qiaseq mirna library kit  (Qiagen)


Bioz Verified Symbol Qiagen is a verified supplier
Bioz Manufacturer Symbol Qiagen manufactures this product  
  • Logo
  • About
  • News
  • Press Release
  • Team
  • Advisors
  • Partners
  • Contact
  • Bioz Stars
  • Bioz vStars
  • 99
    Name:
    QIAseq miRNA Library Kit
    Description:
    Gel free miRNA Sample to Insight solution for differential expression analysis and novel discovery using next generation sequencing Kit contents For 12 sequencing prep reactions 3 ligation 5 ligation reverse transcription cDNA cleanup library amplification and library cleanup reagents quality control primers Benefits Gel free miRNA sequencing library prep from as little as 1 ng of total RNA Elimination of adapter dimers and unwanted RNA species resulting in the highest fidelity and most efficient data Bead based method to remove adapter dimers and unwanted RNA species Integrated Unique Molecular Indices UMIs enable quantification of individual miRNA molecules Primary read mapping and differential expression analysis via the GeneGlobe Data Analysis Cen
    Catalog Number:
    331502
    Price:
    1120
    Category:
    QIAseq miRNA Library Kit
    Buy from Supplier


    Structured Review

    Qiagen qiaseq mirna library kit
    QIAseq miRNA Library Kit
    Gel free miRNA Sample to Insight solution for differential expression analysis and novel discovery using next generation sequencing Kit contents For 12 sequencing prep reactions 3 ligation 5 ligation reverse transcription cDNA cleanup library amplification and library cleanup reagents quality control primers Benefits Gel free miRNA sequencing library prep from as little as 1 ng of total RNA Elimination of adapter dimers and unwanted RNA species resulting in the highest fidelity and most efficient data Bead based method to remove adapter dimers and unwanted RNA species Integrated Unique Molecular Indices UMIs enable quantification of individual miRNA molecules Primary read mapping and differential expression analysis via the GeneGlobe Data Analysis Cen
    https://www.bioz.com/result/qiaseq mirna library kit/product/Qiagen
    Average 99 stars, based on 7 article reviews
    Price from $9.99 to $1999.99
    qiaseq mirna library kit - by Bioz Stars, 2020-04
    99/100 stars

    Images

    1) Product Images from "Evaluation of methodologies for microRNA biomarker detection by next generation sequencing"

    Article Title: Evaluation of methodologies for microRNA biomarker detection by next generation sequencing

    Journal: RNA Biology

    doi: 10.1080/15476286.2018.1514236

    Overview of the small RNA sequencing workflow, compared methodologies for library preparation and computational analysis pipeline. (a) Schematic illustration of small RNA sequencing (sRNA-seq) library preparation. With exception of the SMARTer smRNA-Seq kit, all kits employed a ligation-based approach to attach 3′ and 5′ adapter to the miRNA. In the QIAseq protocol, a unique barcode is attached at the RT stage (orange dotted line), so-called unique molecular indices (UMI). Illumina adapter (purple and blue) and sequencing index (light purple) for multiplexing are added during the PCR amplification. Several steps of the protocol may introduce bias to the sequencing libraries as indicated by the yellow warning triangles. (b) Table summary of the key features of the four assessed sRNA-seq kits. (c) Small RNA sequencing data analysis pipeline. In the case of QIAseq, UMIs were trimmed alongside the adapters to allow side-by-side comparison by a single computational pipeline. Abbreviations: Nextflex Small RNA-Seq Kit v3 (Nextflex), NEBNext Small RNA Library Prep Set (NEBNext) and QIAseq miRNA Library Kit (QIAseq).
    Figure Legend Snippet: Overview of the small RNA sequencing workflow, compared methodologies for library preparation and computational analysis pipeline. (a) Schematic illustration of small RNA sequencing (sRNA-seq) library preparation. With exception of the SMARTer smRNA-Seq kit, all kits employed a ligation-based approach to attach 3′ and 5′ adapter to the miRNA. In the QIAseq protocol, a unique barcode is attached at the RT stage (orange dotted line), so-called unique molecular indices (UMI). Illumina adapter (purple and blue) and sequencing index (light purple) for multiplexing are added during the PCR amplification. Several steps of the protocol may introduce bias to the sequencing libraries as indicated by the yellow warning triangles. (b) Table summary of the key features of the four assessed sRNA-seq kits. (c) Small RNA sequencing data analysis pipeline. In the case of QIAseq, UMIs were trimmed alongside the adapters to allow side-by-side comparison by a single computational pipeline. Abbreviations: Nextflex Small RNA-Seq Kit v3 (Nextflex), NEBNext Small RNA Library Prep Set (NEBNext) and QIAseq miRNA Library Kit (QIAseq).

