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  • Baseclear - Order forms
    Epigenetics DNA purification RNA purification Other products Sample kits Epigenetic services Bio Basic Gene Synthesis Protein expression and purification Peptide synthesis Custom antibody service Kisker Biotech Lab disposables Lab equipment Microparticles Industries Industrial Biotechnology Food Ingredients Pharma Health Water Environment Clinical Diagnostics laboratories Agro Sciences Academic Research institutes About BaseClear Our company Meet our team History Partners Distributors Why BaseClear Reasons to work with BaseClear Research development Quality assurance Technologies Information News Ordering Career Jobs Internships Contact Contact details Contact form Request quotation Order forms Blog Home Our services Lab Products Industries About BaseClear Blog Our company Why BaseClear Information Contact Contact details Contact form Request quotation Order forms ORDER FORMS This is the list of all our current order forms For most services it is also possible to use our online platform https orders baseclear com to create order forms Is your service not listed or can we be of any assistance don t hesitate to contact us info baseclear com or 31 0 71 523 3917 Synthetic Biology Gene synthesis Orderform PCR cloning Orderform Sanger Sequencing Project sequencing Orderform Full 24H sequencing Orderform Quick Shot Orderform 96 well sequencing Orderform 96 well premix sequencing Orderform 96 well load

    Original URL path: http://www.baseclear.com/contact/orderforms (2016-02-12)
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  • Baseclear - Blog
    consists of assembly and annotated draft genomes and researchers are required to submit these to the National Center for Biotechnology Information NCBI archive prior to publication of the manuscript Although this seems a small step of the research process it may become quite a complex task to share sequence data with the scientific community through these databases as many validation criteria apply Read more Nucleid acid extraction is an essential part of your sequencing project Microbial profiling studies depend heavily on obtaining high molecular weight sufficient concentration and adequate quality DNA As different extraction methods differ in their principle of obtaining nucleic acids and the outcome in terms of quantity as well as quality this post describes basic considerations that help microbial ecologists select an appropriate extraction method for their sequencing project Read more DNA RNA Sequencing Platforms A Short Overview With this blog Björn te Boekhorst provides a short overview of the history of DNA and RNA sequencing the market leading sequencing platforms and a brief selection of emerging technologies Read more Oxford Nanopore is here to stay ready for the challenges A rollercoaster with many ups this is how Hans Jansen Senior scientist at ZF screens describes their experiences with the MinION Nanopore sequencer so far About a year ago ZF screens decided to take part to the early access program of Oxford Nanopore Technologies ONT to experience first hand the promises of this new technology Read more How to close your bacterial genome using Oxford Nanopore sequencing technology The latest long read sequencing technologies in particular that of Oxford Nanopore Technologies have the potential to further ease the process of bacterial genomic research and breakdown the analysis costs So called USB stick DNA sequencing is promised to have an enormous strong impact on genomic research as the

    Original URL path: http://www.baseclear.com/blog (2016-02-12)
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  • Baseclear - Disclaimer
    INFORMATION WE GATHER We require this information to understand your needs and provide you with a better service and in particular for the following reasons Internal record keeping We may use the information to improve our products and services We may periodically send promotional emails about new products special offers or other information which we think you may find interesting using the email address which you have provided From time to time we may also use your information to contact you for market research purposes We may contact you by email phone fax or mail We may use the information to customise the website according to your interests SECURITY We are committed to ensuring that your information is secure In order to prevent unauthorised access or disclosure we have put in place suitable physical electronic and managerial procedures to safeguard and secure the information we collect online How we use cookies A cookie is a small file which asks permission to be placed on your computer s hard drive Once you agree the file is added and the cookie helps analyse web traffic or lets you know when you visit a particular site Cookies allow web applications to respond to you as an individual The web application can tailor its operations to your needs likes and dislikes by gathering and remembering information about your preferences We use traffic log cookies to identify which pages are being used This helps us analyse data about webpage traffic and improve our website in order to tailor it to customer needs We only use this information for statistical analysis purposes and then the data is removed from the system Overall cookies help us provide you with a better website by enabling us to monitor which pages you find useful and which you do not

