridge.com/enzyme-assays/ ArrayBridge] The have ~850 enzymes listed that they say they have assays for, but little detail on what services they actually provide.<br />
* [http://www.sbdrugdiscovery.com/screening-assays SB Drug Discovery] 50 PDEs, 50 Ion Channels, NHRs, GPCRs, Inflammation<br />
* [http://www.discoverx.com/services/drug-discovery-development-services DiscoverRX] Kinase, Epigenetic, GPCR<br />
* [http://metislabs.com/radioligand-binding-assays.html MetisLab] Radioligand assays for GPCRs<br />
* [http://www.creative-biogene.com/ Creative Biogene] Transfected Stable Cell Lines<br />
<br />
== CRO sourcing services ==<br />
* [https://www.scienceexchange.com]<br />
* [https://www.assaydepot.com]<br />
<br />
https://www.genoway.com/services/catalog-models/mouse-knockouts.htm?utm_source=emailing&utm_medium=email&utm_content=01122015&utm_campaign=01122015</div>Wendywilsonhttp://wiki.docking.org/index.php?title=Contract_Research_Organizations&diff=9728Contract Research Organizations2016-11-18T05:57:35Z<p>Wendywilson: /* Other CROs */</p>
<hr />
<div>Contract research organizations are companies that will perform specific in vitro and in vivo assays to testing the activity of compounds or therapies. Listed here are companies that the Shoichet lab has either worked with or considered working with in the past.<br />
<br />
==[http://pdsp.med.unc.edu PDSP]==<br />
The NIMH Psychoactive Drug Screening Program run by the Roth lab at UNC Chapel Hill, has been a close collaborator in performing in vitro binding and functional assays for almost all GPCR targets and and several transporters. If the PDSP has the assay, they are typically our first choice.<br />
<br />
To submit compounds for screening:<br />
# Login to the [https://pdspdb.unc.edu/html/pdspV2/web/index.php PDSP].<br />
# Create a new request<br />
** Provide the grant number, name name, known activity and rational<br />
** Add the compounds and requested assays<br />
<br />
Here is the address to send compounds vis FedEx (good as of 11/2014)<br />
<br />
PDSP<br />
Attn: Xi-Ping Huang<br />
120 Mason Farm Rd<br />
2113 Genetic Medicine Bldg<br />
Chapel Hill, NC 27514<br />
TEL: (919)-966-8777<br />
<br />
When sending compounds provide:<br />
* Shoichet Lab<br />
* project name<br />
* compound id, amount submitted, molecular weight (they usually would like at least 10 mg)<br />
* label the vials with the ID/name and the PDSP# assigned (they will send you labels)<br />
<br />
==[https://www.eurofinspanlabs.com/Panlabs Eurofins Panlabs]==<br />
Located in Taiwan, they have 1,350 assays covering the following target classes<br />
*Cytokine/Chemokine (41)<br />
*GPCR (270)<br />
*Ion Channel (41)<br />
*Kinase (154)<br />
*Nuclear Receptor (16)<br />
*Other (15)<br />
*Phosphatase (31)<br />
*Phosphodiesterase (19)<br />
*Protease (51)<br />
*Transporter (19)<br />
They were used by both Henry Lin and Matthew O'Meara (2013-2014) and they gave reasonable results at reasonable prices.<br />
<br />
The shoichet lab contact there has been (10/14):<br />
Judy Winslow, phone #: 425-785-3736, email: JudyWinslow@eurofins.com.<br />
<br />
==[http://www.reactionbiology.com Reaction Biology]==<br />
Located in Pennsylvania, Reaction Biology specializes in Kinase assays and have a few epigenetic and other assays:<br />
*HMT/DNMT Assays<br />
*HDAC/HAT Assays<br />
*Bromodomain Assays<br />
*DUB Assays<br />
*Protease Assays<br />
*PDE Assays<br />
*CYP/hERG/Bcl/HSP90 Assays<br />
*Cell Assays<br />
*Phosphatase Assays<br />
<br />