    Techniques Used: RNA Sequencing Assay, Ligation, Sequencing, Multiplexing, Polymerase Chain Reaction, Amplification, Introduce

    2) Product Images from "Multisite Evaluation of Next-Generation Methods for Small RNA Quantification"

    Article Title: Multisite Evaluation of Next-Generation Methods for Small RNA Quantification

    Journal: Journal of Biomolecular Techniques : JBT

    doi: 10.7171/jbt.20-3102-001

    miRNA detection and bias. Percentages of Miltenyi Biotec miRXplore miRNA detected above 5 CPM in MUR ( A ) and in MUR-D ( B ) are shown. Percentages and amplitude of Miltenyi Biotec miRXplore miRNA detected that deviated from the median are shown in MUR ( C ) or MUR-D ( D ). The darkest shade is within 2-fold of the median; the medium shade is 2–10-fold either up or down vs. the expected value; the lightest shade is > 10× either increased or decreased. Percentages of reads increased > 10× from median in MUR ( E ) or MUR-D ( F ). CLO-S and C, Takara Bio (Clontech) SMARTer smRNA-Seq Kit; DIA and D, Diagenode CATS Small RNA-Seq Kit; ILMN and I, Illumina TruSeq Small RNA Library Prep Kit; LEX and L, Lexogen Small RNA-Seq Library Prep Kit; Nano, NanoString nCounter miRNA Expression Assay; NEB and N, New England Biolabs NEBNext Small RNA Library Prep Set; PEB and P, PerkinElmer NextFlex Small RNA-Seq Kit v.3; QIA and Q, Qiagen QIAseq miRNA Library Kit; SOM and S, Somagenics RealSeq-AC miRNA Library Kit; TRI and T, Trilink CleanTag Small RNA Library Prep Kit.
    Figure Legend Snippet: miRNA detection and bias. Percentages of Miltenyi Biotec miRXplore miRNA detected above 5 CPM in MUR ( A ) and in MUR-D ( B ) are shown. Percentages and amplitude of Miltenyi Biotec miRXplore miRNA detected that deviated from the median are shown in MUR ( C ) or MUR-D ( D ). The darkest shade is within 2-fold of the median; the medium shade is 2–10-fold either up or down vs. the expected value; the lightest shade is > 10× either increased or decreased. Percentages of reads increased > 10× from median in MUR ( E ) or MUR-D ( F ). CLO-S and C, Takara Bio (Clontech) SMARTer smRNA-Seq Kit; DIA and D, Diagenode CATS Small RNA-Seq Kit; ILMN and I, Illumina TruSeq Small RNA Library Prep Kit; LEX and L, Lexogen Small RNA-Seq Library Prep Kit; Nano, NanoString nCounter miRNA Expression Assay; NEB and N, New England Biolabs NEBNext Small RNA Library Prep Set; PEB and P, PerkinElmer NextFlex Small RNA-Seq Kit v.3; QIA and Q, Qiagen QIAseq miRNA Library Kit; SOM and S, Somagenics RealSeq-AC miRNA Library Kit; TRI and T, Trilink CleanTag Small RNA Library Prep Kit.

