Genomic Characterization defines Human Glioblastoma genes and core pathways

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Molecular portraits of human breast tumours.

Human breast tumours are diverse in their natural history and in their responsiveness to treatments. Variation in transcriptional programs accounts for much of the biological diversity of human cells and tumours. In each cell, signal transduction and regulatory systems transduce information from the cell’s identity to its environmental status, thereby controlling the level of expression of every gene in the genome. Here we have characterized variation in gene expression patterns in a set of 65 surgical specimens of human breast tumours from 42 different individuals, using complementary DNA microarrays representing 8,102 human genes.

 

These patterns provided a distinctive molecular portrait of each tumour. Twenty of the tumours were sampled twice, before and after a 16-week course of doxorubicin chemotherapy, and two tumours were paired with a lymph node metastasis from the same patient. Gene expression patterns in two tumour samples from the same individual were almost always more similar to each other than either was to any other sample.

 

Sets of co-expressed genes were identified for which variation in messenger RNA levels could be related to specific features of physiological variation. The tumours could be classified into subtypes distinguished by pervasive differences in their gene expression patterns.

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Normal DNA Marker (100-2000 bp)

MKD2002-500mL
EUR 9.6

Normal DNA Marker (100-5000 bp)

MKD2003-500mL
EUR 13.2

Normal DNA Marker (100-15000 bp)

MKD2004-500mL
EUR 13.2

Accurate DNA Marker (100-600 bp)

MKD3003-500mL
EUR 9.6

Accurate DNA Marker (100-1000 bp)

MKD3004-250mL
EUR 9.6

Accurate DNA Marker (100-1500 bp)

MKD3005-250mL
EUR 9.6

Accurate DNA Marker (100-2000 bp)

MKD3006-250mL
EUR 13.2

Accurate DNA Marker (100-5000 bp)

MKD3007-250mL
EUR 13.2

Prestained DNA Marker (100-600 bp)

MKD1002-500mL
EUR 18

Prestained DNA Marker (100-1000 bp)

MKD1003-250mL
EUR 14.4

Prestained DNA Marker (100-1500 bp)

MKD1004-250mL
EUR 14.4

Prestained DNA Marker (100-2000 bp)

MKD1005-500mL
EUR 18

Prestained DNA Marker (100-5000 bp)

MKD1006-500mL
EUR 21.6

Image Green? 100 bp DNA Marker

M1155-500
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Universal Genomic DNA Kit

MBS278033-200Preps
EUR 380

Universal Genomic DNA Kit

MBS278033-50Preps
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SeraMir 3'-Universal Primer (10,000 qPCR reactions)

RA800P-3
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QuantiMir 3'-Universal Primer (10,000 qPCR reactions)

RA420AU-3
EUR 125

QPCR Kit DNA Universal f - EACH

MOL6606
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QPCR Kit DNA Universal m - EACH

MOL6610
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Agrisera Universal Stabilizer (100 ml)

AS18-MacroStab-100
EUR 179

Genorise® Universal DNA Mini Kit 50

GR101076
EUR 223

Genorise® Universal DNA Mini Kit 200

GR101077
EUR 567

Genorise® Universal DNA Mini Kit 500

GR101077-500
EUR 1272

Methylamp Universal Methylated DNA Kit 

P-1011
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QPCR Kit DNA Universal f Mmix - EACH

MOL6608
EUR 1581.9

QPCR Kit DNA Universal m Mmix - EACH

MOL6612
EUR 1581.9

VAHTS Universal DNA Library Prep Kit for MGI

NDM607-01
EUR 879.6

VAHTS Universal DNA Library Prep Kit for MGI

NDM607-02
EUR 2563.2

Universal Solution for DNA isolation (GeDI)

E3760-01
EUR 30.52

Universal Solution for DNA isolation (GeDI)

