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BaseClear

Contact Details

Baseclear BV

Einsteinweg 5 2333 CC Leiden

B. J. Reichert

+31715233917

Hotel Description

BaseClear, founded in 1993, is an independent contract research laboratory in the field of DNA research. BaseClear’s enthusiastic, 65-strong team works on development of DNA technology from its laboratory in Leiden Bioscience Park. This technology is applied in contract research for BaseClear customers worldwide operating in many sectors, from the food and pharmaceutical industries to plant breeding. Innovation and quality are the top priorities in the services provided by this specialist laboratory. 

Our departments and facilities:

Genome sequencing department
We have access to state of art Next Generation DNA sequencing technology from Oxford Nanopore technologies, Illumina (HiSEQ2500, MiSEQ) and Pacific Biosciences (PacBio Sequel and RS II). Our key scientist have developed and optimised a large set of protocols and techniques to run a variety of sample types and sample quantities. Service include genome sequencing, RNA-seq, metagenomics and microbial profiling. Automated, robotic sample prep methods are available to handle samples in a High Throughput manner.

Bioinformatics
Our Bio-informaticians handle the output of our NextGen sequencers and develop methods and protocols to do challenging analyses of complex data. We have an in-house large server/computing platform to do these analysis and co-operate with specialised partners to offer a broad range of analysing solutions. Further the team develops state of the art software which is in some cases published and offered to the scientific community

Molecular and synthetic biology lab
A variety of cloning, PCR and synthetic biology approaches (from small genes to chromosomes) in laboratories capable of working at ML2 level and ample experience in handling and cloning in several host organisms (E.coli, Bacillus, yeast, fungi)

Genomics
Private
  • Industrial biotech
  • Other
  • Biodiversity & ecology
  • Biomedical & health
  • Agri & Food
  • Bio-informatics expertise
  • Custom genomics assays
  • DNA extraction
  • Assay validation
  • Microbial genomics
  • Strain characterization
  • Microbiome analysis
  • Biomolecule and gene discovery
  • Biomarker and vaccine development
  • Antibiotic resistance screening

Expertise and Track Record

43500984115 Unravel the genetic characteristics of mcr-1 positive Enterobacteriaceae isolated from chicken meat in the Netherlands with E.J. Schrauwen (Avans Hogeschool). 43500984077 Characterizing antibiotic resistance development of clinical dose regimens using next-generation sequencing to enable personalized treatments of bacterial infections with J.G.C. van Hasselt (LACDR). 43500984049 The role of microbe-microbe interactions in the evolution of antibiotic resistance with M.G.J. de Vos (Wageningen University)

BaseClear has access to all the latest sequencing technologies, including those of Oxford Nanopore Technologies, Pacific Biosciences and Illumina. BaseClear has been offering convenient and high-quality solutions for over 20 years. BaseClear distinguishes itself by having a highly customer-oriented approach, direct communication and a close collaboration with our customers to develop solutions specifically matched to their needs.

Our team will take care of the full process from start-to-finish and make sure you are always up to date about the status of your project. You can always ask our specialists to provide consultancy and support to define the optimal setup for your project (e.g. sample or DNA/RNA extration method, library prep protocol, run type, data amount). The data generated is carefully processed and analysed by our specialized bioinformatics team, thus offering you a complete analysis solution from wet lab to data interpretation.

Toward single contig high quality genomes with our PacBio Sequel: https://www.baseclear.com/blog/towards-single-contig-high-quality-genomes_40_13.html

Optimized protocols for DNA extraction: https://www.baseclear.com/blog//nucleic-acid-extraction-is-an-essential-part-of-your-sequencing-project_40_7.html

Close your bacterial genomes using Oxford Nanopore sequencing technology: https://www.baseclear.com/blog/bacterial-genome-analysis-using-oxford-nanopore-sequencing-technology_40_4.html

In-house developed bioinformatics tool, SSPACE: https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-15-211

The king cobra genome reveals dynamic gene evolution and adaptation in the snake venom system: http://www.pnas.org/content/110/51/20651.abstract

At this moment we have limited experience with the integration of different data-sets, but this is one of our focus areas for which we are interested to partner.

  • A case of Ignatzschineria bacteraemia in an unconscious man from the Netherlands.: https://www.ncbi.nlm.nih.gov/pubmed/28348762
  • Comparative genomics reveals high biological diversity and specific adaptations in the industrially and medically important fungal genus Aspergillus: https://www.ncbi.nlm.nih.gov/pubmed/28196534
  • Characterisation of clinical Staphylococcus aureus isolates harbouring mecA or Panton-Valentine leukocidin genes from four tertiary care hospitals in Indonesia: https://www.ncbi.nlm.nih.gov/pubmed/26970318
  • Genome Sequence of EU-Unauthorized Genetically Modified Bacillus subtilis Strain 2014-3557 Overproducing Riboflavin, Isolated from a Vitamin B2 80% Feed Additive: https://www.ncbi.nlm.nih.gov/pubmed/25858836
  • Bioinformatics approaches for viral metagenomics in plants using short RNAs: model case of study and application to a Cicer arietinum population: https://www.ncbi.nlm.nih.gov/pubmed/25674078
  • Next-generation sequencing-based genome diagnostics across clinical genetics centers: implementation choices and their effects: https://www.ncbi.nlm.nih.gov/pubmed/25626705
  • RNA structural constraints in the evolution of the influenza A virus genome NP segment: https://www.ncbi.nlm.nih.gov/pubmed/25180940
  • Multiple Sequence Alignment: https://www.ncbi.nlm.nih.gov/pubmed/27896722
  • Scaffolding pre-assembled contigs using SSPACE: https://www.ncbi.nlm.nih.gov/pubmed/21149342
  • Toward almost closed genomes with GapFiller: https://www.ncbi.nlm.nih.gov/pubmed/22731987

Generade is the center of expertise genomics, developing new knowledge and technology in the field of genomics. Generade is a collaboration between BaseClear, LUMC, Naturalis Biodiversity Center, Hogeschool Leiden and the University of Leiden. Generade focuses on education and training, research and entrepeneurship.

Generade supports the regular education and post graduate courses of future-proof professionals so they can respond to the rapid technological developments and translate them into their professional practice in the Life Sciences. Generade also promotes innovation in business through performing and financing applied research in the field of genomics. Generade offers support in the organization of research projects and in finding the right partners for co-creation. In addition Generade stimulates innovation in the area of Life Sciences by supporting small (start-up) companies.

Hotel Characteristics

  • PhD-level scientists: 8
  • Dedicated technicians: 22
  • Lab managers: 6
  • Biostaticians: 8
  • IT_specialists: 8

100

  • Oxford Nanopore Technologies GridION X5
  • Oxford Nanopore Technologies MinION
  • Illumina HiSeq2500
  • Illumina MiSeq
  • PacBio Sequel
  • PacBio RS II
  • Vitek MS Maldi-TOF from bioMérieux
  • ABI3730(XL) from Thermo Fisher Scientific
  • MicroSEQ system from Life Technologies
  • Beckman FX lab automation workstation

Our labs are ISO17025 accredited and GMP compliant.

Data is usually deliverd via our internally build order portals. Server security and data integrity is guaranteed through through SSH server-client connections and additional security measures.