BACKGROUND
Understanding Mycobacterium tuberculosis (Mtb) is very important to guide the transmission control strategy efficiently. typing traditional sports do not have enough discriminatory power to overcome the great plague. Here, we examine the potential of using the next-generation genome sequencing to identify the transmission chains associated outbreaks.
RESULTS
Over the long term (1997-2010) prospective, population-based molecular epidemiological surveillance consisting of a total of 2,301 patients, we identified a large outbreak caused by a strain of Mtb lineage Haarlem. The main measure performance results of whole genome sequencing (WGS) is the analysis of the degree of correlation with the analysis WGS contact tracing data and spatio-temporal distribution of plague cases. WGS analysis of 86 isolates revealed 85 single nucleotide polymorphisms (SNPs), grouping plague genome into seven groups (two to 24 isolates each), plus 36 unique SNP profile. WGS Results show that the first outbreak isolates were detected in 1997 were counterfeit clustered by classical genotype.
In 1998, one of the clones (called “Hamburg clone”) began to grow, apparently independently of differences in social environments initial case. genome-based grouping patterns that fit well with contact tracing data and geographic distribution of cases of grouping patterns based on the classic genotype. A maximum of three SNPs identified in the eight confirmed the chain of transmission from human to human, which involved 31 patients. We estimate the Mtb genome evolution rate of 0.4 mutations per genome per year. This level indicates that Mtb grown in natural hosts with a doubling time of about 22 h (400 generations per year). Based on genome variation is found, the emergence of clones Hamburg is dated back to the period between 1993 and 1997, then shortly before the discovery of the outbreak through epidemiological surveillance.
CONCLUSION
Our findings indicate that WGS is superior to conventional genotyping for tracking and investigating Mtb pathogenic micro-epidemics. WGS provides Mtb genome size evolution over time in the context of the natural host.
Highly multiplexed molecular inversion probe genotyping: SNP targeted more than 10,000 genotypes in a single test tube.
Large-scale genetic studies are very dependent on the multiplex SNP tests efficient and scalable. In this study, we report the development of Molecular Inversion Probe technology with four-color, single-array detection, applied to large scale genotyping of up to 12,000 SNPs per reaction. While generating 38 429 SNPs tests using this technology in a population of 30 trios of the family panel Humain Center d’Etude polymorphisms as part of the International HapMap project, we set up a conversion rate of approximately 90% of SNP with a concordance rate of> 99.6% and the level of completeness of> 98% to test the level of multiplexing up to 12,000plex.
Yeast Autolysate |
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| RM194-500G | EWC Diagnostics | 1 unit | EUR 33.33 |
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Description: Yeast Autolysate |
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Casitone Glycerol Yeast Autolysate |
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| M381-100G | EWC Diagnostics | 1 unit | EUR 15.93 |
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Description: Casitone Glycerol Yeast Autolysate |
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Casitone Glycerol Yeast Autolysate |
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| M381-500G | EWC Diagnostics | 1 unit | EUR 39.2 |
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Description: Casitone Glycerol Yeast Autolysate |
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Casitone Glycerol Yeast Autolysate |
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| MV381-100G | EWC Diagnostics | 1 unit | EUR 15.93 |
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Description: Casitone Glycerol Yeast Autolysate |
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Casitone Glycerol Yeast Autolysate |
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| MV381-500G | EWC Diagnostics | 1 unit | EUR 39.2 |
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Description: Casitone Glycerol Yeast Autolysate |
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Czapek Yeast Autolysate Agar (CYA Agar) |
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| M2061-100G | EWC Diagnostics | 1 unit | EUR 18.16 |
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Description: Czapek Yeast Autolysate Agar (CYA Agar) |
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Czapek Yeast Autolysate Agar (CYA Agar) |
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| M2061-500G | EWC Diagnostics | 1 unit | EUR 55.59 |
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Description: Czapek Yeast Autolysate Agar (CYA Agar) |
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Yeast Autolysate (Yeast Peptone) BactoBio for microbiology |
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| 67146 | Sisco Laboratories | 100 Gms | EUR 5.99 |
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Description: Part D |
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Yeast Autolysate (Yeast Peptone) BactoBio for microbiology |
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| 67146-1 | Sisco Laboratories | 500 Gms | EUR 22.24 |
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Description: Part D |
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Perfringens S.F.P. Supplement ( S.F.P. Supplement ) |
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| 92096 | Sisco Laboratories | 5 vl | EUR 9.41 |
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Description: Part D |
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Perfringens S.F.P. Supplement ( S.F.P. Supplement ) |