Their tag line is ''With the largest functional kinase activity assay panel in the industry, RBC provides kinase, epigenetic, and other profiling services to over 590 companies worldwide. RBC specializes in custom assay conditions, high quality reproducible data, and outstanding service.''<br />
<br />
* ~104.00USD for 10 dose IC50 singlet curve (with 20% academic discount)<br />
*They have a minimum order of 300USD order<br />
<br />
==[http://www.carnabio.com/english CarnaBio]==<br />
Located in Japan, CarnBio has an extensive Kinase pannel of 311 targets and a 2-week turn around. Christian Laggner used them for the kinase assays in [http://www.nature.com/nchembio/journal/v8/n2/abs/nchembio.732.html (Laggner NatChemBio 2012)].<br />
<br />
==[http://www.multispaninc.com Multispan]==<br />
In Hayward CA, Multispan 230 validated GPCR assays. 320 human GPCR and 180 murine GPCR cDNAs are cloned for custom assays. Apparently Mike Keiser has used them, though if PDSP has the target/assay that is the way to go.<br />
<br />
==[http://www.chantest.com ChanTest - Now part of Charles River]==<br />
In Cleveland OH, they have a range of Ion Channel assays. Brian says we've used them before and they were reasonable.<br />
They've now been acquired by Charles River.<br />
<br />
''ChanTest has developed the world’s most complete library of validated human ion channel-expressing cell lines to serve all the ion channel needs of its pharmaceutical and biotech customers.''<br />
<br />
==[http://www.aurorabiomed.com/ion-channel-screening-assays/ Aurora Biomed]==<br />
Aurora’s product range includes automated liquid-handling equipment, atomic absorption spectrometers, atomic fluorescence spectrometers, ion channel screening technology and microwave digestion systems, increasing the efficiency of sample management in a wide range of research applications. We are headquartered in Vancouver, BC, Canada.<br />
<br />
Matt worked with Andy Hegel (andrew.hegle@aurorabiomed.com) to test compounds with patch-clamp assays for the Systems SEA project in 2014. They gave us a discount of 200$ per datapoint.<br />
<br />
<br />
==[http://www.perkinelmer.com/ PerkinElmer]==<br />
AS OF JAN 1 2015 THEY ARE DISCONTINUING THEIR ASSAY SERVICES DIVISION<br />
<br />
Large collection of in vitro services including:<br />
* Cytochrome P450<br />
* Cytokine/Chemokine Secretion<br />
* GPCRs<br />
* Ion Channels (Ligand- & Voltage-Gated)<br />
* Kinases<br />
* Nuclear Receptors<br />
* Other - Enzymes<br />
* Other - Receptors<br />
* Phosphodiesterases (PDEs)<br />
* Transporters<br />
and some in vivo services<br />
<br />
[http://www.perkinelmer.com/Catalog/Category/ID/Complete-Services-Assay-List Complete Assay Services List]<br />
<br />
==[http://optiviabio.com/ Optivia]==<br />
Specialized in transporters, based in the Bay Area.<br />
<br />
==[http://www.solvobiotech.com/ Solvo]==<br />
Specialized in transporters, based in the Bay Area.<br />
<br />
==[http://www.genscript.com/bio-assay_center.html GenScript]==<br />
They have few assays for different classes of targets<br />
<br />
In particular they have a protease panel covering over 70 proteases and can possibly develop further targets<br />
<br />
==[http://bpsbioscience.com/ BPS Biosciences]==<br />
Mostly enzymes<br />
<br />
==[http://www.invivogen.com/innate-immunity InvivoGen]==<br />
Located in San Diego, focusing on immune response<br />
<br />
Assays for Pattern Recognition Receptor activity<br />
* Toll-Like Receptors<br />
* NOD-Like Receptors<br />
* RIG-I-Like Receptors<br />
* C-type Lectin Receptors<br />
* Cytosolic dsDNA Sensors<br />