E3760-02
EUR 95.92

ACTGene? DNA Marker, 100 bp Ladder, 11 Fragments, 100 loads

ACT-IDMWD100
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25-500 bp DNA Marker

abx461022-1096tests
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25-500 bp DNA Marker

abx461022-596tests
EUR 525

25-500 bp DNA Marker

abx461022-96tests
EUR 400

VAHTS Universal DNA library Prep Kit for MGI V4

NDM610-01
EUR 235.2

VAHTS Universal DNA library Prep Kit for MGI V4

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EUR 880

VAHTS Universal DNA library Prep Kit for MGI V3

NDM607-00-6rxns
EUR 1.09

VAHTS Universal DNA library Prep Kit for MGI V3

NDM607-01-24rxns
EUR 304.66

VAHTS Universal DNA library Prep Kit for MGI V3

NDM607-02-96rxns
EUR 1139.05

GeneMATRIX UNIVERSAL DNA/RNA/Protein Purification Kit

E3597-01
EUR 81.75
Description: Kit for isolation of total DNA/RNA/Protein from the same biological sample(bacteria, tissue, plant, yeast, cell culture)

GeneMATRIX UNIVERSAL DNA/RNA/Protein Purification Kit

E3597-02
EUR 299.75
Description: Kit for isolation of total DNA/RNA/Protein from the same biological sample(bacteria, tissue, plant, yeast, cell culture)

50 bp Ladder DNA Marker

FYD004-500UL Ask for price

Methylamp Universal Methylated DNA Preparation Kit

P-1019
EUR 416.7

TIP,100-1000UL,UNIVERSAL,BLU,NS,BAG,1K/10K

4846
EUR 315.6
Description: Non Filter Tips; Core Tips

VAHTS Universal DNA Library Prep Kit for Illumina V3

ND607-01
EUR 529.2

VAHTS Universal DNA Library Prep Kit for Illumina V3

ND607-02
EUR 1686

VAHTS Universal DNA Library Prep Kit for Illumina V4

ND610-01
EUR 294

VAHTS Universal DNA Library Prep Kit for Illumina V4

ND610-02
EUR 1100

VAHTS Universal DNA Library Prep Kit for Ion Torrent

ND701-01
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VAHTS Universal DNA Library Prep Kit for Ion Torrent

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VAHTS Universal DNA Library Prep Kit for Illumina V4

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VAHTS Universal DNA Library Prep Kit for Illumina V4

ND610-02-96rxns
EUR 1139.05

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ND610-03-24rxns
EUR 269.23

VAHTS Universal DNA Library Prep Kit for Illumina V4

ND610-04-96rxns
EUR 999.53

AFTSpin Universal Plant Fast DNA Extraction Kit

RK30111
EUR 69

EpiMag High Throughput DNA Isolation Universal Kit

P-1022-96
EUR 227.7

EpiMag High Throughput DNA Isolation Universal Kit

P-1022
EUR 215

Universal-1

OD308-1PK
EUR 2.65
Description: Universal-1

Universal-1

OD308R-1PK
EUR 2.65
Description: Universal-1

VAHTS Universal DNA Library Prep Kit for Ion Torrent V2

ND702-01
EUR 294

VAHTS Universal DNA Library Prep Kit for Ion Torrent V2

ND702-02
EUR 1100

Universal Kit for DNA isolation with GeDI Solution

E3765-01
EUR 59.95

Universal Kit for DNA isolation with GeDI Solution

E3765-02
EUR 210.37

VAHTS Universal Pro DNA Library Prep Kit for MGI

NDM608-01
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VAHTS Universal Pro DNA Library Prep Kit for MGI

NDM608-02
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100 bp LadderDNA Marker HighConcentration

FYD005-500UL Ask for price

Normal DNA Marker (200-2000 bp)

MKD2005-500mL
EUR 9.6

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MKD2006-250mL
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MKD2007-250mL
EUR 13.2

Normal DNA Marker (250-10000 bp)

MKD2008-500mL
EUR 12

Normal DNA Marker (250-12000 bp)

MKD2009-250mL
EUR 9.6

Normal DNA Marker (500-8000 bp)

MKD2010-500mL
EUR 7.2

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MKD2011-250mL
EUR 7.2

Normal DNA Marker (1000-15000 bp)

MKD2012-500mL
EUR 7.2

VAHTS Universal Plus DNA Library Prep Kit for MGI

NDM617-01
EUR 988.8

VAHTS Universal Plus DNA Library Prep Kit for MGI

NDM617-02
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Universal heat peel sheets 125x78mm 100 sheets - PK100