    Techniques Used: RNA Sequencing Assay, Expressing

    Study design and workflow metrics. A ) Schematic of study design is shown. MUR, MUR-D, and HBR were processed using 9 different smRNA profiling methods at 4 sites each. The general methodologies included sequential ligation (Illumina, TriLink, Qiagen, NEB, PerkinElmer, Lexogen), template switching (Takara, Diagenode), circularization (Somagenics), and NanoString probe-based hybridization. B ) Total start-to-finish preparation time for each kit as reported by sites. C ) Mean “ease of use” reported by each site (scale: 1 = uncomfortable, 5 = comfortable). D ) Library preparation success rates. Light color blocks are successfully produced libraries. Dark colors are failed libraries. CLO and CLO-S, Takara Bio (Clontech) SMARTer smRNA-Seq Kit; DIA, Diagenode CATS Small RNA-Seq Kit; ILL and ILMN, Illumina TruSeq Small RNA Library Prep Kit; LEX, Lexogen Small RNA-Seq Library Prep Kit; NANO, NanoString nCounter miRNA Expression Assay; NEB, New England Biolabs NEBNext Small RNA Library Prep Set; PEB, PerkinElmer NextFlex Small RNA-Seq Kit v.3; QIA, Qiagen QIAseq miRNA Library Kit; SOM, Somagenics RealSeq-AC miRNA Library Kit; TRI, Trilink CleanTag Small RNA Library Prep Kit.
    Figure Legend Snippet: Study design and workflow metrics. A ) Schematic of study design is shown. MUR, MUR-D, and HBR were processed using 9 different smRNA profiling methods at 4 sites each. The general methodologies included sequential ligation (Illumina, TriLink, Qiagen, NEB, PerkinElmer, Lexogen), template switching (Takara, Diagenode), circularization (Somagenics), and NanoString probe-based hybridization. B ) Total start-to-finish preparation time for each kit as reported by sites. C ) Mean “ease of use” reported by each site (scale: 1 = uncomfortable, 5 = comfortable). D ) Library preparation success rates. Light color blocks are successfully produced libraries. Dark colors are failed libraries. CLO and CLO-S, Takara Bio (Clontech) SMARTer smRNA-Seq Kit; DIA, Diagenode CATS Small RNA-Seq Kit; ILL and ILMN, Illumina TruSeq Small RNA Library Prep Kit; LEX, Lexogen Small RNA-Seq Library Prep Kit; NANO, NanoString nCounter miRNA Expression Assay; NEB, New England Biolabs NEBNext Small RNA Library Prep Set; PEB, PerkinElmer NextFlex Small RNA-Seq Kit v.3; QIA, Qiagen QIAseq miRNA Library Kit; SOM, Somagenics RealSeq-AC miRNA Library Kit; TRI, Trilink CleanTag Small RNA Library Prep Kit.

    Techniques Used: Ligation, Hybridization, Produced, RNA Sequencing Assay, Expressing

    Relative expression of miRNAs. A ) Correlation scatter plots of miRNAs detected in MUR and MUR-D for the QIA method, with miRNAs scored in log2 mapped reads per million. B ) Correlation scatter plot of miRNAs detected in MUR-D using LEX vs. ILL kits, with miRNAs scored in log2 mapped reads per million. C ) Unsupervised hierarchical clustering heatmap of log2 transformed CPM across all methods. C (prep kit), Takara Bio (Clontech) SMARTer smRNA-Seq Kit; C (prep type), circularization; D, Diagenode CATS Small RNA-Seq Kit; ILL and I, Illumina TruSeq Small RNA Library Prep Kit; L (prep type), sequential ligation; LEX and L (prep kit), Lexogen Small RNA-Seq Library Prep Kit; N, New England Biolabs NEBNext Small RNA Library Prep Set; Nano, NanoString nCounter miRNA Expression Assay; NO, No size selection; P, PerkinElmer NextFlex Small RNA-Seq Kit v.3; QIA and Q, Qiagen QIAseq miRNA Library Kit; S, Somagenics RealSeq-AC miRNA Library Kit; SAGE, pippin prep; SPRI, solid phase reversible immobilization; T (prep kit), Trilink CleanTag Small Library Prep Kit; T (prep type), template switching.
    Figure Legend Snippet: Relative expression of miRNAs. A ) Correlation scatter plots of miRNAs detected in MUR and MUR-D for the QIA method, with miRNAs scored in log2 mapped reads per million. B ) Correlation scatter plot of miRNAs detected in MUR-D using LEX vs. ILL kits, with miRNAs scored in log2 mapped reads per million. C ) Unsupervised hierarchical clustering heatmap of log2 transformed CPM across all methods. C (prep kit), Takara Bio (Clontech) SMARTer smRNA-Seq Kit; C (prep type), circularization; D, Diagenode CATS Small RNA-Seq Kit; ILL and I, Illumina TruSeq Small RNA Library Prep Kit; L (prep type), sequential ligation; LEX and L (prep kit), Lexogen Small RNA-Seq Library Prep Kit; N, New England Biolabs NEBNext Small RNA Library Prep Set; Nano, NanoString nCounter miRNA Expression Assay; NO, No size selection; P, PerkinElmer NextFlex Small RNA-Seq Kit v.3; QIA and Q, Qiagen QIAseq miRNA Library Kit; S, Somagenics RealSeq-AC miRNA Library Kit; SAGE, pippin prep; SPRI, solid phase reversible immobilization; T (prep kit), Trilink CleanTag Small Library Prep Kit; T (prep type), template switching.