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| 92096-1 | Sisco Laboratories | 4 x5 vl | EUR 31.64 |
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Description: Part D |
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Perfringens T.S.C. Supplement (T.S.C Supplement) (200mg/vl) |
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| 55688 | Sisco Laboratories | 5 vl | EUR 10.26 |
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Description: Part D |
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Perfringens T.S.C. Supplement (T.S.C Supplement) (200mg/vl) |
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| 55688-1 | Sisco Laboratories | 4 x5 vl | EUR 29.08 |
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Description: Part D |
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KV Supplement |
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| 70663 | Sisco Laboratories | 5 vl | EUR 13.68 |
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Description: Part D |
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V.C.N. Supplement |
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| FD023-5VL | EWC Diagnostics | 1 unit | EUR 37.09 |
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Description: V.C.N. Supplement |
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*V.C.N. Supplement |
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| FD023-5X5VL | EWC Diagnostics | 1 unit | EUR 137.06 |
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Description: *V.C.N. Supplement |
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V.C.N.T. Supplement |
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| FD024-5VL | EWC Diagnostics | 1 unit | EUR 37.09 |
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Description: V.C.N.T. Supplement |
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*V.C.N.T. Supplement |
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| FD024-5X5VL | EWC Diagnostics | 1 unit | EUR 145.42 |
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Description: *V.C.N.T. Supplement |
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C.B.I. Supplement |
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| FD049-5VL | EWC Diagnostics | 1 unit | EUR 23.52 |
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Description: C.B.I. Supplement |
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KV Supplement |
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| FD116-5VL | EWC Diagnostics | 1 unit | EUR 27.32 |
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Description: KV Supplement |
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V.P. Supplement |
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| FD349-5VL | EWC Diagnostics | 1 unit | EUR 19.86 |
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Description: V.P. Supplement |
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V.C.A.T. Supplement |
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| FD353-5VL | EWC Diagnostics | 1 unit | EUR 28.98 |
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Description: V.C.A.T. Supplement |
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CN Supplement |
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| PHS007-5VL | EWC Diagnostics | 1 unit | EUR 21.79 |
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Description: CN Supplement |
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VCN Supplement |
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| 34123 | Sisco Laboratories | 5 vl | EUR 19.67 |
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Description: Part D |
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VCN Supplement |
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| 34123-1 | Sisco Laboratories | 5 x5 vl | EUR 69.28 |
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Description: Part D |
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CNA Supplement |
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| 64078 | Sisco Laboratories | 5 vl | EUR 13.68 |
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Description: Part D |
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CPC Supplement |
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| 65165 | Sisco Laboratories | 5 vl | EUR 17.96 |
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Description: Part D |
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CFC Supplement |
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| 70984 | Sisco Laboratories | 5 vl | EUR 12.83 |
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Description: Part D |
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CFC Supplement |
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| 70984-1 | Sisco Laboratories | 5 x5 vl | EUR 39.34 |
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Description: Part D |
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CBI Supplement |
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| 18871 | Sisco Laboratories | 5 vl | EUR 11.97 |
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Description: Part D |
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CFC Supplement |
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| FD036-5VL | EWC Diagnostics | 1 unit | EUR 24.15 |
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Description: CFC Supplement |
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*CFC Supplement |
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| FD036-5X5VL | EWC Diagnostics | 1 unit | EUR 74.37 |
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Description: *CFC Supplement |
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GTC Supplement |
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| FD044-5VL | EWC Diagnostics | 1 unit | EUR 19.78 |
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Description: GTC Supplement |
