Proteomic and Genomic Sample Preparation and Enrichment
Proteomics Sample Preparation, Biomarker Discovery & Protein Products Enrichment Reagents and Kits
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P R O T E OAlbuSorb™ MICS SAMPLE PREP A
Albumin depletion from serum or Lplasma. B U MIsI N EPLETION economical new surface technology, not EMOGLOBIN based on affinity chromatography.
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Cleanascite™
Lipid adsorption and clarification reagent. Selectively removes lipids, cell debris, Elipoproteins, P L E T I Oand N mucinous impurities from biological samples.
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LOW ABUNDANCE ENRICHMENT info | buy HemogloBind™ Hemoglobin capture reagent. Is a polyelectrolytes are polymers with repeating units of stationary charges.
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CLASS SPECIFIC ENRICHMENT Enter Product Name / Number
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FUNCTIONAL PROTEOMICS
Superior Substitute to phenol/Chloroform for DNA & RNA • isolation. Is a unique protein • extraction reagent • based upon • patented • elastomeric polyelectrolytes. •
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info | buy SeraFILE™ SeraFILE™ is a sorting, or subfractionation methodology designed for comparative proteome analysis.
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C H E M 02-12-2008 ICAL PROTEOMICS
BSG Partner- Profact Proteomics, Launches New 12-31-2007
G E N OSupport M I C SGroup S A MLaunches P L E PProteomics REP Biotech Po 10-12-2007
A New Functional Proteomic Profiling Method 10-11-2007
SeraFILE™-Derived Proteomic Profiles: Implica Clinical Proteomics and Biomarker Discovery 09-29-2007
Biotech Support Group Launches new website! 09-1-2007
New Albumin Depletion Strategies For Proteom view all
Biotech Support Group LLC
1 Deer Park Drive, Suite M Monmouth Junction, NJ 08852 800-935-0628 North America Biotech Support Group is a New Jersey based company which produces licensed and proprietary products for genomics and proteomics732-274-2866 Worldwide research. www.biotechsupportgroup.com home | products | catalog | services | corporate | career | order | contact | sitemap Copyright © 2007 Biotech Support Group Inc. All Rights Reserved.
Albumin Depletion Enrichment of Low Abundance Serum/Plasma Proteins All of our proteomics
AlbuVoid™
products have these common features and
Selectively Voids Albumin
collective advantages:
•
Albumin voids in flowthrough, >95%
Enriched proteins are intact,
•
<30 minute protocol
with their native structure
•
Low abundance enrichment equivalent or better than hexapeptides or antibodies
•
On-bead digestion protocols, efficient LC-MS workflows
•
Disposable, costeffective, no column regeneration or cross-contamination
•
Mild elution maintains native structure with retained enzymatic and functional activities
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Species agnostic
•
uncompromised, and can be employed for interrogations of structure (activityprobes), and functional properties •
Consumable, one-time use with no potential for crosscontamination or reduced performance upon regeneration
•
Adaptable to high-
Typical Performance* Serum Sample Volume
200 µl
Albumin Removal
>95%
LC-MS unique peptides Total Low Abundance Protein Recovery
600-800
Protocol Time
30 min.
>95%
2DE analysis of AlbuVoid™ treated sheep serum. Samples were reduced, alkylated and total protein normalized. The circled regions indicate the albumin zone. Gel 1: Sheep serum sample. Gel2: AlbuVoid™ Eluate. Gel 3: Same as 2 AlbuVoid™ Eluate but restained with SilverQuest (Invitrogen) silver stain. The differences between the gels illustrate the efficiency of albumin removal, with no intrinsic pI or MW bias.
throughput protocols, no specialized instruments or HPLC •
Product AlbuVoid™ AlbuVoid™ AlbuVoid™
Size 5 Preps 10 Preps 50 Preps
Item No. AVK-05 AVK-10 AVK-50
* Estimates based on SDS-PAGE visualization combined with Total Protein Assay.