    Techniques Used: Expressing, Transformation Assay, RNA Sequencing Assay, Ligation, Selection

    Related Articles

    Amplification:

    Article Title: Bulky DNA adducts, microRNA profiles, and lipid biomarkers in Norwegian tunnel finishing workers occupationally exposed to diesel exhaust
    Article Snippet: Small RNA sequencing (sRNA-seq) Libraries for sRNA-seq were prepared using QIAseq miRNA Library kit (Qiagen, Hilden, Germany). .. Briefly, adapters were ligated to the 3' and 5' ends of miRNAs. sRNAs with ligated adapters underwent reverse transcription with unique molecular identifier (UMI) assignment followed by library amplification (16 cycles) on a Mastercycler Nexus (Eppendorf, Hamburg, Germany). sRNA libraries were validated on an Agilent 2100 Bioanalyzer (Agilent, Santa Clara, California, USA) using high-sensitivity DNA chips.

    Article Title: Evaluation of methodologies for microRNA biomarker detection by next generation sequencing
    Article Snippet: As such, certain adapter-miRNA pairs or sequence compositions may be favoured over others during ligation and PCR amplification, and thereby result in over- or underrepresentation of these miRNAs in the sequencing library [ , ]. .. In this study, we have benchmarked four commercial kits intended for Illumina sequencing: Nextflex Small RNA-Seq Kit v3, Bioo Scientific (BSC); SMARTer smRNA-Seq Kit, Clontech/Takara (CLT); NEBNext Small RNA Library Prep Set, New England Biolabs (NEB) and QIAseq miRNA Library Kit, Qiagen (QIA).

    Article Title: HNRNPA2/B1 is upregulated in endocrine-resistant LCC9 breast cancer cells and alters the miRNA transcriptome when overexpressed in MCF-7 cells
    Article Snippet: Libraries were prepared using QIAseq miRNA Library Kit (Qiagen). cDNA samples were barcoded with QIAseq miRNA NGS ILM IP primers. .. Adaptor dimers were removed from amplified libraries using QIAseq miRNA NGS beads.

    Construct:

    Article Title: Systematic Analysis of Transcriptomic Profile of the Effects of Low Dose Atropine Treatment on Scleral Fibroblasts using Next-Generation Sequencing and Bioinformatics
    Article Snippet: Samples were prepared with the QIAseq miRNA Library Kit (QIAGEN) following the instruction manual. .. Following the sequential ligation of adaptors to the 3' and 5' ends of miRNAs, universal cDNA synthesis was carried out, and the cDNA constructs containing 18-40 nucleotide (140-155 nucleotides in length with both adaptors) RNA fragments were chosen.