4TI05231
EUR 108

Accurate DNA Marker (50-500 bp)

MKD3001-250mL
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Accurate DNA Marker (50-1000 bp)

MKD3002-250mL
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Universal Aspergillus Taqman qPCR Detection, 100 reactions

TBS42020
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Prestained DNA Marker (250-12000 bp)

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VAHTS Universal Pro DNA Library Prep Kit for Illumina

ND608-01
EUR 558

VAHTS Universal Pro DNA Library Prep Kit for Illumina

ND608-02
EUR 1858.8

 

Comprehensive genomic characterization defines human glioblastoma genes and core pathways.

Human cancer cells typically harbour multiple chromosomal aberrations, nucleotide substitutions and epigenetic modifications that drive malignant transformation. The Cancer Genome Atlas (TCGA) pilot project aims to assess the value of large-scale multi-dimensional analysis of these molecular characteristics in human cancer and to provide the data rapidly to the research community.
Here we report the interim integrative analysis of DNA copy number, gene expression and DNA methylation aberrations in 206 glioblastomas–the most common type of adult brain cancer–and nucleotide sequence aberrations in 91 of the 206 glioblastomas.
This analysis provides new insights into the roles of ERBB2, NF1 and TP53, uncovers frequent mutations of the phosphatidylinositol-3-OH kinase regulatory subunit gene PIK3R1, and provides a network view of the pathways altered in the development of glioblastoma.
Furthermore, integration of mutation, DNA methylation and clinical treatment data reveals a link between MGMT promoter methylation and a hypermutator phenotype consequent to mismatch repair deficiency in treated glioblastomas, an observation with potential clinical implications.
Together, these findings establish the feasibility and power of TCGA, demonstrating that it can rapidly expand knowledge of the molecular basis of cancer.

The sequence of the human genome.

A 2.91-billion base pair (bp) consensus sequence of the euchromatic portion of the human genome was generated by the whole-genome shotgun sequencing method.
The 14.8-billion bp DNA sequence was generated over 9 months from 27,271,853 high-quality sequence reads (5.11-fold coverage of the genome) from both ends of plasmid clones made from the DNA of five individuals.
Two assembly strategies-a whole-genome assembly and a regional chromosome assembly-were used, each combining sequence data from Celera and the publicly funded genome effort.
The public data were shredded into 550-bp segments to create a 2.9-fold coverage of those genome regions that had been sequenced, without including biases inherent in the cloning and assembly procedure used by the publicly funded group.
This brought the effective coverage in the assemblies to eightfold, reducing the number and size of gaps in the final assembly over what would be obtained with 5.11-fold coverage.
The two assembly strategies yielded very similar results that largely agree with independent mapping data. The assemblies effectively cover the euchromatic regions of the human chromosomes.
More than 90% of the genome is in scaffold assemblies of 100,000 bp or more, and 25% of the genome is in scaffolds of 10 million bp or larger. Analysis of the genome sequence revealed 26,588 protein-encoding transcripts for which there was strong corroborating evidence and an additional approximately 12,000 computationally derived genes with mouse matches or other weak supporting evidence.
Although gene-dense clusters are obvious, almost half the genes are dispersed in low G+C sequence separated by large tracts of apparently noncoding sequence.
Only 1.1% of the genome is spanned by exons, whereas 24% is in introns, with 75% of the genome being intergenic DNA. Duplications of segmental blocks, ranging in size up to chromosomal lengths, are abundant throughout the genome and reveal a complex evolutionary history.
Comparative genomic analysis indicates vertebrate expansions of genes associated with neuronal function, with tissue-specific developmental regulation, and with the hemostasis and immune systems.
DNA sequence comparisons between the consensus sequence and publicly funded genome data provided locations of 2.1 million single-nucleotide polymorphisms (SNPs). A random pair of human haploid genomes differed at a rate of 1 bp per 1250 on average, but there was marked heterogeneity in the level of polymorphism across the genome.
Less than 1% of all SNPs resulted in variation in proteins, but the task of determining which SNPs have functional consequences remains an open challenge.