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GBS Supplement |
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| FD054-5VL | EWC Diagnostics | 1 unit | EUR 17.21 |
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Description: GBS Supplement |
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CPC Supplement |
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| FD110-5VL | EWC Diagnostics | 1 unit | EUR 37.25 |
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Description: CPC Supplement |
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CNA Supplement |
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| FD115-5VL | EWC Diagnostics | 1 unit | EUR 27.32 |
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Description: CNA Supplement |
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*NYC Supplement |
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| FD150-5VL | EWC Diagnostics | 1 unit | EUR 23.97 |
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Description: *NYC Supplement |
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VIA Supplement |
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| FD312-5VL | EWC Diagnostics | 1 unit | EUR 35.83 |
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Description: VIA Supplement |
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NAD Supplement |
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| FD327-5VL | EWC Diagnostics | 1 unit | EUR 27.95 |
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Description: NAD Supplement |
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LCN Supplement |
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| FD338-5VL | EWC Diagnostics | 1 unit | EUR 21.07 |
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Description: LCN Supplement |
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LCN Supplement |
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| FD338-5X5VL | EWC Diagnostics | 1 unit | EUR 60.93 |
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Description: LCN Supplement |
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PCP Supplement |
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| FD347-5VL | EWC Diagnostics | 1 unit | EUR 25.86 |
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Description: PCP Supplement |
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CNC Supplement |
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| PHS001-5VL | EWC Diagnostics | 1 unit | EUR 27.22 |
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Description: CNC Supplement |
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CNP Supplement |
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| PHS003-5VL | EWC Diagnostics | 1 unit | EUR 22.72 |
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Description: CNP Supplement |
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CNF Supplement |
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| PHS006-5VL | EWC Diagnostics | 1 unit | EUR 26.12 |
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Description: CNF Supplement |
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CNV Supplement |
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| PHS014-5VL | EWC Diagnostics | 1 unit | EUR 26.12 |
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Description: CNV Supplement |
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NNB Supplement |
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| PHS015-5VL | EWC Diagnostics | 1 unit | EUR 22.72 |
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Description: NNB Supplement |
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PSA Supplement |
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| PHS018-5VL | EWC Diagnostics | 1 unit | EUR 19.23 |
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Description: PSA Supplement |
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VCNT Supplement |
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| 32249 | Sisco Laboratories | 5 vl | EUR 19.67 |
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Description: Part D |
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VCNT Supplement |
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| 32249-1 | Sisco Laboratories | 5 x5 vl | EUR 69.28 |
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Description: Part D |
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CCDA Supplement |
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| FD135F-5VL | EWC Diagnostics | 1 unit | EUR 28.41 |
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Description: CCDA Supplement |
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XLT4 Supplement |
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| FD152-1VL | EWC Diagnostics | 1 unit | EUR 27.01 |
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Description: XLT4 Supplement |
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CATC Supplement |
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| FD235-5VL | EWC Diagnostics | 1 unit | EUR 23.84 |
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Description: CATC Supplement |
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TSBV Supplement |
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| FD323-5VL | EWC Diagnostics | 1 unit | EUR 23.44 |
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Description: TSBV Supplement |
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OADS Supplement |
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| FD348-5VL | EWC Diagnostics | 1 unit | EUR 34.65 |
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Description: OADS Supplement |
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OADS Supplement |
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| FD348-5X5VL | EWC Diagnostics | 1 unit | EUR 142.01 |
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Description: OADS Supplement |