    Microarray:

    Article Title: Multisite Evaluation of Next-Generation Methods for Small RNA Quantification
    Article Snippet: RNA from the HBR (AM7962; Thermo Fisher Scientific), a commercially available sample from the 2006 Microarray Quality Control study, was used as a second standard because it is commonly used to characterize miRNA chemistries by other studies and provides a highly complex normal sample. .. Most of the kits tested, including Illumina TruSeq Small RNA Library Prep Kit, Lexogen Small RNA-Seq Library Prep Kit, New England Biolabs NEBNext Small RNA Library Prep Set, PerkinElmer (formerly Bioo Scientific) NextFlex Small RNA-Seq Kit v.3, Qiagen QIAseq miRNA Library Kit, and Trilink CleanTag Small RNA Library Prep Kit all use variants of this methodology.

    Significance Assay:

    Article Title: Immunophenotyping and transcriptional profiling of in vitro cultured human adipose tissue derived stem cells
    Article Snippet: Transcripts that showed significant and consistent differences between conditions in our dataset (FDR corrected p-value, q-value < 0.05) were subjected to further interpretation with Ingenuity Pathway Analysis. .. 2 combination (Supplementary Table ). miRNA-seq was performed for the same set of five biological replicate experiments using QIAseq miRNA Library Kit (Qiagen, Hilden, Germany) following the manufacturer protocol, starting with 500 ng of input RNA for each sample.

    Expressing:

    Article Title: PIWI proteins contribute to apoptosis during the UPR in human airway epithelial cells
    Article Snippet: Small RNA sequencing libraries were prepared using QIAseq miRNA library kit (Qiagen) following the manufacturer’s instructions and followed by sequencing on an Illumina NextSeq instrument. .. The analysis of the differential expression of small RNAs between control and experimental samples were performed with geNorm in the Gene Globe Software.

    Article Title: Systematic Analysis of Transcriptomic Profile of the Effects of Low Dose Atropine Treatment on Scleral Fibroblasts using Next-Generation Sequencing and Bioinformatics
    Article Snippet: Paragraph title: Next-Generation Sequencing (NGS) for miRNA and mRNA Expression Profiling ... Samples were prepared with the QIAseq miRNA Library Kit (QIAGEN) following the instruction manual.

    Article Title: Transforming Growth Factor-β1 Selectively Recruits microRNAs to the RNA-Induced Silencing Complex and Degrades CFTR mRNA under Permissive Conditions in Human Bronchial Epithelial Cells
    Article Snippet: Experiments were performed in polarized human bronchial epithelial cell models CFBE41o- expressing WT- or F508del-CFTR (WT-CFBE and F508del-CFBE cells, respectively). .. Cells were treated with TGF-β1 or vehicle for 24 h, total RNA was isolated and used with QIAseqTM miRNA Library Kit (Qiagen), and analyzed on the Illumina platform.

    Modification:

    Article Title: A comparison of RNA extraction and sequencing protocols for detection of small RNAs in plasma
    Article Snippet: CleanTag™ Small RNA Library Prep Kit (TriLink) uses modified adapters to reduce adapter dimer formation from low inputs of RNA [ ]. .. QIAseq miRNA Library Kit (QIAGEN) claims to employ optimised reaction chemistry to reduce bias, minimise adapter dimer formation and contaminating non-miRNAs, facilitating low inputs of RNA.

    Derivative Assay:

    Article Title: Evaluation of methodologies for microRNA biomarker detection by next generation sequencing
    Article Snippet: In this study, we have benchmarked four commercial kits intended for Illumina sequencing: Nextflex Small RNA-Seq Kit v3, Bioo Scientific (BSC); SMARTer smRNA-Seq Kit, Clontech/Takara (CLT); NEBNext Small RNA Library Prep Set, New England Biolabs (NEB) and QIAseq miRNA Library Kit, Qiagen (QIA). .. All methodologies can generate miRNA sequencing libraries from low input amounts (1–100 ng) and are therefore suitable to process RNA derived from biofluids.

