QIAseq miRNA Library Kit
Gel-free miRNA Sample to Insight solution for differential expression analysis and novel discovery using next-generation sequencing
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QIAseq miRNA 12 Index Kit IL UDI (12)
Cat. No. / ID: 331601
The QIAseq miRNA 12 Index Kit UDI is for indexing 12 samples using QIAseq miRNA library Kits. The sample indices are supplied as a liquid, in 96-well hard plastic plates, along with the UDI 5' Adapter (96) and the UDI RT Initiator (96). NOTE: In order to ensure data consistency, we recommend that all samples in a data set have UDIs. This ensures that the protocol and sequencing will be the same for all samples. Compatible UDI indices are 331601, 331615, 331625, 331635, 331645, 331655, 331665, 331675, 331685, 331717, 331727 and 331738
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KitIndex
Library Kit
miRNA Index Kit Version 1
miRNA Index Kit UDI Version 2
For platform
Illumina
Thermo Fisher
Number of indices
12
48
96
Samples
12 CDI
12 UDI
The QIAseq miRNA Library Kit is intended for molecular biology applications. This product is not intended for the diagnosis, prevention, or treatment of a disease.
✓ 24/7 automatic processing of online orders
✓ Knowledgeable and professional Product & Technical Support
✓ Fast and reliable (re)-ordering
Features
- Gel-free miRNA sequencing library prep speeds up library construction time
- Elimination of adapter dimers and hY4 RNA resulting in the highest fidelity and most efficient data from low input serum, plasma and exosome samples
- Integrated Unique Molecular Indices (UMIs) enable quantification of individual miRNA molecules
- Includes access to the RNA-seq Analysis Portal for human, mouse and rat samples
- Available with 768 unique dual indices for high-throughput sequencing on Illumina NovaSeq instruments
Product Details
Optimized reaction chemistry enables robust, miRNA-specific libraries while minimizing reaction biases and eliminating adapter dimers. Unique Molecular Indices (UMIs) tag each miRNA at an early stage, eliminating PCR and sequencing bias. Analyze miRNA-seq data with ease using the GeneGlobe-integrated RNA-seq Analysis Portal – an intuitive, web-based data analysis solution created for biologists and included with QIAseq Stranded RNA Library Kits.
High-throughput sequencing on Illumina NovaSeq instruments is now possible with 768 unique dual indices.
Important note: We highly recommend that data is only compared with RNA-seq libraries that use the same type of indices (single or unique dual indices) in order to ensure experimental consistency. Samples and data generated with single-end indexed libraries should only be compared with other samples and data generated with single-end indices. Samples and data generated with unique dual indices should only be compared to other samples and data generated with unique dual indices.
Want to try this solution for the first time? Request a quote for a trial kit.
Performance
QIAseq miRNA sequencing enables superior data generation through an improved workflow. The standard QIAseq miRNA procedure does not require gel purification, excision and elution, providing substantial sample handling/loss and time savings.
A huge issue with miRNA sequencing workflows is the presence of adapter dimer contamination. The QIAseq miRNA Library Kit has fully optimized library process to virtually eliminate adapter dimerization, even from very low inputs of total RNA (see figure Adapter dimers (AD) and contaminating RNA steal your reads during miRNAseq experiments). In addition, the reaction chemistry facilitates the preparation of robust, miRNA-focused libraries while all but eliminating biases and background contaminants. Together, these benefits highlight that the QIAseq miRNA Library Kit is designed to maximize the yield of miRNA available to sequence.
Due to the growth of circulating miRNAs as potential biomarkers, the QIAseq miRNA Library Kit is optimized to map miRNA down to ultralow input levels. In addition, the kit integrates Unique Molecular Indices (UMIs) into the reverse-transcription process, enabling unbiased and accurate miRNome-wide quantification of mature miRNAs by NGS. Collectively, QIAseq miRNA offers an unrivaled Sample to Insight solution for differential expression analysis and discovery of novel miRNAs using next-generation sequencing (see figure QIAseq miRNA workflow).
A huge issue with miRNA sequencing workflows is the presence of adapter dimer contamination. The QIAseq miRNA Library Kit has fully optimized library process to virtually eliminate adapter dimerization, even from very low inputs of total RNA (see figure Adapter dimers (AD) and contaminating RNA steal your reads during miRNAseq experiments). In addition, the reaction chemistry facilitates the preparation of robust, miRNA-focused libraries while all but eliminating biases and background contaminants. Together, these benefits highlight that the QIAseq miRNA Library Kit is designed to maximize the yield of miRNA available to sequence.