    Original URL path: http://www.baseclear.com/privacy-policy (2016-02-12)
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  • Baseclear - Terms Of Service
    5 The carrying out of orders by BaseClear will take place according to procedures determined by BaseClear All rights to these procedures and other inventions developed by BaseClear pursuant to a given assignment shall belong to BaseClear BaseClear shall be entitled to perform similar procedures for other clients unless otherwise stipulated 6 1 A deadline agreed upon for work to be performed by BaseClear must always be considered a guideline and is never binding for BaseClear unless otherwise expressly agreed upon in writing 6 2 In the event the time taken to perform the work threatens to exceed the agreed upon deadline BaseClear will notify the client as soon as practicable 7 1 BaseClear is at all times authorised to have work performed by third parties and does not require prior consent from the client for such subcontracting 7 2 BaseClear does not accept any responsibility or liability for assistance provided by third parties who upon request of the client have been involved in performing the commissioned work 8 1 BaseClear shall maintain secrecy with regard to information and results ensuing from an order and shall destroy such information no later than five years following completion of said order Unless required in compliance with legal obligations this information will be disclosed only to the client who issued the order 8 2 The client is obliged to maintain secrecy regarding all information that becomes known to said client pursuant to an order regarding BaseClear or BaseClear s operating procedures The client may only disclose information other than the direct results to third parties subject to express written consent by BaseClear The client is obliged to refer to the name BaseClear when disclosing such information 9 1 BaseClear will use reasonable skill and care in performing the contracted work Claims regarding the achievement of results can however only be made following the issue of an express written guarantee by BaseClear that such results will indeed be achieved 9 2 BaseClear shall repeat the work performed free of charge if the set requirements for reasonable skill and care have not been satisfied provided the client submits a request for this within two weeks of obtaining the results and provided that new samples for insofar as this is necessary are made available to BaseClear 9 3 BaseClear s liability to the client will be limited to damages which will never exceed the fees paid to BaseClear or the agreed upon fees for the order in question 9 4 BaseClear will never be liable to the client for subsequent damages incurred by the client or any third party arising from faults or errors in the results of the order unless such faults or errors can be attributed to gross negligence or proven intent 9 5 Under no circumstances can BaseClear be held liable with the exception of and insofar as its business liability insurance and or professional indemnity Insurance covers such damages should the occasion arise 10 The client must ensure that the samples to

    Original URL path: http://www.baseclear.com/terms-of-service (2016-02-12)
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  • Baseclear
    data output and a delivery time of only 4 weeks These sharp delivery times are made possible by dedicated internal processes together with automation of lab protocols and the recent upgrade of our sequencer to HiSeq 2500 The first RAPID projects have now been completed with great success and customers are very satisfied with this new service For specific projects we can even arrange faster delivery times on request please don t hesitate to contact us for more info RNA SEQ UPDATE We now offer complete RNA seq solutions including optional rRNA depletion and Meta transcriptomics services Additionally our bioinformatics team has further optimized the RNA seq pipeline for denovo transcriptome assembly annotation and gene expression analysis This unique assembly pipeline combines Trinity software and BLAST resulting in a fully annotated transcriptome including EC CAZy GO and KO terms Additional quality controls are standardly performed to evaluate the assembly quality including checking the presence or absence of core transcripts that are conserved among most species Transcript expression is measured using advanced CLCbio analysis software and comparative analyses are carried out using rigorous statistical criteria The pipeline is also well suited for analysis of meta transcriptomes RECENT TRANSCRIPTOMICS PROJECT COMPLETED Meta transcriptomics on waste water samples identification of all active species and functions of organisms in a water sample Rapid RNA seq data analysis provided a full RNA seq report and data analysis within 2 weeks Rapid RNA seq on 10 Yeast strains including RNA isolation and sequencing 10 yeast transcriptomes within 4 weeks Gene expression analysis of Streptomyces strains including rRNA depletion 20 Mio reads sequence data and gene expression analysis for 5 Streptomyces strains ZonMW NWO ALW call closes in one week Just before the summer ZonMW published a call for proposals for public private research partnerships to get