    Article Title: Multisite Evaluation of Next-Generation Methods for Small RNA Quantification
    Article Snippet: This standard is derived by using total RNA from Dicer-deleted mesenchymal stem cells, which lack almost all mature miRNA, and supplementing it with the MUR, which gives both rigorous known quantification as well as a more biologically representative context for the study. smRNA chemistries were derived from a broad variety of sources, reflecting several different methods for library preparation. .. Most of the kits tested, including Illumina TruSeq Small RNA Library Prep Kit, Lexogen Small RNA-Seq Library Prep Kit, New England Biolabs NEBNext Small RNA Library Prep Set, PerkinElmer (formerly Bioo Scientific) NextFlex Small RNA-Seq Kit v.3, Qiagen QIAseq miRNA Library Kit, and Trilink CleanTag Small RNA Library Prep Kit all use variants of this methodology.

    Hybridization:

    Article Title: Multisite Evaluation of Next-Generation Methods for Small RNA Quantification
    Article Snippet: Most of the kits tested, including Illumina TruSeq Small RNA Library Prep Kit, Lexogen Small RNA-Seq Library Prep Kit, New England Biolabs NEBNext Small RNA Library Prep Set, PerkinElmer (formerly Bioo Scientific) NextFlex Small RNA-Seq Kit v.3, Qiagen QIAseq miRNA Library Kit, and Trilink CleanTag Small RNA Library Prep Kit all use variants of this methodology. .. Finally, NanoString small RNA hybridization was used as a nonsequencing methodology for comparison.

    Ligation:

    Article Title: Evaluation of methodologies for microRNA biomarker detection by next generation sequencing
    Article Snippet: As such, certain adapter-miRNA pairs or sequence compositions may be favoured over others during ligation and PCR amplification, and thereby result in over- or underrepresentation of these miRNAs in the sequencing library [ , ]. .. In this study, we have benchmarked four commercial kits intended for Illumina sequencing: Nextflex Small RNA-Seq Kit v3, Bioo Scientific (BSC); SMARTer smRNA-Seq Kit, Clontech/Takara (CLT); NEBNext Small RNA Library Prep Set, New England Biolabs (NEB) and QIAseq miRNA Library Kit, Qiagen (QIA).

    Article Title: Multisite Evaluation of Next-Generation Methods for Small RNA Quantification
    Article Snippet: Typical smRNA library preparation for Illumina sequencing is based on sequential ligation of oligonucleotides to the 5′ and 3′ ends of the smRNAs. .. Most of the kits tested, including Illumina TruSeq Small RNA Library Prep Kit, Lexogen Small RNA-Seq Library Prep Kit, New England Biolabs NEBNext Small RNA Library Prep Set, PerkinElmer (formerly Bioo Scientific) NextFlex Small RNA-Seq Kit v.3, Qiagen QIAseq miRNA Library Kit, and Trilink CleanTag Small RNA Library Prep Kit all use variants of this methodology.

    Article Title: Systematic Analysis of Transcriptomic Profile of the Effects of Low Dose Atropine Treatment on Scleral Fibroblasts using Next-Generation Sequencing and Bioinformatics
    Article Snippet: Samples were prepared with the QIAseq miRNA Library Kit (QIAGEN) following the instruction manual. .. Following the sequential ligation of adaptors to the 3' and 5' ends of miRNAs, universal cDNA synthesis was carried out, and the cDNA constructs containing 18-40 nucleotide (140-155 nucleotides in length with both adaptors) RNA fragments were chosen.

    Biomarker Assay:

    Article Title: A comparison of RNA extraction and sequencing protocols for detection of small RNAs in plasma
    Article Snippet: Issues particularly pertinent for blood-based biomarker discovery are the ability to work with low miRNA concentrations and reduction of bias. .. QIAseq miRNA Library Kit (QIAGEN) claims to employ optimised reaction chemistry to reduce bias, minimise adapter dimer formation and contaminating non-miRNAs, facilitating low inputs of RNA.

    Indirect Immunoperoxidase Assay:

    Article Title: Immunophenotyping and transcriptional profiling of in vitro cultured human adipose tissue derived stem cells
    Article Snippet: Differentially expressed genes were grouped in functional pathways using Ingenuity Pathway Analysis (IPA Spring Release 2017, Redwood City, USA) on gene level using RefSeq annotation. .. 2 combination (Supplementary Table ). miRNA-seq was performed for the same set of five biological replicate experiments using QIAseq miRNA Library Kit (Qiagen, Hilden, Germany) following the manufacturer protocol, starting with 500 ng of input RNA for each sample.