Due to the growth of circulating miRNAs as potential biomarkers, the QIAseq miRNA Library Kit is optimized to map miRNA down to ultralow input levels. In addition, the kit integrates Unique Molecular Indices (UMIs) into the reverse-transcription process, enabling unbiased and accurate miRNome-wide quantification of mature miRNAs by NGS. Collectively, QIAseq miRNA offers an unrivaled Sample to Insight solution for differential expression analysis and discovery of novel miRNAs using next-generation sequencing (see figure QIAseq miRNA workflow).
Principle
Mature miRNAs are naturally occurring, 22-nucleotide, non-coding RNAs that mediate posttranscriptional gene regulation. Alterations in miRNA can be correlated with gene expression changes in development, differentiation, signal transduction, infection, aging and disease. Continually growing evidence associates circulating miRNA expression with both normal and disease biology as miRNAs expressed in virtually all biofluids, including serum, plasma, cerebrospinal fluid (CSF) and urine. Specifically with cancers, numerous studies and reviews have associated the presence of various miRNAs with cancer cell proliferation, resistance to apoptosis, invasiveness and differentiation.
Quantification of miRNA expression can be performed using a variety of technologies including next-generation sequencing (NGS) and real-time PCR (qPCR). While NGS is the default tool for novel miRNA discovery, commercially available library preparation kits are tedious and introduce biases. As a result, qPCR has been the “go to” technology for quantification of miRNA expression, until now. QIAseq miRNA defines a new generation in small RNA sequencing products and includes several distinct features not found in other sequencing kits. With the QIAseq miRNA Library Kit, the power of NGS has been combined with single molecule quantification from UMIs to produce the most representative expression data possible.Procedure
QIAGEN offers a true Sample to Insight workflow, from sample isolation to data analysis and interpretation. Total RNA is first extracted from biofluids (such as serum, plasma, CSF and urine), cells, fresh/frozen tissues or FFPE tissues using a miRNeasy kit. From there, miRNA sequencing libraries are prepared using the QIAseq miRNA Library Kit (see figure Under a day prep).
In an unbiased reaction, adapters are ligated sequentially to the 3’ and 5’ ends of miRNAs. Subsequently, universal cDNA synthesis with UMI assignment, cDNA cleanup, library amplification and library cleanup are performed. Proprietary methodology, using modified oligonucleotides, virtually eliminates the presence of adapter dimers in the sequencing library and effectively removes a major contaminant often observed during sequencing. Bead-based cleanups eliminate the majority of unwanted background noise that steals sequencing reads from a budget. The UMIs ensure that during data analysis, the sample is analyzed specifically, not amplification or sequencing artifacts. To go from sample to sequencer, the process takes only eight hours, with minimal hands-on time. Up to a maximum of 48 samples can be multiplexed.
After sequencing, “.fastq” or “.fastq.gz” file formats can be uploaded directly to the GeneGlobe Data Analysis Center for primary mapping and molecular tag counting. For well-characterized species, such as human, mouse and rat, reads are mapped to species-specific miRBase and genome databases. For poorly-characterized or novel species, read are mapped to the entire miRBase database. Secondary differential expression analysis is then performed with multiple methods for molecular tag count normalization and visualization of the resulting data.
In an unbiased reaction, adapters are ligated sequentially to the 3’ and 5’ ends of miRNAs. Subsequently, universal cDNA synthesis with UMI assignment, cDNA cleanup, library amplification and library cleanup are performed. Proprietary methodology, using modified oligonucleotides, virtually eliminates the presence of adapter dimers in the sequencing library and effectively removes a major contaminant often observed during sequencing. Bead-based cleanups eliminate the majority of unwanted background noise that steals sequencing reads from a budget. The UMIs ensure that during data analysis, the sample is analyzed specifically, not amplification or sequencing artifacts. To go from sample to sequencer, the process takes only eight hours, with minimal hands-on time. Up to a maximum of 48 samples can be multiplexed.
After sequencing, “.fastq” or “.fastq.gz” file formats can be uploaded directly to the GeneGlobe Data Analysis Center for primary mapping and molecular tag counting. For well-characterized species, such as human, mouse and rat, reads are mapped to species-specific miRBase and genome databases. For poorly-characterized or novel species, read are mapped to the entire miRBase database. Secondary differential expression analysis is then performed with multiple methods for molecular tag count normalization and visualization of the resulting data.
