Diagenode

D-Plex Small RNA-seq Kit for Illumina




Catalog Number
Format
Price
C05030001
24 rxns
$1,475.00

Product Features

  • Ultra-low input capability, down to 10 pg for small RNAs and 100 pg for total RNA samples
  • High library complexity providing novel and diverse transcript detection
  • Versatile integartion into numerpus transcriptomic analysis workflow: ribosome profiling, CLIP-seq, RIP-seq and other
  • Improved quantification accuracy through the use of UMIs
  • Easy to use with minimal hands-on time: one day, one tube protocol

Download the manual

D-Plex Small RNA-seq Library Prep Kit is a tool designed for the study of the small non-coding transcriptome. The kit is using the D-Plex technology to generate small RNA libraries for Illumina sequencing directly from total RNAs or enriched small RNAs.

The D-Plex technology utilizes two innovative ligation-free mechanisms - poly(A) tailing and template switching - to produce sequencing libraries from ultra-low input amounts, down to 10 pg for small RNAs and 100 pg for total RNAs. Combined with unique molecular identifiers (UMI), this complete solution ensures a realistic and accurate representation of diverse small RNA species (such as microRNAs, piRNAs, tRNAs, and siRNAs) with minimized quantitative bias.

D-Plex Small RNA-seq Kit offers a time saving protocol that can be completed within 5 hours and requires minimal hands-on time. The library preparation takes place in a single tube, increasing the efficiency tremendously. 

D-Plex Small RNA-seq Kit includes all buffers and enzymes necessary for the library preparation. Specific D-Plex Indexes were designed and validated to fit the D-Plex technology and are available separately:

For D-Plex UDI library construction:

The use of UDI is highly recommended to mitigate errors introduced by read misassignment, including index hopping frequently observed with patterned flow cells such as Illumina’s NovaSeq system.

For D-Plex SI library construction:

D-Plex is also available for MGI sequencing, check here!

The D-Plex smRNA-seq is a versatile tool for a plethora of transciptomic analysis

With low-input capability, accuracy and ability to incorporate different transcript classes independent of chemical moieties, the strong D-Plex library-preparation method can be included in various analysis workflows (i.e., ribosome profiling, genome-wide mapping of protein: RNA binding sites).

  • Characteristics and library prep. workflow

    High library diversity for ultra-low inputs

    D-Plex smRNA-seq captures the smRNA complexity of the sample in a sensitive manner. A large number of features is detected for each biotype at a CPM ≥5, as shown above for different species.

    Accurate representation of the smRNA content of a sample

    Accurate identification of PCR duplicates in low-input samples using unique molecular identifiers (UMIs).
    The UMI read deduplication that is embedded in the D-Plex construct is used to avoid over-estimation of transcripts by identifying clones generated during the PCR amplification of the library. Despite limiting starting RNA input, the UMI correction removed technical copies of transcripts, maintaining the initial sample abundance.

    D-Plex (template switching) technology enables recovery of the initial miRNA distribution of the miRXplore Universal Reference (Miltenyi Biotech Inc., Cat. No. 130-093-521). In contrast, ligation-based kits display a strong distortion of the miRNA equimolar distribution initially present in the pool, indicating sample incorporation bias.

    D-Plex smRNA-seq in association with the MGcount analysis correlates strongly (R² > 0.8) with the RT-qPCR analysis, which is considered the gold-standard for accuracy.
    The figures shows a fold-change accuracy of a panel of 20 different small-RNA (figure taken from MGcount publication - Hita et al., BMC bioinformatics, 23-39(2022).

    Maximize information from the regulatory transcriptome using D-Plex small RNA-seq kit and MGcount*

    By analyzing D-Plex dataset with MGcount, more reads are kept during the analysis, which ultimately preserves biological complexity linked to ncRNA expression without decreasing the accuracy of detection.
    *Hita, A., Brocart, G., Fernandez, A. et al. MGcount: a total RNA-seq quantification tool to address multi-mapping and multi-overlapping alignments ambiguity in non-coding transcripts. BMC Bioinformatics 23, 39 (2022). https://doi.org/10.1186/s12859-021-04544-3

    The D-Plex technology uses two innovative ligation-free mechanisms, poly(A) tailing and template switching, to produce sequencing libraries from ultra-low input amounts.