Based on 200 µl serum preps
Economical surface chemistries, not derived from biological sources
AlbuSorb™ Selectively Binds Albumin •
Removes 30 mg albumin/ml, >90%
•
Economical small ligand-type surface architecture, affinity-type selectivity
On-Bead Digestion Protocols
•
Disposable, cost-effective, no column regeneration or cross-contamination
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Much Simpler Workflows
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Mild elution maintains native structure with retained enzymatic and functional activities
•
No Precipitations
•
Species agnostic
•
Compatible with o LC-MS o Chemical o Functional proteomics
And for LC-MS applications:
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Shorter Preparation Time
•
Less Potential for keratin
Product
Size
AlbuSorb™ 6 gm AlbuSorb™ 18 gm Based on 25 µl serum preps
Albumin Zone
# of preps 170 510
Plasma
AlbuSorb
Control
Eluate
AlbuVoid™ FT Item CNo. C: Control Serum FT: Flow Through A185-6 EL: Eluate A185-18
contamination
AlbuTrial™ Kit For more information about onbead digestion, visit http://biotechsupportgroup.co m/news/new-bead-digestion-lcms-applications-proteomicstudies
Don’t know which one to try? Try both. AlbuTrial™ kit is a combination of AlbuSorb™ and AlbuVoid™ with respective buffers. Product
Size
Item No.
AlbuTrial™ Kit
1 gram AlbuSorb™ 5 Preps AlbuVoid™
AVS-05
EL
Hemoglobin Depletion and/or Enrichment
HemoVoid™
HemogloBind™
Hemoglobin Depletion For Erythrocyte Proteomics
Removes Hemoglobin Interference •
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Hemoglobin voids in flow-through >98%
Has a high degree of specificity for hemoglobin binding up to 10 mg/ml
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depletion from hemolyzed serum and whole blood
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<30 minute bind/wash/elute protocol
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applicable to hemoglobin variant analysis
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ideal for erythrocyte proteomics
•
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depletion from heavily hemolyzed serum, blood and dried blood spot/blood card
Native structure uncompromised with simple transfer to post-treatment interrogations
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Species and tissue agnostic
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Compatible with LC-MS, activity-probe profiling and proteomic analyses
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applicable to hemoglobin variant analysis
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Low abundance protein and enzyme enrichment
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Disposable, cost-effective
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Native structure uncompromised with simple transfer to post-treatment interrogations
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Species and tissue agnostic
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Compatible with LC-MS, activity-probe profiling and virtually all proteomic analyses
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On-bead digestion protocols
2DE Comparison. Red circles indicate the Hemoglobin subunits region. The HemoVoid™ eluate (bottom) has been severely depleted of Hemoglobin. The remainder of the red cell proteins are substantially enriched (visualized) and are better resolved in the HemoVoid™ eluate. Many more proteins are detectable after HemoVoid™ treatment with extensive protein coverage across both dimensions.
Product Size HemoVoid™ 10 Preps HemoVoid™ 50 Preps HemoVoid™ 100 Preps Based on 300 µl preps
Item No. HVK-10 HVK-50 HVK-100
Product
Size
Item No.
HemogloBind™
15 ml
H0145 -15
HemogloBind™
50 ml
H0145 -50
1:1 v:v ratio processes up to 10 mg/ml hemolyzed serum
HemoTrial™ Kit Don’t know which one to try? Try both. HemoTrial™ kit is a combination of HemogloBind™ and HemoVoid™ with respective buffers. Product
Size
Item No.
HemoTrial™ Kit
5 ml HemogloBind™ + 5 Preps HemoVoid™
HTK-05
HemoVoid™ Blood Card Kit The HemoVoid™ Blood Card kit was designed to substantially reduce hemoglobin interference from dried blood card protein analytes. Product
Size
Item No. HemoVoid™ 10 HVBCBlood Card Preps 10 HemoVoid™ 50 HVBCBlood Card Preps 50 Based on 0.5” dried blood spot, ~ 15 µl whole blood
from
Class Specific Enrichment KinaSorb™
PDEnrich™
Kinase (& ATP binding proteins) enrichment reagent
Cyclic Nucleotide Phosphodiesterase Enrichment Reagent
Non-covalent immobilization of phosphate group with optimal nucleotide orientation & specificity
Enrichment 3-5X, binding protein recoverable, ~200 µg
•
Enrichment 4-10X, PDE protein recoverable, ~70 µg
60 minute, scaleable protocol compatible with functional assays, electrophoresis and LC-MS
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Up to 50X concentration of PDE volume
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45 minute, scaleable protocol
Phosphatase activity & cyclic nucleotide phosphodiesterase (PDE) activity not detectable
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Improves protein normalization when comparing heterogeneous tissues
Improves protein normalization when comparing heterogeneous tissues
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On-bead digestion protocols
On-bead digestion protocols
Top – Rat Brain Homogenate. Bottom – after KinaSorb™, ATP binding proteins, and presumably some small carryover proteins are visualized. Methods to monitor drug response are provided in the example on right.