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NMPT Supplement |
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| PHS002-5VL | EWC Diagnostics | 1 unit | EUR 22.72 |
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Description: NMPT Supplement |
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CNNP Supplement |
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| PHS004-5VL | EWC Diagnostics | 1 unit | EUR 38.62 |
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Description: CNNP Supplement |
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CNTB Supplement |
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| PHS005-5VL | EWC Diagnostics | 1 unit | EUR 22.72 |
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Description: CNTB Supplement |
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CNVB Supplement |
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| PHS009-5VL | EWC Diagnostics | 1 unit | EUR 27.22 |
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Description: CNVB Supplement |
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CCTP Supplement |
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| PHS010-5VL | EWC Diagnostics | 1 unit | EUR 21.79 |
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Description: CCTP Supplement |
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CNFT Supplement |
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| PHS012-5VL | EWC Diagnostics | 1 unit | EUR 22.72 |
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Description: CNFT Supplement |
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CCFT Supplement |
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| PHS017-5VL | EWC Diagnostics | 1 unit | EUR 27.22 |
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Description: CCFT Supplement |
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PEMBA Supplement |
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| FD200-5VL | EWC Diagnostics | 1 unit | EUR 21.02 |
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Description: PEMBA Supplement |
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*PEMBA Supplement |
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| FD200-5X5VL | EWC Diagnostics | 1 unit | EUR 64.1 |
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Description: *PEMBA Supplement |
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FRIIS Supplement |
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| FD317-5VL | EWC Diagnostics | 1 unit | EUR 32.68 |
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Description: FRIIS Supplement |
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TYCSB Supplement |
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| FD321-5VL | EWC Diagnostics | 1 unit | EUR 14.2 |
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Description: TYCSB Supplement |
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CNBGM Supplement |
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| PHS016-5VL | EWC Diagnostics | 1 unit | EUR 38.62 |
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Description: CNBGM Supplement |
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Lactic Supplement |
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| 84282 | Sisco Laboratories | 5 vl | EUR 11.12 |
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Description: Part D |
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Sulpha Supplement |
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| 34050 | Sisco Laboratories | 5 vl | EUR 13.68 |
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Description: Part D |
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Sulpha Supplement |
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| FD068-5VL | EWC Diagnostics | 1 unit | EUR 26.51 |
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Description: Sulpha Supplement |
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Fraser Supplement |
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| FD141-5VL | EWC Diagnostics | 1 unit | EUR 18.14 |
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Description: Fraser Supplement |
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Fraser Supplement |
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| FD141-5X5VL | EWC Diagnostics | 1 unit | EUR 85.24 |
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Description: Fraser Supplement |
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Poctri Supplement |
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| FD241-5VL | EWC Diagnostics | 1 unit | EUR 6.15 |
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Description: Poctri Supplement |
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CCFTNB Supplement |
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| PHS011-5VL | EWC Diagnostics | 1 unit | EUR 38.62 |
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Description: CCFTNB Supplement |
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Strepto Supplement |
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| 11475 | Sisco Laboratories | 5 vl | EUR 10.26 |
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Description: Part D |
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Strepto Supplement |
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| 11475-1 | Sisco Laboratories | 5 x5 vl | EUR 32.5 |
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Description: Part D |
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Strepto Supplement |
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| FD031-5VL | EWC Diagnostics | 1 unit | EUR 20.06 |
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Description: Strepto Supplement |
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*Strepto Supplement |
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| FD031-5X5VL | EWC Diagnostics | 1 unit | EUR 62.85 |
