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SIRVs - RNA control designed for splice variant detection

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  • SIRVs - RNA control designed for splice variant detection

    Many RNA-Seq researches aim to elucidate the quantitative nature of transcript variants. However, no RNA controls so far have been able to provide proper guidance for the correct assembly of transcript variants from RNA-Seq data.

    To address this issue, Lexogen has developed Spike-in RNA Variant Control Mixes (SIRVs).

    They include artificial transcripts which reflect variations such as alternative splicing, alternative transcription start- and end-sites, overlapping genes, and antisense transcripts. Therefore, with SIRVs spiked into the samples, the performance of RNA preparation, library generation, sequencing, and bioinformatics algorithms can be assessed adequately.

    For more details please visit the SIRVs web page or contact us at [email protected].

  • #2
    Has anyone used this reagent? Are there sequencing data available on samples spiked with SIRV and/or ERCC as comparisons?

    Would love to hear what users think of this reagent, given the conversation threads about ERCC here on SeqAnswers (not very positive).

    Cheers.

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    • #3
      SIRVs RNA-Seq data - available soon at www.lexogen.com

      @ methylnick

      Thank you for your interest in the Spike-In RNA Variants! The SIRV transcripts and the derived mixes were prepared in a highly controlled and documented way to ensure the best possible spike-in input for your RNA-Seq experiments. For example, RNA integrity is of highest priority since the SIRVs constitute transcript variants, and degradation products could interfer with the assignment of reads to the correct isoform. Please consult the SIRVs User Guide - available at https://www.lexogen.com/sirvs/#sirvsdownloads - for further details and a comparison between ERCC and SIRV spike-in transcripts.

      Prior to their commercial launch, the SIRVs mixes were distributed within the SIRVs Test program. The data from this program are currently evaluated, and RNA-Seq data of reference RNAs spiked with ERCCs and SIRVs will be available soon at www.lexogen.com.

      If you cannot wait until then - and to get the most comprehensive and appropriate results - please co-spike SIRV and ERCC mixes into the RNA samples you are working with and evaluate them using your NGS pipeline. We see that already 20-25 M reads / library are sufficient for a useful SIRV coverage.

      For further information and if you want to be informed personnally about the SIRV NGS data release, please e-mail to [email protected].

      Lukas Paul
      Lexogen GmbH

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      • #4
        Great thank you Lukas. I look forward to it when it is available.

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        • #5
          Upcoming Webinar – Controlling RNA-Seq Experiments Using Spike-In RNA Variants

          DATE: October 19, 2016
          TIME: 9:00 AM PT, 12:00 PM ET, 6:00 PM CEST

          PRESENTED BY:Lukas Paul, PhD
          Head of Services, Lexogen

          Hardly anyone would run an RNA gel without a ladder, but transcriptomes are mostly sequenced without the use of external standards. The added layer of transcript isoform complexity in eukaryotes as well as incomplete or incorrect gene annotations further challenge RNA-Seq pipelines to correctly calculate and compare gene expression values. Lexogen, a specialized transcriptomics company, addresses this problem by providing Spike-In RNA Variant Control Mixes (SIRVs) to the RNA-Seq community. These controls are processed together with the RNA sample to allow for an evaluation of the RNA-Seq workflow and, in particular, of transcript isoform detection and gene expression quantification. The mixes contain 69 transcript variants that map to 7 human model genes and mirror the native transcriptome complexity by comprehensively representing splicing isoforms, transcription start-site and end-site variants, overlapping transcripts and antisense transcription. Lukas Paul, Head of Services at Lexogen, describes in this webinar how the SIRVs have been used to estimate absolute accuracy and consistency, as well as concordance in gene expression measurements at the level of workflows, experiments, and samples. A “SIRVs dashboard” is introduced that brings together spike-in derived NGS data, annotations and data evaluation in an easily navigable way, and the webinar will highlight how condensed SIRVs data can function as a “RNA-Seq fingerprint” that enables comparisons across experiments, samples and platforms.

          Learning Objective 1: Learn practical considerations on the use of spike-in transcripts in RNA-Seq experiments

          Learning Objective 2: Learn how RNA-Seq spike-in reads can be evaluated to assess gene expression quantification

          (find out more...)
          Last edited by lexogen; 09-14-2016, 07:31 AM. Reason: Title added

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          • #6
            Research Award - "Controlling RNA-Seq Experiments Using SIRVs"

            Lexogen has launched the Research Award - "Controlling RNA-Seq Experiments Using SIRVs"!

            The Award is about our Spike-in RNA Variant Control Mixes. If you plan to do RNA-Seq project soon and consider to use spike-ins, apply for this Award and get a chance to win SIRVs and a free sequencing run on Illumina HiSeq 2500. The deadline for your application is November 21, 2016.

            Please also forward this information about the Award to your colleague or a friend, who would be interested and get a chance to receive a treat for your lab from Lexogen!

            Learn more and apply: https://www.lexogen.com/award-2016-2/[/QUOTE]

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            • #7
              I wonder if you would be able theoretically to compare SIRVs design to RNA Sequin pointing possible advantages of SIRVs.

              http://www.sequin.xyz/about/rnaseq/

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              • #8
                New, comprehensive SIRVs thread and web-site

                For updated information on the SIRVs please follow this seqanswers thread: "SIRVs (Spike-In RNA Variants): external controls for RNA sequencing".

                For comprehensive information on the SIRVs, access to SIRVs RNA-Seq data, and to order the SIRVs visit Lexogen's SIRVs webpage.

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