Clarified rat brain homogenate was enriched with KinaSorb™ and then processed through several multi-dimensional separations surfaces (PROspector™). The bars reflect kinetic activity in the various sub-proteome fractions as a percentage of activity in the load applied to the surfaces. The numbers designate the different surface architectures. FT: Flow through, E: elution, L: low Imatinib inhibitor concentration, H: high Imatinib inhibitor concentration.
On the left is a comparison of enriched Bovine Brain Homogenate (BBH) and Rat Brain Homogenate (RBH) before and after treatment with PDEnRich™. A substantial amount of cAMP hydrolysis activity* is recovered in both cases with a severe reduction in total protein content.
Product # of preps Item No. PDEnRich™ 10 PD545-10 PDEnRich™ 50 PD545-50 Based on 100 µl tissue homogenate
NuGel™ PBA Kit Glycoprotein Enrichment Using Phenyl Boronic Acid
Product # of preps KinaSorb™ 10 10 KinaSorb™ 50 50 Based on 100 µl tissue homogenate preps
Item No. KE785-10 KE785-50
• Sorbitol elution; compatible with functional assays, electrophoresis and LC-MS
Virus Enrichment & Purification •
Purifies whole infectious non-enveloped virus, isolates antigenic virions
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Enriches for viral proteins and nucleic acids
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No ultracentrifugation
•
Used for monitoring vaccine immune response Size 15 ml reagent only 50 ml reagent only For 40 ml cell culture For 400 ml cell culture
• Disposable, no column regeneration • Species and tissue agnostic
Viraffinity™ / ViraPrep™
Product Viraffinity™ Viraffinity™ ViraPrep™ Mammal ViraPrep™ Mammal
• Enriches heterogeneous sets of glycoprotein’s, N-linked & O-linked
Item No. V1062-15 V1062-50 VPM-40 VPM-400
ViraPrep™ Lambda processes Lambda DNA. See Price List for order information.
Sample Type Mouse Plasma Rat Serum Sheep Serum Bovine Serum Bovine Brain Homogenate
%Glycoprotein relative to starting sample (Sorbitol Elution) 33 44 18 40 9
Product # of preps NuGel™ PBA Kit 10 NuGel™ PBA Kit 50 Based on 50 µl serum preps
Item No. NGPBA-10 NGPBA-50
Sample Preparation Cleanascite™
UPCK™ Kit
Lipid Adsorption & Clarification
Urine Protein Enrichment & Concentration
•
Effectively replaces chlorinated/fluorinated hydrocarbons (eg. freon)
•
Helps purify antibodies, proteins, nucleic acids, proteoglycans, and assorted serum components
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Ideal for clarifying ascites, serum, cell & tissue culture, bile and organ homogenates
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Clarifies saliva and feces
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Cited in over 35 bioseparation articles
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Extends the life of membrane and chromatographic apparatus
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Ideal for bioprocessing of recombinant proteins, monoclonol antibodies
Egg Yolk Clarification
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Linearly scaleable, unlike ultrafiltration
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Alternative to solvent/alcohol precipitation
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On-bead digestion protocols
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<60 min. bind, wash and elute protocol
•
Applicable to >1 & 2 DE > LC-MS >microarrays
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The eluted fractions retain their enzymatic and biological activity
Product UPCK™ Kit UPCK™ Kit
>
# of Preps 10 25
Item No. UPCK-10 UPCK-25
Based on 10 ml urine samples
BindPro™ Metabolomics Product Cleanascite™ Cleanascite™
Quantity (ml) 100 1000
Process Volume (ml)* 400 4000
Item No. X2555-100 X2555-1000
*Based on typical volume ratios, can be adjusted to lipid load
Cleanascite™ PRO
Lipid Adsorption for Proteomics
Protein Removal & Enrichment of Metabolites/Analytes •
Serum and plasma protein removal, >95%
•
Linearly scaleable, unlike chemical precipitation or membrane filtration.