10 mm Diameter Solid Titanium Tip

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13 mm Diameter Tapped Titanium Tip

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13 mm Diameter Solid Titanium Tip

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19 mm Diameter Tapped Titanium Tip

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19 mm Diameter Solid Titanium Tip

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25 mm Diameter Tapped Titanium Tip

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25 mm Diameter Solid Titanium Tip

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Flat Replaceable Tips 13 mm Diameter Flat Titanium Tip

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Flat Replaceable Tips 19 mm Diameter Flat Titanium Tip

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Description: use with corresponding Tapped Tips and Tapped Extender Tips

Flat Replaceable Tips 25 mm Diameter Flat Titanium Tip

0-120-0018
EUR 100
Description: use with corresponding Tapped Tips and Tapped Extender Tips

Titanium Cup Tip, 250 ml

0-120-0019
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Microtube Tray, 8 Position (for 250 ml Cup Tip)

0-120-0021
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Continuous Flow Chamber

0-120-0026
EUR 774
Description: includes Interface Washers

Interface Washers 1.5” Diameter, 5/Pkg

0-120-003
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13 mm Diameter Solid Titanium Extender Tip

0-120-0032
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13 mm Diameter Tapped Titanium Extender Tip

0-120-0033
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19 mm Diameter Solid Titanium Extender Tip

0-120-0034
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19 mm Diameter Tapped Titanium Extender Tip

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25 mm Diameter Solid Titanium Extender Tip

0-120-0036
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25 mm Diameter Tapped Titanium Extender Tip

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KoldPod, 1.5ml Micro Tube

0-120-0038
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Description: Thermo conductive tube pods

KoldPod, 15ml Conical Tube

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EUR 275
Description: Thermo conductive tube pods

KoldPod, 50ml Conical Tube

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Description: Thermo conductive tube pods

Model 150 V/T Ultrasonic Homogenizer

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Model 300 V/T Ultrasonic Homogenizer

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Description: Delivers up to 300 Watts of ultrasonic power to the Titanium Tip. The Timer and Duty Cycle function increase preciosion in sample.

SONABOZ Sound Abating Chamber

0-125-0001
EUR 1020
Description: Reduces cavitational sound emitted during processing.

Model 3000 Ultrasonic Homogenizer

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Model 3000MP Ultrasonic Homogenizer

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OMNICON® Zone Reader, 210-240V/50-60Hz

0-131-0002
EUR 35200
Description: Designed to Perform multi-plate Assays on round 90/100mm Petri Dishes. The integrated LED illumination system provides transmitted light for brightfield and darkfield illumination of transparent media.

OMNI-Noculator Peni Cylinder Filler, 210-240V/50-60Hz

0-134-0002
EUR 32200
Description: A robotic liquid handling system designed to dispense Peni Cylinders and fill Peni Cylinders with the corresponding antibiotic liquid sample.

Peni Cylinder Dispenser with Manual Hopper

0-144-0002
EUR 5406
Description: Dispenser can be configured to dispense 4 or 6 Peni Cylinders onto a petri dish.

Peni Cylinder Dispenser with Motorized Hopper, 100-240V/50-60Hz

0-144-0003
EUR 6254
Description: The motorized hopper can be configured to dispense 4 or 6 Peni Cylinders onto a petri Dispenser can be disassembled for disinfection.

Stainless Steel Peni Cylinder with Flat Face

0-144-0005
EUR 399
Description: sold in packages of 100 pieces

Stainless Steel Peni Cylinder with Chamfered Face

0-144-0006
EUR 412
Description: sold in packages of 100 pieces

Custom development of ELISAs for other species or antibody isotypes not listed in the catalog. Custom testing of samples for IgG/IgM/IgA or total (IgG+IgM+IgA)

000-CUS
EUR 602

Alpha-Bungarotoxin, CF®405S, 500 ug

00002
EUR 527
Description: Alpha-bungarotoxin from Krait snake venom (Bungarus multicinctus)

Alpha-bungarotoxin, CF405s

00002
EUR 594
Description: Minimum order quantity: 1 unit of 500uG

Alpha-Bungarotoxin, CF®405S, 500 ug

00002-1
EUR 527

Alpha-Bungarotoxin, CF®405S 100ug

00002-100ug
EUR 132
Description: Alpha-bungarotoxin from Krait snake venom (Bungarus multicinctus)