* Inflammasome<br />
* Autophagy & Innate Immunity<br />
* PRR & PAMPs Detection<br />
<br />
==[http://indigobiosciences.com/screening-services/nuclear-receptor-assays/ INDIGO Biosciences]==<br />
Located in Pennsylvania, they can do nuclear hormone assay.<br />
<br />
3,500 minimum order size e.g. 1 compound at 5 receptors at 10 doses each<br />
<br />
==[http://www.soralabs.com/services/ Sora Labs]==<br />
It looks like they have some enzyme assays that they can run.<br />
<br />
==[http://www.fluofarma.com/ FlouFarma]==<br />
Located in France, high content screening of live cells<br />
<br />
==[http://www.cytoskeleton.com/custom-services/compound-screening Cytoskeleton]==<br />
Compound screening against tubulin, microtubule, myosin, sarcomere, kinesin and small G-proteins.<br />
<br />
==[https://www.caymanchem.com/app/template/services%2CHome.vm Cayman Chemical]==<br />
* Assay Services<br />
Biochemists with experience in the areas of eicosanoids, steroids, oxidative stress, and inhibitor screening<br />
Use Cayman’s extensive line of well-characterized biochemical kits<br />
Enzyme immunoassay, colorimetric, and fluorometric assays available<br />
* Screening Services<br />
Comprehensive screening laboratory focused on epigenetics<br />
Backed by our core strengths in protein production, assay development, chemical synthesis, and medicinal chemistry<br />
Capacity to test compounds at a rate of up to 100,000 compounds per week<br />
Ability to profile compounds against a broad epigenetic enzyme panel<br />
Includes assays for methyltransferases, demethylases, acetyltransferases, deacetylases (HDACs and SIRTS), and histone code readers (ex. bromodomain proteins)<br />
<br />
==[http://www.discoverx.com/ DiscoveRx]==<br />
GPCR, Kinases, Nuclear Receptors, Epigenetic Targets and Signaling Pathways<br />
<br />
==[http://www.hdbiosciences.com/EngHTS.htm HD Biosciences]==<br />
HD Biosciences Co., Ltd. is a Shanghai-based, biology-focused preclinical drug discovery contract research organization (CRO). They do hit identification, hit-to-lead, assay development in major target classes, such as GPCRs, kinases, ion channels and transporters, and in a high-throughput screening format using plate-based platforms. Our screening capabilities span from cell line generation, biochemical, and cell-based functional assays for receptors, enzymes and ion channels in a variety of techniques, including:<br />
<br />
* Fluorescence (e.g. HTRF, FP, FRET, FLIPR, Flexstation) <br />
* Absorbance <br />
* Luminescence (e.g. luciferase, b-lactamase, deGFP, reporter gene)<br />
* Radiometrics (e.g. SPA, MicroBeta, Filtration) <br />
* Electrophysiology (e.g. patch clamps) <br />
* ImageXpress (e.g. live cell image HCA/HCS)<br />
<br />
<br />
==[http://www.absorption.com/resources/assay-data-sheets/ Absorption Systems]==<br />
Absorption Systems is a preclinical CRO. They have locations in Exton, PA, San Diego, CA, and Panama City, Panama. They work with a wide variety of customers in the pharmaceutical and biotech industry, including small virtual pharma companies, large pharma companies with weekly programs, and specialty CROs looking for services that complement their own offerings. In vitro and in vivo areas of speciality include:<br />
<br />
* BCS + Biowaivers<br />
* Wound healing and psoriasis disease models<br />
* Formulation<br />
* Metabolism<br />
* Permeability<br />
* Pharmacokinetics<br />
* Protein binding (e.g. fraction bound in plasma)<br />
* Toxicology<br />
* Transporters<br />
<br />