    WORKFLOW


    RNA molecules are polyadenylated at the 3’-end and primed with an oligo(dT) primer containing part of the ILMN 3’-adapter sequence. The addition of a template-switching oligonucleotide during cDNA synthesis enables fusion of part of the ILMN 5’-adapter during reverse transcription. After PCR, the library comprises double stranded DNA constructs that are ready for sequencing.



  • Data analysis

    A specific bioinformatics pipeline has been developed to process the special sequences present in the D-Plex construct, namely the UMI, the A-tail, and the template switch motif. All guidelines and free softwares are shared in the user manual. Subject to the compatibility of D-Plex constructs, other specific pipelines can be used.

    small RNA sequencing bioinformatics pipeline

    Need help for your bioinformatics analysis of miRNA?

     

     

    Diagenode has collaborated with Andreas Keller and Tobias Fehlmann to develop a new bioinformatics pipeline for the prediction of novel miRNAs.

     

     

  • Data analysis - Counting using MGcount

    The counting or expression level calculation is the last step of the processing to generate an expression level matrix. We recommend using MGcount*, a counting tool developed at Diagenode with a suitable annotations file that include the small RNA transcripts that are object of study. MGcount, built on top of featureCounts, employs a flexible quantification approach to deal with datasets containing multiple RNA biotypes such as D-plex libraries. Non-coding RNAs varying in length, biogenesis, and function, may overlap in a genomic region, and are sometimes present in the genome with a high copy number. Consequently, reads may align equally well to more than one position in the reference genome or/and align to a position where more than one annotated transcript is located. MGcount employs two strategies to quantify these reads. Firstly, it assigns reads in rounds prioritizing small-RNAs over long-RNAs ensuring the unbiased read attribution to intergenic and intragenic small RNAs while preventing host-genes transcription over-estimation. Secondly, MGcount collapses loci where reads consistently multi-map into communities of loci with a graph-based approach. The resultant communities are groups of biologically related loci with nearly identical sequence. Subsequently, quantification of reads is performed at the loci-community level, reducing multi-alignments ambiguity at individual locus. Ultimately, this strategy maximizes the transcriptome information analysed and improves the interrogation of non-coding RNAs. MGcount software repository provides annotation files for A. thaliana, H. sapiens, M. musculus and C. elegans. The required input files for MGcount are a .txt file listing the paths to the alignment input files (.bam format) and the annotations file (.gtf format). The output directory path has to be provided as an input as well.

    Example command:

    MGcount -T 2 --gtf Homo_sapiens.GRCh38.gtf --outdir outputs --bam_infiles input_bamfilenames.txt

    MGcount provides the choice to enable/disable the quantification of all RNA biotypes included in the annotation file in the form of "communities" as optional parameters for small-RNA (--ml_flag_small) and long-RNA (--ml_flag_long). Both are enabled by default. The main output of MGcount is the count_matrix.csv file containing an expression matrix that can be imported to R or any other software for downstream analyses.
    A full user guide for MGCount is available here: https://filedn.com/lTnUWxFTA93JTyX3Hvbdn2h/mgcount/UserGuide.html.

    Other standard counting tools such as featureCounts or HTSeq-counts can also be used alternatively. Given the high complexity of D-Plex libraries, we recommend having a clear understanding of the scientific question and the goal of the project before proceeding to the choice of the counting method as this will strongly impact downstream analyses. Diagenode provides bioinformatics support as a service (please, contact us if you need help with data analysis).

    Notice that D-Plex produces forward-stranded data. Stranded libraries have the benefit that reads map to the genome strand where they were originated from. Therefore, when estimating transcript expression, reads aligned to the forward strand should be assigned only to transcript features in the forward strand whereas reads aligned to the reverse strand should be assigned only to transcript features in the reverse strand. For this, make sure you select “stranded mode” in any tool of choice. Stranded mode is selected by default in MGcount.