Alpha-Bungarotoxin, CF®680R, 500 ug

9-00003
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Description: Alpha-bungarotoxin from Krait snake venom (Bungarus multicinctus)

Alpha-Bungarotoxin, CF®680R, 500 ug

00003-1
EUR 527

Alpha-Bungarotoxin, CF®680R 100ug

9-00003
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Description: Alpha-bungarotoxin from Krait snake venom (Bungarus multicinctus)

Alpha-Bungarotoxin, CF®640R, 500 ug

9-00004
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Description: Alpha-bungarotoxin from Krait snake venom (Bungarus multicinctus)

Alpha-Bungarotoxin, CF®640R, 500 ug

00004-1
EUR 527

Alpha-Bungarotoxin, CF®640R 100ug

9-00004
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Description: Alpha-bungarotoxin from Krait snake venom (Bungarus multicinctus)

Alpha-Bungarotoxin, CF®488A, 500 ug

9-00005
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Description: Alpha-bungarotoxin from Krait snake venom (Bungarus multicinctus)

Alpha-Bungarotoxin, CF®488A, 500 ug

00005-1
EUR 527

Alpha-Bungarotoxin CF®488A 100ug

9-00005
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Description: Alpha-bungarotoxin from Krait snake venom (Bungarus multicinctus)

Alpha-Bungarotoxin, CF®568, 500 ug

9-00006
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Description: Alpha-bungarotoxin from Krait snake venom (Bungarus multicinctus)

Alpha-Bungarotoxin, CF®568, 500 ug

00006-1
EUR 527

Alpha-Bungarotoxin, CF®568 100ug

9-00006
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Description: Alpha-bungarotoxin from Krait snake venom (Bungarus multicinctus)

Alpha-Bungarotoxin, CF®594, 500 ug

9-00007
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Description: Alpha-bungarotoxin from Krait snake venom (Bungarus multicinctus)

Alpha-Bungarotoxin, CF®594, 500 ug

00007-1
EUR 527

Alpha-Bungarotoxin CF®594 100ug

9-00007
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Description: Alpha-bungarotoxin from Krait snake venom (Bungarus multicinctus)

Alpha-Bungarotoxin, CF®633, 500 ug

9-00009
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Description: Alpha-bungarotoxin from Krait snake venom (Bungarus multicinctus)

Alpha-Bungarotoxin, CF®633, 500 ug

00009-1
EUR 527

Alpha-Bungarotoxin, CF®633 100ug

9-00009
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Description: Alpha-bungarotoxin from Krait snake venom (Bungarus multicinctus)

SARS-CoV-2 Indicator Cell Line for RNA Replication - GFP Reporter only

0001-PP-001
EUR 12000
Description: SARS-CoV-2 GFP reporter cell line using HEK293T (ACE2/TMPRSS2) cells

Alpha-Bungarotoxin, 1 mg

00010-1
EUR 193
Description: Alpha-bungarotoxin from Krait snake venom (Bungarus multicinctus)

Alpha-Bungarotoxin, 1 mg

00010-1-1
EUR 193

Fluorescein-Alpha-Bungarotoxin, 500 ug

00011
EUR 376
Description: Alpha-bungarotoxin from Krait snake venom (Bungarus multicinctus)

Fluorescein-Alpha-Bungarotoxin, 500 ug

00011-1
EUR 376

Tetramethylrhodamine-Alpha-Bungarotoxin, 500 ug

00012
EUR 394
Description: Alpha-bungarotoxin from Krait snake venom (Bungarus multicinctus)

Tetramethylrhodamine-Alpha-Bungarotoxin, 500 ug

00012-1
EUR 394

Fluorescein-alpha-bungarotoxin, 10x50ug

00013
EUR 436
Description: Alpha-bungarotoxin from Krait snake venom (Bungarus multicinctus)

Fluorescein-alpha-bungarotoxin, 10x50ug

00013-1
EUR 436

Tetramethylrhodamine-A-Bungarotoxin, 10x50 ug

00014
EUR 494
Description: Alpha-bungarotoxin from Krait snake venom (Bungarus multicinctus)

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