....for RNA-Seq data analysis software!
Lexogen, an NGS and transcriptomics company, has developed a new bioinformatics tool - Mix² model for detecting multiple positional bias types in RNA-Seq data and accurate transcript concentration estimation. Altogether this yields more reliable FPKM values.
Mix², a new algorithm for accurate quantification of transcript isoforms in RNA-Seq data
Fragment bias in RNA-Seq poses a serious challenge to the accurate quantification of gene isoforms. The novel Mix² algorithm makes no assumption about fragment bias but fits a mixture model to the data, thus inferring the bias automatically. Mix² model leads to considerably better correlation between known and estimated transcript isoform concentration than Cufflinks and PennSeq, which results in substantially increased accuracy in the detection of differential expression. Further details can be found in the manuscript on BioRxiv.
Application and participation - Applications should be completed by January 31 through the following web page Application form
All applicants will be given a stand-alone executable of the Mix² software for free use on their own RNA-Seq data.
Reports - We ask the participants to submit reports in free format including results generated with the Mix² software. The emphasis of these reports should be on the comparison with their previous algorithms.
Prizes
1st place (1 person) : Mac Book Air (11 inch, Intel Core i5, 125Gb) / 2nd places (2 people) : iPad Mini 2 Retina (16Gb, Wifi)
Have you done your Christmas gifts shopping yet? And what about your lab? Is it ready for 2015?
Just 14 days are left before 2014 Year-End Special Offer on all RNA-Seq products of Lexogen expires.
Hurry up and get all the reagents you need for your RNA-Seq experiments in 2015 already now at a special price!
Lexogen webshop
The QuantSeq protocol generates NGS libraries of the sequences close to the 3’ end of the polyadenylated RNA within 4.5 hours.
SENSE is an all-in-one >99.9% strand-specific library prep protocol designed to produce mRNA-Seq and total RNA-Seq libraries in less than 5 hours.
The TeloPrime Full-Length cDNA Amplification Kit is an all-in-one protocol for generating full-length cDNA from total RNA.
The SPLIT RNA Extraction Kit enables a fast and highly efficient extraction of RNA that is free of genomic DNA contamination without usage of DNase. The RNA can be recovered as total RNA or split into two fractions, large RNA and small RNA.
Learn more about our products
Offers valid until December 31, 2014, or while the stocks last.
QuantSeq 3’mRNA-Seq Library Prep has been automated on PerkinElmer Sciclone/Zephyr Workstations
3’mRNA-Seq with minimum manual intervention for cost-effective, fast, accurate gene expression analysis and 3’UTR mapping
Lexogen is glad to announce the launch of autoQuantSeq on PE Sciclone/Zephyr, which is an automated version of the QuantSeq 3’mRNA-Seq Library Prep protocol and uses the same kit reagents. Hence, it features automated all-in-one library preparation protocol designed to generate up to 96 Illumina-compatible libraries of the sequences close to the 3’ end of the polyadenylated RNA within just 7 hours.
Automating the process of library preparation has the advantage of avoiding sample tracking errors, dramatically increasing throughput and saving hands-on time.
QuantSeq will be further automated on all major liquid handlers used for Next Generation Sequencing library preparation.
The new QuantSeq 3’mRNA-Seq Library Prep is the best alternative for microarrays and conventional RNA-Seq for gene expression analysis and eQTL studies, and a great tool for detection of the 3'UTR.
Lexogen has launched the QuantSeq 3’mRNA-Seq Library Prep kit. This protocol generates Illumina-compatible libraries of the 3' end of transcripts from 100 pg - 2 µg of total RNA within 4.5 hours. As only one fragment per transcript is produced no length normalization is required, and an accurate determination of gene expression values is possible. Sequencing from the poly(A) tail makes it furthermore possible to assess the exact 3'UTR. By maintaining the strand-specificity (> 99.9%) the protocol allows an efficient detection of the antisense transcripts, overlapping and fusion genes.
With the high level of multiplexing (96 samples/lane) and the low price per reaction, QuantSeq is an cost-efficient alternative for gene expression analysis.
Lexogen’s SPLIT RNA extraction kit is designed to extract RNAs of all lengths from various sources, either as total RNA or split by size into a large RNA fraction and a small RNA fraction. Size-selection is achieved by adjusting the isopropanol volume used to precipitate the RNA onto the silica column.
The SPLIT RNA Extraction Kit enables a fast and highly efficient extraction of RNA
that is free of genomic DNA contamination. The RNA can be recovered as total RNA
or split into a large and a small RNA fraction, facilitating the analysis of e.g. mRNA
and miRNA from the same sample. Thus the RNA obtained is ideal for seamlessly
preparing libraries for Next Generation Sequencing of total RNA or its large and
small fractions.
QuantSeq 3‘mRNA-Seq Library Prep Kit generates Illumina-compatible libraries of the sequences close to the 3’end of the polyadenylated RNA. Only one fragment per transcript is generated and therefore no length normalization of reads is needed. This results in extremely accurate gene expression values.
QuantSeq is available in two versions: using the first kit (Cat. No. 015.96) NGS reads are generated towards the oligodT, and to pinpoint the exact 3’ end paired-end sequencing may be required. This version of QuantSeq results in reads directly reflecting the mRNA sequence. With the second version of the kit (Cat.No. 016.96) it is possible to exactly pinpoint the 3’ end during Read 1. The reads generated here during Read 1 reflect the cDNA sequence. In order to achieve cluster calling on the Illumina platform a T-fill reaction is required first for this version of the kit.
QuantSeq maintains exceptional strand-specificity of more than 99.9 % and allows to map reads to their corresponding strand on the genome, enabling the discovery and quantification of antisense transcripts and overlapping genes.
The quantification and control of technical variability is an essential part of any experiment. By minimizing technical variation introduced during steps such as RNA extraction, library construction, and sequencing, quantification more accurately reflects the true biological concentrations of transcripts and permits more repeatable and precise sample-to-sample comparisons. This technical note briefly examines the precision and repeatability of transcript quantification with the SENSE mRNA-Seq library preparation kit
The SENSE mRNA-seq library preparation kit generates ready-to-sequence libraries from low amounts of total RNA within 4 h. SENSE libraries are significantly more strand specific (>99.9%) than leading alternatives and are virtually free of rRNA contamination. The protocol does not rely on RNA or cDNA fragmentation or additional kits for rRNA depletion, library amplification or size selection and is available for Illumina, Ion Torrent and SOLiD sequencing platforms.
The majority of RNA-seq library preparation protocols quantify the expression of genes without taking into account the numerous transcript variants which contribute to this overall expression. SQUARE mRNA-seq uses a selective matrix to separate transcript variants and to enable the assembly and quantification of individual transcripts. The protocol is highly specific for full-length, polyadenylated mRNA, and transcript hypotheses are supported by directional transcription start and polyadenylation site tagging.
