Īs additional capabilities were added to the software platform, it was eventually split into several themed Workbenches and pugins with collections of features relevant to different applications (e.g. In 2010, CLC bio was notable as the first commercial platform for bioinformatics analysis that utilized a graphical user interface for building, managing, and deploying analysis workflows as well as command-line tools, a SOAP and REST API, and later, the ability to run containerized tools. CLC bio developed some of their own open source algorithms, as well as their own SIMD-accelerated implementations of several exiting popular applications. Software ĬLC bio's main activities were in software development for desktop ( Mac OS X, Windows, and Linux), enterprise, and cloud software for analysis of biological data. ĬLC bio was acquired by QIAGEN in 2013 and merged into its bioinformatics research and development division with several other purchased platforms in 2014. By 2012, it had additional offices in Cambridge, Massachusetts, Tokyo, Taipei and Delhi, with staff largely from research backgrounds (30% having a PhD) and had built a userbase of around 250,000 users in both academic institutions and biotechnology companies. Its product's development was also partly funded by collaborating with reserachers on grant-funded projects. GEO help: Mouse over screen elements for information.Ĭells were grown in LB broth until mid-exponential phase (OD600 = 0.5-0.CLC bio was a bioinformatics software company that developed software suite subsequently purchased by QIAGEN.ĬLC bio started commercial activities on Januheadquartered in Aarhus, Denmark. Total RNA was isolated from cells using hot phenol method. High quality total RNA was further processed by removing 23S and 16S rRNAs using the MicrobExpress bacterial mRNA enrichment kit (Life Technologies, USA). Final concentrations and purity grades of the samples were determined using Bioanalyzer 2100 (Agilent, USA). Samples with the amount at least 0.5-1 µg were used for library construction and RNA sequencing. Libraries of depleted RNA were prepared using the Illumina TruSeq RNA LT v2 kit according to the manufacturer's instructions. RNA libraries were prepared for sequencing using Illumina protocols Review by Ana Marculescu on September 11, 2014. CLC Main Workbench is a professional software application specialized in advanced protein sequence analyses, data management, as well visual. Raw data for each sample was analyzed using CLC Genomics Workbench version 12.0.1 software (QIAGEN Aarhus, Denmark), with default settings, based on their proprietary algorithms. They encoded the generation sequencing data supporting the results of this. Pairwise comparison of the expression results was performed using the total mapping results for deletion mutants vs wild type.ĭifferential gene lists were created with 2-fold expression cutoff and significant p-values of <0.05 to identify genes that were up- or down-regulated under each condition. Supports all major next-generation sequencing platforms Product Details CLC Genomics Workbench is a comprehensive analysis package for the analysis and visualization of data and supports all typical NGS workflows. 1997) was used in modelling, and CLC sequence viewer (CLC bio, a QIAGEN. Additionally, it includes all the sequence analysis tools of CLC Main Workbench. Learn more about QIAGEN CLC Genomics Workbench. Genome_build: Raw sequence reads were mapped to the A.
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