    Original URL path: http://www.baseclear.com/news/New-BaseClear-Premium-NGS-Rapid-Sequencing-services!_90_16.html (2016-02-12)
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  • Baseclear
    to overview New high throughput assembly and annotation pipeline Our bioinformatics team has now completed the setup of a high throughput HT assembly and annotation pipeline which rapidly turns nucleotides into meaningful genomes at an incredibly low price After an extensive filtering i e removal of adapters and phix and trimming i e removal of low quality bases of the raw reads the polished reads are fed to our de novo assembly pipeline This unique masterpiece connects the best available assembly software tools to guarantee high quality assemblies First a draft assembly is computed using CLCbio s de novo assembly tool currently considered the state of the art assembler in the field The draft genome is further polished using our highly cited BaseTools SSPACE Premium for scaffolding and GapFiller for automated gap closure Second the finished genomes are annotated using our brand new annotation pipeline which is based on the Prokka Prokaryotic Genome Annotation System It includes a number of features among which CDS prediction annotation using BLAST on the UniProt sequence database PFAM protein family prediction rRNA identification and Signal peptide prediction The annotations are delivered in a number of standard formats Excel GFF GenBank Sequin and more but we also provide free access to our online annotation browser which allows interactive analyses of the results Different search options provide our customers with a unique tool to scan their genomes for genes or enzymes of interest Also a local BLAST search is implemented to screen assembled genomes for particular gene of protein query sequences High throughput solutions to sequence entire bacterial strain collections Using Robotics like the Beckman Coulter Ffix we are able to prep 96 wells plates of bacterial genome libraries in a cost effective and very short time The multiplexed libraries will be sequenced using our Illumina

    Original URL path: http://www.baseclear.com/news/New-high-throughput-assembly-and-annotation-pipeline_90_17.html (2016-02-12)
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  • Baseclear
    transcriptome sequencing services Novel long non coding and strand specific RNA library preparation services BaseClear has recently introduced a new dedicated library preparation method to analyze Long non coding RNAs These transcripts long ncRNAs lncRNA are non protein coding transcripts longer than 200 nucleotides Long non coding RNAs are currently a hot research topic and are associated with epigenetics gene transcription and post transcriptional regulation Last year we introduced strand specific library preparation making it possible for researchers to specifically identify which strand of a genomic locus is transcribed To date we have received very positive feedback on this technique The information gained with both these techniques greatly improves the quality of genome annotations and supports studies of anti sense transcription and non coding RNA For more information or if you wish to discuss specific project please contact us Improved de novo transcriptome assembly pipeline Recent updates to our de novo transcriptome assembly and annotation pipeline have resulted in significantly improved results These improvements were made possible through the introduction of a number of state of the art analysis tools to our unique yet standardized pipeline This pipeline now delivers high quality transcriptomes without any prior need for a reference Additional features which are now also introduced are the inclusion of non annotated transcripts in the downstream analysis and an improved quality evaluation method The recent upgrade of our Illumina platform to the HiSeq2500 with read lengths up to paired end 150 cycles also helps with the assembly process providing longer reads of higher quality The cutting edge meta transcriptomics PacBio sequencing Recently we successfully completed a number of meta transcriptomics projects and we are actively looking for partners who are interested in performing new projects in this area Additionally we are investigating the options for transcriptome sequencing and analysis

    Original URL path: http://www.baseclear.com/news/BaseClear-has-further-expanded-its-transcriptome-sequencing-services_90_15.html (2016-02-12)
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  • Baseclear
    These technologies allow the study of functional genes and gene clusters and their influence on an organism s phenotype When microbial organisms are used in fermentation or food production genomic studies can be applied to gain improved understanding and influence their behaviour Both NIZO and BaseClear have a long history of developing microbial genetics knowledge and have in recent years specialized and invested in state of the art genomic and bioinformatics technologies The partnership offers new approaches for realizing an integrated metagenomics pipeline for efficient analyses of microbial communities which can be applied to different habitats including the gut skin or oral microbiome This solution includes detailed advice on the experimental design i e quality controls the efficient extraction of DNA a state of the art taxonomic annotation pipeline an interactive browser for the visualisation and first line interpretation of the results Further solutions will be added later this year and will include genome comparison risk assessment and functional gene content analyses The NIZO BaseClear collaboration will also work closely with customers to develop new solutions to address the most challenging issues faced in the coming years About NIZO Good food needs good science NIZO food research is a leading center in proteins bacteria and processing Our passion is to help make better foods and to be an incubator of innovation NIZO is an independent company and one of the most advanced contract research centers in the world NIZO brings the latest food technologies to life in their food grade pilot plant Customers value their gains in product quality sustainability cost effectiveness and speed to market Innovation is teamwork Only when people work together share results and continuously look for the earliest opportunity to apply results progress can be made Since 1948 NIZO s experts have worked in joint teams

    Original URL path: http://www.baseclear.com/news/NIZO-and-BaseClear-join-forces-to-offer-state-of-the-art-microbial-genomic-solutions_90_22.html (2016-02-12)
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