==[http://www.cyprotex.com/toxicology Cyprotex]==<br />
Cyprotex is a contract research organization specializing in preclinical ADME-Tox with offices in the UK and US.<br />
<br />
Permeability & Transporters<br />
* Caco-2 permeability<br />
* Transporter interactions<br />
* PAMPA-GI and PAMPA-BBB<br />
* MDCK and MDR1-MDCK<br />
* Transdermal absorption<br />
* Intranasal absorption<br />
<br />
Distribution - reversible/time dependent<br />
* Plasma protein binding<br />
* Whole blood binding<br />
* Blood to plasma ratio<br />
* Brain tissue binding<br />
* Microsomal binding<br />
<br />
Metabolism<br />
* Metabolic stability microsomes, hepatocytes, S9, plasma/blood<br />
* Metabolite profiling and identification<br />
* Reaction phenotyping<br />
* CYP inhibition<br />
* UGT inhibition<br />
* MAO inhibition<br />
* CYP induction<br />
* PXR and AhR nuclear <br />
<br />
receptor activation<br />
* 3D microtissues<br />
<br />
==[http://www.brunswicklabs.com/biological-analysis Brunswick Labs]==<br />
Brunswick Laboratories is an independent, full-service bioanalytical laboratory specializing in the science of Antioxidants, Oxidative Stress, Anti-inflammatory, Synthetic and Natural Compound Bioanalysis.<br />
<br />
+1-508-281-6660<br />
blservices@brunswicklabs.com<br />
200 Turnpike Road, Southborough, MA 01772, USA<br />
<br />
* Bioavailability, BioAbsorption, and BioUptake study via Caco-2 human intestinal cells<br />
* Anti-inflammatory: LOX, COX, TNF-alpha, NFkB, Interleukins (ILs), and PGE2 as biomarkers<br />
* Oxidative Stress Analysis for biological samples<br />
* Antioxidation effect in a biological system: Nrf2, Cellular Antioxidant Assay (CAA) <br />
* Diabetes and Weight Management: insulin secretion, insulin receptor activity, glucose uptake, glucose metabolism, and carbohydrate digestion as biomarkers<br />
* Detoxification and Liver Function: Phase I and Phase II liver enzymes, liver function biomakers in serum<br />
* Energy metabolism investigation via human cells <br />
* Anti-cancer Function evaluation: cancer cell viability, proliferation, apoptosis, and invasion as biomarkers <br />
* Anti-aging Assays: SIRT-1, telomerase activity as biomarkers<br />
* Preclinical Investigations for Skin Care Products: UV protection, melanin (age spot) inhibition, anti-aging, anti-inflammatory<br />
<br />
==[http://biotoxsciences.com/In_Vitro_Services BioToxSciences]==<br />
http://biotoxsciences.com/In_Vitro_Services<br />
<br />
Based in San Diego, they have a range of in-vitro functional assays<br />
<br />
==Other CROs==<br />
* [http://www.ricerca.com Ricerca]<br />
* [http://www.amsbio.com/ amsbio] not really a CRO but apparently they can do assays<br />
* [http://stores.arraybridge.com/enzyme-assays/ ArrayBridge] The have ~850 enzymes listed that they say they have assays for, but little detail on what services they actually provide.<br />
* [http://www.sbdrugdiscovery.com/screening-assays SB Drug Discovery] 50 PDEs, 50 Ion Channels, NHRs, GPCRs, Inflammation<br />
* [http://www.discoverx.com/services/drug-discovery-development-services DiscoverRX] Kinase, Epigenetic, GPCR<br />
* [http://metislabs.com/radioligand-binding-assays.html MetisLab] Radioligand assays for GPCRs<br />
* [http://www.creative-biogene.com/ Creative Biogene]<br />
<br />
== CRO sourcing services ==<br />
* [https://www.scienceexchange.com]<br />
* [https://www.assaydepot.com]<br />
<br />
https://www.genoway.com/services/catalog-models/mouse-knockouts.htm?utm_source=emailing&utm_medium=email&utm_content=01122015&utm_campaign=01122015</div>Wendywilson