    *Hita, A., Brocart, G., Fernandez, A. et al. MGcount: a total RNA-seq quantification tool to address multi-mapping and multi-overlapping alignments ambiguity in non-coding transcripts. BMC Bioinformatics 23, 39 (2022). https://doi.org/10.1186/s12859-021-04544-3

  •  Documents
    D-Plex Small RNA-seq Kit for Illumina MANUAL
    Note: The D-Plex Small RNA-seq Kit manual describes the protocol for both UDI and SI li...
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    True and accurate small RNA-seq: Use the power of UMIs without ligation FLYER
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    D-Plex RNA-seq library preparation solutions FLYER
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    D-Plex Small RNA-seq Library Prep Kit FLYER
    Go deeper with your RNA research & Biomarker discovery
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  •  Publications

    How to properly cite this product in your work

    Diagenode strongly recommends using this: D-Plex Small RNA-seq Kit for Illumina (Diagenode Cat# C05030001). Click here to copy to clipboard.

    Using our products in your publication? Let us know!

    Pervasive translation of Xrn1-sensitive unstable long non-coding RNAs in yeast
    Andjus S. et al.
    Despite being predicted to lack coding potential, cytoplasmic long non-coding (lnc)RNAs can associate with ribosomes. However, the landscape and biological relevance of lncRNAs translation remains poorly studied. In yeast, cytoplasmic Xrn1-sensitive lncRNAs (XUTs) are targeted by the Nonsense-Mediated mRNA Decay (NM...

    Aseptic loosening around total joint replacement in humans is regulated by miR-1246 and miR-6089 via the Wnt signalling pathway
    Yi Deng at al.
    Background: Total joint replacement for osteoarthritis is one of the most successful surgical procedures in modern medicine. However, aseptic loosening continues to be a leading cause of revision arthroplasty. The diagnosis of aseptic loosening remains a challenge as patients are often asymptomatic until the la...

    An inappropriate decline in ribosome levels drives a diverse set of neurodevelopmental disorders
    Ni C. et al.
    Many neurodevelopmental defects are linked to perturbations in genes involved in housekeeping functions, such as those encoding ribosome biogenesis factors. However, how reductions in ribosome biogenesis can result in tissue and developmental specific defects remains a mystery. Here we describe new allelic variants ...

    Challenges in characterization of transcriptomes of extracellular vesicles and non-vesicular extracellular RNA carriers
    Makarova J. et al.
    Since its original discovery over a decade ago, extracellular RNA (exRNA) has been found in all biological fluids. Furthermore, extracellular microRNA has been shown to be involved in communication between various cell types. Importantly, the exRNA is protected from RNases degradation by certain carriers including m...

    Guidelines for Performing Ribosome Profiling in Plants Including Structural Analysis of rRNA Fragments
    Ting M.K.Y. et al.
    Ribosome profiling (or Ribo-seq) is a technique that provides genome-wide information on the translational landscape (translatome). Across different plant studies, variable methodological setups have been described which raises questions about the general comparability of data that were generated from diverging meth...

    Integrated multiplexed assays of variant effect reveal cis-regulatory determinants of catechol-O-methyltransferase gene expression
    Hoskins I. et al.
    Multiplexed assays of variant effect are powerful methods to profile the consequences of rare variants on gene expression and organismal fitness. Yet, few studies have integrated several multiplexed assays to map variant effects on gene expression in coding sequences. Here, we pioneered a multiplexed assay based on ...

    The Ribosome Assembly Factor Reh1 is Released from the Polypeptide Exit Tunnel in the Pioneer Round of Translation
    Musalgaonkar S. et al.
    Assembly of functional ribosomal subunits and successfully delivering them to the translating pool is a prerequisite for protein synthesis and cell growth. In S. cerevisiae, the ribosome assembly factor Reh1 binds to pre-60S subunits at a late stage during their cytoplasmic maturation. Previous work shows ...