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< 30 minute protocol
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Applicable for drug binding/screening and metabolomics
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Tissue, species agnostic
nd
•
2 generation product based on highly cited lipid removal platform; < non-specific binding
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Removes phospholipid matrix interference
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Enrich lipid associated proteins
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On-bead digestion protocols
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Compatible with N-Octyl Glucoside and other membrane protein detergents
•
Simple and fast Product
Cleanascite™ PRO Cleanascite™ PRO
Quantity (ml) 15 100
# of preps* 75 500
Item No. XPRO5-15 XPRO5-100
*Based on 100 µl tissue homogenate and typical volume ratios, can be adjusted to lipid load
Product BindPRO™ BindPRO™
# of Preps 15 50
Based on 25-30 µl serum
Item No. BPM55-15 BPM55-50
Functional & Chemical Proteomics Functional Proteomics
NuGel™ PROspector™
Building sequence/structure/function relationships
Functional proteomics and enrichment kit
Functional proteomics relies in part, on the functional or structural features of intact, non-denatured proteins. While the terminology can often overlap, chemical and affinity-based proteomic profiles can be considered a subset of functional proteomics.
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12 differentiated subproteomes with uncompromised functional and structural attributes
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Generate characteristic molecular profiles for comparison and discovery
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Enrich functional biomarkers for sequence and structural annotation
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Kit includes 6 surface chemistries per prep
Thus, functional proteomic annotation complements conventional sequence annotation while supporting the study of mechanism of action and drug promiscuity. Furthermore, the subtleties of protein attributes, when the same or similar underlying sequence can have multiple conformations and functions, and when different sequences sometime perform the same or similar functions, are now open to investigation. A new functional proteomics enrichment toolset based on the NuGel™ platform, can now sift through these biological complexities. Both PROspector™ and PROfessor™ support functional and chemical proteomics and can: •
Optimize drug compounds
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Survey drug-interaction promiscuity
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Elucidate mechanism of action
•
Identify phenotypic biomarkers
Molecular profiles differ under a compound challenge.
small competitive small c
Plotted are the relative changes in cAMP hydrolysis activity of each subproteome in the presence of competitive substrate cGMP.
in
Encircled are the enriched functional specific responses that distinguish the two samples; RBH (rat brain) & BBH (bovine brain).
sample-
Product # of preps* Item No. NuGel™ PROspector™ 5 SR610-5 NuGel™ PROspector™ 25 SR610-25 *Based on processing 0.5-1.0 mg total protein
NuGel™ PROfessor™ Protein Compression & Chemical Proteomics • Can compress protein concentrations*, enrich low abundance proteins • Enablement for compound-centric displacement proteomics (CCDP)*
Protein Compression The low abundance bands are enriched relative to their high abundance bands, visually estimated to be 5 – 10X for most bands. The protein compression is both tissue and species agnostic. IgG (non-reduced), being heterogeneous, is observed as one band.
• Composite of the PROspector™ surfaces • Deconstruction can optimize biomarker enrichment • Tissue and species agnostic
*patent pending
Protein Description Hemoglobin subunit beta-1 Glucose-6-phosphate isomerase Malate dehydrogenase transketolase Cytochrome c, somatic Succinyl-CoA:3-ketoacid coenzyme A transferase Transgelin Annexin A2 fumarate hydratase annexin A3 glutathione reductase
Product NuGel™ PROfessor™ NuGel™ PROfessor™
# of preps* 10 50
Item No. SRPRO-10 SRPRO-50
*Based on processing ~1.0 mg total protein. Protein compression may require higher loads.
Caffeine 87 192 117 72 47
Imatinib 550 459 356 160 123
Neg.Cont. 53 76 35 24 3
69 0 26 17 5 9
122 84 66 42 36 36
19 0 0 2 0 0
A partial list of LC-MS/MS identification and spectral counts demonstrate Imatinib interaction (displaced) proteins from a common tissue homogenate, using CCDP. Caffeine was employed as a non-specific control compound, negative control was the final wash buffer.
NuGel™ Polymer Coated Silica Affinity Matrices for Ligand Immobilization Product Name NuGELTM PolyEpoxy NuGELTM PolyAmine NuGELTM PolyAldehyde NuGELTM PolyHydroxy NuGELTM PolyCarboxy NuGELTM PolyNHS
Matrix Reactive Group
Ligand Reactive Group
Immobilization Conditions
Quantity (Grams)
Item No.