Applications
Biofluids (such as serum, plasma, CSF and urine), cells, fresh/frozen tissue and FFPE tissues containing total and miRNA are compatible with the QIAseq miRNA Library Kit. Use the QIAseq miRNA Library Kit to characterize the next circulating miRNA biomarker. Uncover miRNA signatures locked away in FFPE tissues. Completely characterize a new species. The QIAseq miRNA Library Kit has been designed to enhance yields from biofluids such as serum. In the figure Detection of miRNA, the QIAseq miRNA Library Kit shows robust detection of miRNA from serum samples. Mapped reads were then compared to adapter dimers in serum samples. QIAseq miRNA still shows superior mapping of miRNAs even with limited samples (see figure Read distribution in serum samples). With the QIAseq miRNA Library Kit, determine the differential expression of any known or novel miRNAs from any total RNA sample derived from any species.
QIAseq miRNA is the ultimate tool to enhance discovery and expression from large-scale projects with hundreds of samples down to the small pilot focused on a group of target miRNA. QIAseq miRNA offers an unrivaled Sample to Insight solution for differential expression analysis and discovery of novel miRNAs using next-generation sequencing.
Supporting data and figures
Adapter dimers (AD) and contaminating RNAs steal your reads during miRNA sequencing experiments
While gels can be used to eliminate adapter dimers and contaminating RNAs, there is still a possibility for high prevalence in sequencing reads even after gel excision. On the above left, QIAseq miRNA shows a robust miRNA library with no adapter dimers or contaminating RNA after the basic protocol that includes a bead-based purification. Compared to libraries generated with competitor kits (prior to a required tedious gel excision), the QIAseq-derived miRNA library is much more robust and devoid of adapter dimers and contaminating RNAs.
Resources
Instrument Technical Documents (13)
Kit Handbooks (5)
Quick-Start Protocols (2)
Scientific Posters (1)
Safety Data Sheets (1)
miRNA Research (2)
Supplementary Protocols (2)
Application Notes (1)
Certificates of Analysis (1)
Publications
Multisite Evaluation of Next-Generation Methods for Small RNA Quantification.
J Biomol Tech; 2020; 31 (2):47-56 2020 Jul PMID:31966025
Evaluation of methodologies for microRNA biomarker detection by next generation sequencing.
RNA Biol; 2018; 15 (8):1133-1145 2018 Sep 18 PMID:30223713
Validation of RNA extraction procedures focused on micro RNA expression analysis.
Folia Biol (Praha); 2013; 59 (1):47-50 2013 PMID:23537528
PIWI-interacting RNAs are aberrantly expressed and may serve as novel biomarkers for diagnosis of lung adenocarcinoma.
Thorac Cancer; 2021; 12 (18):2468-2477 2021 Aug 3 PMID:34346164
Epigenetic regulation of triple negative breast cancer (TNBC) by TGF-β signaling.
Sci Rep; 2021; 11 (1):15410 2021 Jul 29 PMID:34326372
FAQ
What is the recommended read length for libraries prepared using the QIAseq miRNA Library Kit?
Can you perform qPCR analysis of miRNAs from libraries prepared with the QIAseq miRNA Library Kit?
Total RNA from what sample types are compatible with the QIAseq miRNA Library Kit?
What method is used to eliminate adapter dimers from the QIAseq miRNA library?
Are any components of the QIAseq miRNA Library Kit interchangeable with components from other QIAGEN kits?
Should total RNA or small enriched RNA be used as the starting material for the QIAseq miRNA Library Kit?
What is the sequence of the QIAseq miRNA NGS 5’ Adapter?
Are the QIAseq miRNA NGS 5’ Adapter and QIAseq miRNA NGS RT Initiator compatible with the QIAseq miRNA UDI kits?
What is the maximum number of available sample indexes?
What can be used to validate results obtained with the QIAseq miRNA Library Kit?
What is the acceptable number of reads per sample per miRNA sequencing run?
How do Unique Molecular Indexes (UMIs) improve quantification?
What are recommended stopping points during the QIAseq miRNA Library Kit procedure?
Does a QIAseq miRNA library include hY4 Y RNA?
Can I still perform sequencing if my miRNA sequencing library concentrations are too low to obtain a 4 nM library?
What are common sized libraries observed on a TapeStation, Bioanalyzer, or similar instruments?
Can miRNA sequencing libraries be prepared from total RNA isolated from heparinized plasma samples?
What is the sequence of the QIAseq miRNA NGS 3’ Adapter?
What is the sequence of the UDI 5' Adapter?