    Knockout of the longevity gene Klotho perturbs aging- and Alzheimer’s disease-linked brain microRNAs and tRNA fragments
    Dubnov S. et al.
    Overexpression of the longevity gene Klotho prolongs, while its knockout shortens lifespan and impairs cognition via altered fibroblast growth factor signaling that perturbs myelination and synapse formation; however, comprehensive analysis of Klotho’s knockout consequences on mammalian brain transcriptomics i...

    Single-cell quantification of ribosome occupancy in early mouse development
    Ozadam H. et al.
    Translation regulation is critical for early mammalian embryonic development1. However, previous studies had been restricted to bulk measurements2, precluding precise determination of translation regulation including allele-specific analyses. Here, to address this challenge, we developed a novel microfluidic isotach...

    DIS3 ribonuclease prevents the cytoplasmic accumulation of lncRNAs carrying non-canonical ORFs, which represent a source of cancer immunopeptides.
    Foretek D. et al.
    Around 12% of multiple myeloma (MM) cases harbour mutations in DIS3, which encodes an RNA decay enzyme that controls the turnover of some long noncoding RNAs (lncRNAs). Although lncRNAs, by definition, do not encode proteins, some can be a source of (poly)peptides with biological importance, such as antigens. T...

    Pyruvate Kinase M (PKM) binds ribosomes in a poly-ADPribosylation dependent manner to induce translational stalling.
    Kejiou N. S. et al.
    In light of the numerous studies identifying post-transcriptional regulators on the surface of the endoplasmic reticulum (ER), we asked whether there are factors that regulate compartment specific mRNA translation in human cells. Using a proteomic survey of spatially regulated polysome interacting proteins, we ident...

    Towards a human brain EV atlas: Characteristics of EVs from different brain regions, including small RNA and protein profiles.
    Huang Y. et al.
    Extracellular vesicles (EVs) are released from different cell types in the central nervous system (CNS) and play roles in regulating physiological and pathological functions. Although brain-derived EVs (bdEVs) have been successfully collected from brain tissue, there is not yet a "bdEV atlas" of EVs from different b...

    RNA landscapes of brain tissue and brain tissue-derived extracellularvesicles in simian immunodeficiency virus (SIV) infection andSIV-related central nervous system pathology.
    Huang Yiyao and Abdelmagid Abdelgawad Ahmed Gamal andTurchinovich Andrey and Queen Suzanne and Abreu CelinaMonteiro and Zhu Xianming and Batish Mona and Zheng Leiand Witwer Kenneth W
    Antiretroviral treatment regimens can effectively control HIV replication and some aspects of disease progression. However, molecular events in end-organ diseases such as central nervous system (CNS) disease are not yet fully understood, and routine eradication of latent reservoirs is not yet in reach. Extracellular...

    Immunoregulatory Biomarkers of the Remission Phase in Type 1 Diabetes: miR-30d-5p Modulates PD-1 Expression and Regulatory T Cell Expansion
    Gomez-Munoz L. et al.
    The partial remission (PR) phase of type 1 diabetes (T1D) is an underexplored period characterized by endogenous insulin production and downmodulated autoimmunity. To comprehend the mechanisms behind this transitory phase and develop precision medicine strategies, biomarker discovery and patient stratification are u...

    Ageing-associated small RNA cargo of extracellular vesicles.
    Kern F. et al.
    Previous work on murine models and humans demonstrated global as well as tissue-specific molecular ageing trajectories of RNAs. Extracellular vesicles (EVs) are membrane vesicles mediating the horizontal transfer of genetic information between different tissues. We sequenced small regulatory RNAs (sncRNAs) in two mo...

    The piRNA-pathway factor FKBP6 is essential for spermatogenesis butdispensable for control of meiotic LINE-1 expression in humans.
    Wyrwoll M.J. et al.
    Infertility affects around 7\% of the male population and can be due to severe spermatogenic failure (SPGF), resulting in no or very few sperm in the ejaculate. We initially identified a homozygous frameshift variant in FKBP6 in a man with extreme oligozoospermia. Subsequently, we screened a total of 2,699 men with ...