25
NPEY -25
Terminal Epoxy
Amino
Direct Coupling
Terminal Amine
Carboxylic Acid, Carbohydrate
Carbodiiamide reaction, or NaIO4 derived Aldehyde
25
NPAM -25
Terminal Aldehyde
Amino
Direct Coupling
25
NPAY -25
Terminal Glycol
Amino
Carbodiimidazole mediated reaction
25
NPHX -25
Amino
Carbodiiamide mediated reaction
25
NPCY -25
Amino
Direct Coupling
25
NPHS -25
Terminal Carboxylic Acid Terminal N-Hydroxy Succinimide
NuGel™ Trial Kit Don’t know which one to try? Try all 6. Pick the chemistries and quantities of your choice. Choose 1, 2, 3, 4, 5 or all 6 in any combination of 1 gram increments. Product
Size
Item No.
NuGel™ Trial Kit
6 grams
NUTK06
NuGel™’s unique surface passivation can be applied to any porous silica, particle size or quantity for custom manufacture of ion-exchange, hydrophobic interaction, affinity chromatography or HPLC. Please inquire.
Genomics / DNA Isolation Genomic Sample Preparation Products Especially Suitable for BACs and Multiplex SNPs
ProCipitate™ & ProPrep™ Kits Superior Substitute to Phenol/Chloroform for DNA Isolation • • • •
Used throughout the Human Genome Sequencing Project* Removes protein contaminants & leaves DNA unbound Improves yield of DNA over alternative bind and elute systems ProCipitate™ supports the ProPrep™ line of application specific kits Sample Size 10 ml Yeast Culture Genomic DNA Mouse Tail Genomic DNA 4 mm Plant Leaf 1.5 ml culture BAC Preps 250 µl culture Plasmid Preps 200 ml Large Scale BAC Preps Dried Blood Card (or ~ 15 µl Whole Blood) Product ProCipitate™ ProCipitate™ ProCipitate™ ProPrep™ BAC Mini ProPrep™ BAC Mini ProPrep™ BAC Mini ProPrep™ Genomic 96/100 ProPrep™ Genomic 960/1000
ProCipitate Typical Usage 1-2 ml 250-500 µl 100-200 µl 80 µl 20 µl 5 ml 250 µl
Size 30 ml 100 ml 500 ml 96-100 preps Up to 500 preps Up to 1000 preps 96-100 preps Up to 1000 preps
Item No. P0050-30 P0050-100 P0050-500 PMK-100 PMK-500 PMK-1000 PPG-100 PPG-1000
*References J M Kelley; C E Field; M B Craven; D Bocskai; U J Kim; S D Rounsley; M D Adams. High Throughput Direct End Sequencing of BAC Clones. Nucleic Acids Research.1999.15;27(6):1539-1546
Lane 1: 100-1000 base pair Ladder
PCR from whole blood using ProPrep™ Genomic kit
Lane 2: Negative Control Lanes 3-10: PCR amplicons from 1 ng template DNA purified from whole blood, randomly selected from 96 wells. Amplicons are 280 base pairs from Human HLA-DR-Beta primers at 32 cycles.
D C Bruce; M O Mundt; K K McMurry; L J Meincke; D L Robinson; N A Doggett; L L Deaven. BAC Library End Sequencing in Support of Whole Genome Assemblies DOE Joint Genome Institute and Center for Human Genome Studies, Los Alamos National Laboratory, Research Abstracts from the DOE Genome Contractor-Grantee Workshop IX (2002)
Distributors for Asia Pacific Japan
Taiwan
Funakoshi China
Blossom Biotech China
Beijing Shengkeboyuan Bio-tech Co.,LTD India
Company Information Established in 1995, Biotech Support Group is a New Jersey based company which produces licensed and proprietary consumable products for proteomics and genomics research.
•
Its products are trusted brands with 125+ references, having been supported in peer reviewed journals, patents, and technical posters
•
It is a leader in research consumables and products for hemoglobin, albumin, lipid, glycoprotein, viral genomics and proteomics sample preparation and enrichment.
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Its products are for research use only.
BIOPCR Singapore
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Biotech Support Group LLC Life Sciences-Ltda
1 Deer Park Drive, Suite M Monmouth Junction, NJ 08852 800-935-0628 North America 732-274-2866 Worldwide www.biotechsupportgroup.com