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Description: *Strepto Supplement |
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*Lachica's Supplement |
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| FD209-1VL | EWC Diagnostics | 1 unit | EUR 12.65 |
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Description: *Lachica's Supplement |
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N-2 Supplement (100x) |
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| TBS8081-5ML | Tribioscience | 5mL | EUR 84.5 |
Cetrinix Supplement |
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| 94532 | Sisco Laboratories | 5 vl | EUR 14.54 |
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Description: Part D |
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Cetrinix Supplement |
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| 94532-1 | Sisco Laboratories | 5 x5 vl | EUR 35.92 |
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Description: Part D |
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Cetrinix Supplement |
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| FD029-5VL | EWC Diagnostics | 1 unit | EUR 26.51 |
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Description: Cetrinix Supplement |
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*Cetrinix Supplement |
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| FD029-5X5VL | EWC Diagnostics | 1 unit | EUR 67.27 |
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Description: *Cetrinix Supplement |
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*Neomycin Supplement |
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| FD149-5VL | EWC Diagnostics | 1 unit | EUR 17.84 |
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Description: *Neomycin Supplement |
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Neomycin Supplement |
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| FD174-5VL | EWC Diagnostics | 1 unit | EUR 22.73 |
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Description: Neomycin Supplement |
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Cefexime Supplement |
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| FD246-5VL | EWC Diagnostics | 1 unit | EUR 11.53 |
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Description: Cefexime Supplement |
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Cefexime Supplement |
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| FD246-5X5VL | EWC Diagnostics | 1 unit | EUR 32.23 |
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Description: Cefexime Supplement |
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Hayflick Supplement |
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| FD300-5VL | EWC Diagnostics | 1 unit | EUR 23.23 |
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Description: Hayflick Supplement |
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Diphenyl Supplement |
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| FD356-5VL | EWC Diagnostics | 1 unit | EUR 8.14 |
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Description: Diphenyl Supplement |
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CN Supplement - I |
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| PHS008-5VL | EWC Diagnostics | 1 unit | EUR 26.12 |
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Description: CN Supplement - I |
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Cefoxitin Supplement |
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| FD259-5VL | EWC Diagnostics | 1 unit | EUR 27.32 |
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Description: Cefoxitin Supplement |
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Meropenem Supplement |
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| FD262-5VL | EWC Diagnostics | 1 unit | EUR 30.49 |
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Description: Meropenem Supplement |
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Meropenem Supplement |
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| FD262-5X5VL | EWC Diagnostics | 1 unit | EUR 79.46 |
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Description: Meropenem Supplement |
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Coagulase Supplement |
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| FD362-5VL | EWC Diagnostics | 1 unit | EUR 69.09 |
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Description: Coagulase Supplement |
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Coagulase Supplement |
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| FD362-5X5VL | EWC Diagnostics | 1 unit | EUR 234.73 |
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Description: Coagulase Supplement |
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Ampicillin Supplement |
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| FD082-5VL | EWC Diagnostics | 1 unit | EUR 25.1 |
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Description: Ampicillin Supplement |
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Novobiocin Supplement |
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| FD096-5VL | EWC Diagnostics | 1 unit | EUR 25.1 |
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Description: Novobiocin Supplement |
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*Novobiocin Supplement |
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| FD096-5X5VL | EWC Diagnostics | 1 unit | EUR 62.85 |
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Description: *Novobiocin Supplement |
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Moxalactam Supplement |
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| FD151-5VL | EWC Diagnostics | 1 unit | EUR 26.7 |
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Description: Moxalactam Supplement |
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Vancomycin Supplement |