    The seminal plasma microbiome of men with testicular germ cell tumours described by small RNA sequencing
    Mørup N. et al.
    Background: It has been estimated that microorganisms are involved in the pathogenesis of approximately 20% of all cancers. Testicular germ cell tumours (TGCTs) are the most common type of malignancy in young men and arise from the precursor cell, Germ Cell Neoplasia in Situ (GCNIS). The microbiome of seminal p...

    Neutral sphingomyelinase 2 inhibition attenuates extracellular vesiclerelease and improves neurobehavioral deficits in murine HIV.
    Zhu X. et al.
    People living with HIV (PLH) have significantly higher rates of cognitive impairment (CI) and major depressive disorder (MDD) versus the general population. The enzyme neutral sphingomyelinase 2 (nSMase2) is involved in the biogenesis of ceramide and extracellular vesicles (EVs), both of which are dysregulated in PL...

    A novel, essential trans-splicing protein connects the nematode SL1snRNP to the CBC-ARS2 complex.
    Fasimoye R.Y. et al.
    Spliced leader trans-splicing is essential for gene expression in many eukaryotes. To elucidate the molecular mechanism of this process, we characterise the molecules associated with the Caenorhabditis elegans major spliced leader snRNP (SL1 snRNP), which donates the spliced leader that replaces the 5' untranslated ...

    Interspecies effectors of a transgenerational memory of bacterial infection in Caenorhabditis elegans.
    Legüe M. et al.
    The inheritance of memory is an adaptive trait. Microbes challenge the immunity of organisms and trigger behavioral adaptations that can be inherited, but how bacteria produce inheritance of a trait is unknown. We use and its bacteria to study the transgenerational RNA dynamics of interspecies crosstalk leading to a...

    Diverse Monogenic Subforms of Human Spermatogenic Failure
    Nagirnaja L. et al.
    Non-obstructive azoospermia (NOA) is the most severe form of male infertility and typically incurable with current medicine. Due to the biological complexity of sperm production, defining the genetic basis of NOA has proven challenging, and to date, the most advanced classification of NOA subforms is based on simple...

    Ultrasensitive Ribo-seq reveals translational landscapes during mammalian oocyte-to-embryo transition and pre-implantation development.
    Xiong Z. et al.
    In mammals, translational control plays critical roles during oocyte-to-embryo transition (OET) when transcription ceases. However, the underlying regulatory mechanisms remain challenging to study. Here, using low-input Ribo-seq (Ribo-lite), we investigated translational landscapes during OET using 30-150 mouse oocy...

    Translation is a key determinant controlling the fate of cytoplasmic long non-coding RNAs
    Andjus Sara et al.
    Despite predicted to lack coding potential, cytoplasmic long non-coding (lnc)RNAs can associate with ribosomes, resulting in some cases into the production of functional peptides. However, the biological and mechanistic relevance of this pervasive lncRNAs translation remains poorly studied. In yeast, cytoplasmic Xrn...

    MGcount: a total RNA-seq quantification tool to address multi-mappingand multi-overlapping alignments ambiguity in non-coding transcripts
    Hita Andrea, Brocart Gilles, Fernandez Ana, Rehmsmeier Marc, Alemany Anna, Schvartzman Sol
    Background Total-RNA sequencing (total-RNA-seq) allows the simultaneous study of both the coding and the non-coding transcriptome. Yet, computational pipelines have traditionally focused on particular biotypes, making assumptions that are not fullfilled by total-RNA-seq datasets. Transcripts from distinct RNA biotyp...

    Single cell quantification of ribosome occupancy in early mouse development
    Tori Tonn et al.
    Technological limitations precluded transcriptome-wide analyses of translation at single cell resolution. To solve this challenge, we developed a novel microfluidic isotachophoresis approach, named RIBOsome profiling via IsoTachoPhoresis (Ribo-ITP), and characterized translation in single oocytes and embryos during ...

