Background: Deciphering the 3D structure of the genome is essential for elucidating the regulatory mechanisms of gene expression in detail. Further identification of protein-centric chromatin conformation is enabled by coupling the Hi-C procedure with a conventional chromatin. Results: To simultaneously identify protein-centric chromatin conformation and target protein localization, we have developed Cut-C, a method that combines antibody-mediated cleavage by tethered...

#BMC Genomics #Chromosome conformation #Gene regulation #Next generation sequencing #Chromatin structure #3D structure #Existing methods

Arm-less mitochondrial tRNAs conserved for over 30 millions of years in spiders

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Thanks to the conservation of the gene order and the nucleotide identity across close relatives, we were able to predict the secondary structures even on arm-less tRNAs, which would be otherwise unattainable for a single species. Only 32 mitogenome sequences are available at the organelle genome database at NCBI out of the over 45,000 species currently accepted, representing only 15...

#BMC Genomics #Reduced mitogenome #Secondary structure RNA #Miss-pairing structures #Next generation sequencing #Harbor atypical sequences

GENAVi: A shiny web application for gene expression normalization, analysis and visualization

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Results: We have developed GENAVi (Gene Expression Normalization Analysis and Visualization) to provide a user- friendly interface for normalization and differential expression analysis (DEA) of human or mouse feature count level RNA-Seq data. We provide a panel of 20 cell lines commonly used for the study of breast and ovarian cancer within GENAVi as a foundation for users to bring...

#BMC Genomics #Next generation sequencing #RNA-seq #Differential expression #Large genomic datasets #Normalization methods

A comparison of RNA extraction and sequencing protocols for detection of small RNAs in plasma

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A comparison of RNA extraction and. Although developments in small RNA-Seq technology have improved detection of plasma-based miRNAs, the low RNA content and sequencing bias introduced during library preparation remain challenging. In this study we compare commercially available RNA extraction methods using MagnaZol (Bioo Scientific) or miRNeasy (QIAGEN) and three library preparation methods - CleanTag (TriLink), NEXTflex (Bioo Scientific) and...

#BMC Genomics #Small RNA-seq #Circulating biomarker #Next generation sequencing #Library preparation

Optimized PCR conditions minimizing the formation of chimeric DNA molecules from MPRA plasmid libraries

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Optimized PCR conditions minimizing the formation of chimeric DNA molecules from MPRA plasmid libraries. Typically, this is done by PCR amplification of the BC – ROI regions with flanking primers, followed by next-generation sequencing (NGS) of the products.. However, chimeric DNA molecules formed on templates with identical spacer fragment during the amplification process may substantially hamper the identification of genuine...

#BMC Genomics #Massively parallel reporter assay #Emulsion PCR #Conventional PCR #Chimeric DNA molecules #Next generation sequencing

Reference genome and comparative genome analysis for the WHO reference strain for Mycobacterium bovis BCG Danish, the present tuberculosis vaccine

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BCG Danish 1331, Tokyo 172 – 1 and Russia BCG-1 were established as the WHO reference strains. Both for BCG Tokyo 172 – 1 as Russia BCG-1, reference genomes exist, not for BCG Danish. In this study, we set out to determine the completely assembled genome sequence for BCG Danish and to establish a workflow for genome characterization of engineering-derived...

#BMC Genomics #Live vaccines #Next generation sequencing #Complete genomic sequence #Genetic differences #Tandem duplications

Systematic evaluation of RNA-Seq preparation protocol performance

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Systematic evaluation of RNA-Seq preparation protocol performance. We used three standard input protocols: Illumina TruSeq Stranded Total RNA and mRNA kits, a modified NuGEN Ovation v2 kit, and the TaKaRa SMARTer Ultra Low RNA Kit v3. Conclusions: At the manufacturers ’ recommended input RNA levels, all the RNA-Seq library preparation protocols evaluated were suitable for distinguishing between experimental groups, and...

#BMC Genomics #Next generation sequencing #RNA-seq #Quality control #Facilitate preparing RNA-Seq libraries #Long non-coding RNA

2C-ChIP: Measuring chromatin immunoprecipitation signal from defined genomic regions with deep sequencing

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2C-ChIP: measuring chromatin. 2C-ChIP recapitulates results from benchmark ChIP approaches. The flexible nature of the 2C-ChIP approach allows rapid changes in experimental design at relatively low cost, making it a highly efficient method for chromatin analysis.. multiplex 2C-ChIP primer annealing and ligation. Forward 2C-ChIP primer. Reverse 2C-ChIP primer. 2C-ChIP library. 2C-ChIP library PCR-amplification. 2C-ChIP primers. 2C-ChIP library amplification primers. P1-key...

#BMC Genomics #Chromatin immunoprecipitation #Next generation sequencing #Ligation-mediated amplification #Long non-coding RNA