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| FD233-5VL | EWC Diagnostics | 1 unit | EUR 30.49 |
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Description: Vancomycin Supplement |
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Vancomycin Supplement |
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| FD261-5VL | EWC Diagnostics | 1 unit | EUR 29.23 |
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Description: Vancomycin Supplement |
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Vancomycin Supplement |
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| FD261-5X5VL | EWC Diagnostics | 1 unit | EUR 64.75 |
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Description: Vancomycin Supplement |
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HAT Supplement(50X) |
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| CA010-010 | GenDepot | 100ml | EUR 151.2 |
BSK-H Supplement |
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| FD180-100ML | EWC Diagnostics | 1 unit | EUR 113.69 |
|
Description: BSK-H Supplement |
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Ticarcillin Supplement |
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| FD102-5VL | EWC Diagnostics | 1 unit | EUR 24.65 |
|
Description: Ticarcillin Supplement |
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Chromogenic Supplement |
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| FD270-5VL | EWC Diagnostics | 1 unit | EUR 41.54 |
|
Description: Chromogenic Supplement |
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CDM-XF Supplement |
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| abx298010-5ml | Abbexa | 5 ml | EUR 343.2 |
Linco T Supplement |
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| FD026-5VL | EWC Diagnostics | 1 unit | EUR 26.07 |
|
Description: Linco T Supplement |
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Fraser Supplement (250mg/vl) |
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| 97539 | Sisco Laboratories | 5 vl | EUR 9.41 |
|
Description: Part D |
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Vanclo T Supplement |
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| FD028-5VL | EWC Diagnostics | 1 unit | EUR 31.27 |
|
Description: Vanclo T Supplement |
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CCFTNB Supplement - I |
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| PHS013-5VL | EWC Diagnostics | 1 unit | EUR 38.62 |
|
Description: CCFTNB Supplement - I |
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Cycloheximide Supplement |
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| FD311-5VL | EWC Diagnostics | 1 unit | EUR 28.41 |
|
Description: Cycloheximide Supplement |
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Cycloheximide Supplement |
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| FD311-5X5VL | EWC Diagnostics | 1 unit | EUR 85.26 |
|
Description: Cycloheximide Supplement |
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Antimicrobial Supplement |
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| PCT1106-100ML | EWC Diagnostics | 1 unit | EUR 88.23 |
|
Description: Antimicrobial Supplement |
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Antimicrobial Supplement |
|||
| PCT1106-50ML | EWC Diagnostics | 1 unit | EUR 49.72 |
|
Description: Antimicrobial Supplement |
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Vitamin K1 Supplement |
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| FD114-5VL | EWC Diagnostics | 1 unit | EUR 19.1 |
|
Description: Vitamin K1 Supplement |
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CC Supplement, Modified |
|||
| FD169-5VL | EWC Diagnostics | 1 unit | EUR 22.26 |
|
Description: CC Supplement, Modified |
|||
CC Supplement, Modified |
|||
| FD169-5X5VL | EWC Diagnostics | 1 unit | EUR 54.18 |
|
Description: CC Supplement, Modified |
|||
Sorbic Acid Supplement |
|||
| FD236-5VL | EWC Diagnostics | 1 unit | EUR 11.38 |
|
Description: Sorbic Acid Supplement |
|||
Modified CPC Supplement |
|||
| FD110F-5VL | EWC Diagnostics | 1 unit | EUR 39 |
|
Description: Modified CPC Supplement |
|||
LM Selective Supplement |
|||
| FD330-5VL | EWC Diagnostics | 1 unit | EUR 29.67 |
|
Description: LM Selective Supplement |
|||
Supplement C 5Ml - PK6 |
|||
| 252710 | Scientific Laboratory Supplies | PK6 | EUR 486 |
Oleic Albumin Supplement |
|||
| FD020-5VL | EWC Diagnostics | 1 unit | EUR 23.23 |
|
Description: Oleic Albumin Supplement |
|||
*Oleic Albumin Supplement |
|||
| FD020-5X5VL | EWC Diagnostics | 1 unit | EUR 82.59 |
|
Description: *Oleic Albumin Supplement |
|||
CAT Selective Supplement |
|||
| FD145-5VL | EWC Diagnostics | 1 unit | EUR 27.01 |
|
Description: CAT Selective Supplement |
|||
*CAT Selective Supplement |
|||
| FD145-5X5VL | EWC Diagnostics | 1 unit | EUR 64.75 |
|
Description: *CAT Selective Supplement |
|||
Mycoplasma Supplement - P |
|||
| FD182-1VL | EWC Diagnostics | 1 unit | EUR 49.09 |
|
Description: Mycoplasma Supplement - P |
|||
Iron Sulphate Supplement |
|||
| FD237-5VL | EWC Diagnostics | 1 unit | EUR 11.68 |
|
Description: Iron Sulphate Supplement |
|||
*Iron Sulphate Supplement |
|||
| FD237-5X5VL | EWC Diagnostics | 1 unit | EUR 47.07 |
|
Description: *Iron Sulphate Supplement |
|||
GTC Supplement (1.25mg/vl) |
|||
| 30963 | Sisco Laboratories | 5 vl | EUR 6.84 |
|
Description: Part D |
|||
Furthermore, these individual metrics can be “traded off” and, at the expense of a small portion of the conversion rates, the accuracy can be improved to a very high level. No loss of performance seen when the scale of 6,000plex to 12,000plex the test, it validates the technological capability to suppress cross-reactivity at high multiplex level. These results indicate the suitability of this technology for a comprehensive association study using targeted SNPs in linkage disequilibrium studies indirectly or directly screen for the mutation causes.