    Single cell quantification of ribosome occupancy in early mousedevelopment
    Tonn T. et al.
    Technological limitations precluded transcriptome-wide analyses of translation at single cell resolution. To solve this challenge, we developed a novel microfluidic isotachophoresis approach, named RIBOsome profiling via IsoTachoPhoresis (Ribo-ITP), and characterized translation in single oocytes and embryos during ...

    Functional microRNA targetome undergoes degeneration-induced shift in the retina
    Chu-Tan JA et al.
    Background: MicroRNA (miRNA) play a significant role in the pathogenesis of complex neurodegenerative diseases including age-related macular degeneration (AMD), acting as post-transcriptional gene suppressors through their association with argonaute 2 (AGO2) - a key member of the RNA Induced Silencing Complex...

    Functional microRNA targetome undergoes degeneration-induced shift inthe retina.
    Chu-Tan Joshua A et al.
    BACKGROUND: MicroRNA (miRNA) play a significant role in the pathogenesis of complex neurodegenerative diseases including age-related macular degeneration (AMD), acting as post-transcriptional gene suppressors through their association with argonaute 2 (AGO2) - a key member of the RNA Induced Silencing Complex (RISC)...

    Single-cell microRNA sequencing method comparison and application tocell lines and circulating lung tumor cells
    Hücker S. et al.
    Molecular single cell analyses provide insights into physiological and pathological processes. Here, in a stepwise approach, we first evaluate 19 protocols for single cell small RNA sequencing on MCF7 cells spiked with 1 pg of 1,006 miRNAs. Second, we analyze MCF7 single cell equivalents of the eight best pro...

    Small RNAs in Seminal Plasma as Novel Biomarkers for Germ Cell Tumors
    Mørup N. et al.
    Circulating miRNAs secreted by testicular germ cell tumors (TGCT) show great potential as novel non-invasive biomarkers for diagnosis of TGCT. Seminal plasma (SP) represents a biofluid closer to the primary site. Here, we investigate whether small RNAs in SP can be used to diagnose men with TGCTs or the precursor le...

    Vesicle-bound regulatory RNAs are associated with tissue aging
    F. Kern, T. Kuhn, N. Ludwig, M. Simon, L. Gröger, N. Fabis, A. Salhab, T. Fehlmann, O. Hahn, A. Engel, M. Koch, J. Koehler, K. Winek, H. Soreq, G. Fuhrmann, T. Wyss-Coray, E. Meese, M. W. Laschke and A. Keller
    Previous work on murine models and human demonstrated global as well as tissue-specific molecular aging trajectories in solid tissues and body fluids1–8. Extracellular vesicles like exosomes play a crucial role in communication and information exchange in between such systemic factors and solid tissues9,10. We...

    Small RNAs in Seminal Plasma as Novel Biomarkers for GermCell Tumors.
    Mørup Nina et al.
    Circulating miRNAs secreted by testicular germ cell tumors (TGCT) show great potential as novel non-invasive biomarkers for diagnosis of TGCT. Seminal plasma (SP) represents a biofluid closer to the primary site. Here, we investigate whether small RNAs in SP can be used to diagnose men with TGCTs or the precursor le...

    miRMaster 2.0: multi-species non-coding RNA sequencing analyses at scale
    Tobias Fehlmann, Fabian Kern, Omar Laham, Christina Backes, Jeffrey Solomon, Pascal Hirsch, Carsten Volz, Rolf Müller, Andreas Keller
    Analyzing all features of small non-coding RNA sequencing data can be demanding and challenging. To facilitate this process, we developed miRMaster. After the analysis of over 125 000 human samples and 1.5 trillion human small RNA reads over 4 years, we present miRMaster 2 with a wide range of updates and new featur...

    Bacterial small RNAs and host epigenetic effectors of atransgenerational memory of pathogens in C. elegans
    Legüe M. et al.
    The inheritance of memories is adaptive for survival. Microbes interact with all organisms challenging their immunity and triggering behavioral adaptations. Some of these behaviors induced by bacteria can be inherited although the mechanisms of action are largely unexplored. In this work, we use C. elegans and its b...

    Interspecies RNA Interactome of Pathogen and Host in a Heritable Defensive Strategy.
    Legüe M. et al.
    Communication with bacteria deeply impacts the life history traits of their hosts. Through specific molecules and metabolites, bacteria can promote short- and long-term phenotypic and behavioral changes in the nematode . The chronic exposure of to pathogens promotes the adaptive behavior in the host's progeny called...

    Distinct Extracellular RNA Profiles in Different PlasmaComponents.
    Jia Jing et al.
    Circulating extracellular RNAs (exRNAs) have great potential to serve as biomarkers for a wide range of diagnostic, therapeutic, and prognostic applications. So far, knowledge of the difference among different sources of exRNAs is limited. To address this issue, we performed a sequential physical and biochemical pre...

    Genes with 5′ terminal oligopyrimidine tracts preferentially escape global suppression of translation by the SARS-CoV-2 NSP1 protein
    Shilpa R. et al.
    Viruses rely on the host translation machinery to synthesize their own proteins. Consequently, they have evolved varied mechanisms to co-opt host translation for their survival. SARS-CoV-2 relies on a non-structural protein, NSP1, for shutting down host translation. Despite this, it is currently unknown how viral pr...

    Repeat RNAs associate with replication forks and post-replicative DNA.
    Gylling HM, Gonzalez-Aguilera C, Smith MA, Kaczorowski DC, Groth A, Lund AH
    Non-coding RNA has a proven ability to direct and regulate chromatin modifications by acting as scaffolds between DNA and histone-modifying complexes. However, it is unknown if ncRNA plays any role in DNA replication and epigenome maintenance, including histone eviction and re-instalment of histone-modifications aft...

    The ribosomal protein S1-dependent standby site in tisB mRNA consists of a single-stranded region and a 5′ structure element
    Romilly C. et al.
    In bacteria, stable RNA structures that sequester ribosome-binding sites (RBS) impair translation initiation, and thus protein output. In some cases, ribosome standby can overcome inhibition by structure: 30S subunits bind sequence-nonspecifically to a single-stranded region and, on breathing of the inhibitory struc...

    The sncRNA Zoo: a repository for circulating small noncoding RNAs in animals.
    Fehlmann T, Backes C, Pirritano M, Laufer T, Galata V, Kern F, Kahraman M, Gasparoni G, Ludwig N, Lenhof HP, Gregersen HA, Francke R, Meese E, Simon M, Keller A
    The repertoire of small noncoding RNAs (sncRNAs), particularly miRNAs, in animals is considered to be evolutionarily conserved. Studies on sncRNAs are often largely based on homology-based information, relying on genomic sequence similarity and excluding actual expression data. To obtain information on sncRNA expres...

    NGS analysis of total small non coding RNAs from low input RNA from dried blood sampling
    Marcello Pirritano, Tobias Fehlmann, Thomas Laufer, Nicole Ludwig, Gilles Gasparoni, Yongping Li, Eckart Meese, Andreas Keller, and Martin Simon
    Circulating miRNAs are favored for biomarker candidates as they can reflect tissue specific miRNA dysregulation in disease contexts. Moreover, they have additional advantages that they can be monitored in a minimal invasive manner. Blood-borne miRNAs are therefore currently characterized to identify, describe and va...

    Web-based NGS data analysis using miRMaster: a large-scale meta-analysis of human miRNAs
    Tobias Fehlmann, Christina Backes, Mustafa Kahraman, Jan Haas, Nicole Ludwig, Andreas E. Posch, Maximilian L. Würstle, Matthias Hübenthal, Andre Franke, Benjamin Meder, Eckart Meese, Andreas Keller
    The analysis of small RNA NGS data together with the discovery of new small RNAs is among the foremost challenges in life science. For the analysis of raw high-throughput sequencing data we implemented the fast, accurate and comprehensive web-based tool miRMaster. Our toolbox provides a wide range of modules for qua...

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