    Sequencing:

    Article Title: A comparison of RNA extraction and sequencing protocols for detection of small RNAs in plasma
    Article Snippet: NEXTflex® Small RNA Sequencing Kit v3 (Bioo Scientific) uses randomised adapters to reduce sequencing bias and adapter dimer reduction technology to allow low inputs of RNA [ ]. .. QIAseq miRNA Library Kit (QIAGEN) claims to employ optimised reaction chemistry to reduce bias, minimise adapter dimer formation and contaminating non-miRNAs, facilitating low inputs of RNA.

    Article Title: PIWI proteins contribute to apoptosis during the UPR in human airway epithelial cells
    Article Snippet: .. Small RNA sequencing libraries were prepared using QIAseq miRNA library kit (Qiagen) following the manufacturer’s instructions and followed by sequencing on an Illumina NextSeq instrument. .. Using Qiagen’s Gene Globe Software, sequencing reads were aligned to the human reference genome assembly (hg19) followed by transcript assembly and estimation of the relative abundances.

    Article Title: Immunophenotyping and transcriptional profiling of in vitro cultured human adipose tissue derived stem cells
    Article Snippet: Paragraph title: RNA- and miRNA Sequencing and Bioinformatic Analysis ... 2 combination (Supplementary Table ). miRNA-seq was performed for the same set of five biological replicate experiments using QIAseq miRNA Library Kit (Qiagen, Hilden, Germany) following the manufacturer protocol, starting with 500 ng of input RNA for each sample.

    Article Title: Bulky DNA adducts, microRNA profiles, and lipid biomarkers in Norwegian tunnel finishing workers occupationally exposed to diesel exhaust
    Article Snippet: Small RNA sequencing (sRNA-seq) Libraries for sRNA-seq were prepared using QIAseq miRNA Library kit (Qiagen, Hilden, Germany). .. Sequencing of sRNA libraries was performed on MiSeq system (Illumina, San Diego, California, USA) using MiSeq Reagent Kit V.3.

    Article Title: Evaluation of methodologies for microRNA biomarker detection by next generation sequencing
    Article Snippet: .. In this study, we have benchmarked four commercial kits intended for Illumina sequencing: Nextflex Small RNA-Seq Kit v3, Bioo Scientific (BSC); SMARTer smRNA-Seq Kit, Clontech/Takara (CLT); NEBNext Small RNA Library Prep Set, New England Biolabs (NEB) and QIAseq miRNA Library Kit, Qiagen (QIA). .. All methodologies can generate miRNA sequencing libraries from low input amounts (1–100 ng) and are therefore suitable to process RNA derived from biofluids.

    Article Title: Multisite Evaluation of Next-Generation Methods for Small RNA Quantification
    Article Snippet: Typical smRNA library preparation for Illumina sequencing is based on sequential ligation of oligonucleotides to the 5′ and 3′ ends of the smRNAs. .. Most of the kits tested, including Illumina TruSeq Small RNA Library Prep Kit, Lexogen Small RNA-Seq Library Prep Kit, New England Biolabs NEBNext Small RNA Library Prep Set, PerkinElmer (formerly Bioo Scientific) NextFlex Small RNA-Seq Kit v.3, Qiagen QIAseq miRNA Library Kit, and Trilink CleanTag Small RNA Library Prep Kit all use variants of this methodology.

    Article Title: A comparison of RNA extraction and sequencing protocols for detection of small RNAs in plasma
    Article Snippet: .. Library preparation and sequencing Libraries were prepared from 5 μl of miRNeasy RNA using NEXTflex® Small RNA Sequencing Kit v3 for Illumina® Platforms (Bioo Scientific) and QIAseq miRNA Library Kit (QIAGEN) and from 2 μl miRNeasy RNA using CleanTag™ Small RNA Library Prep Kit (TriLink), following each of the manufacturers’ instructions. .. Additionally, libraries were prepared from 5 μl MagnaZol RNA using NEXTflex® Small RNA Sequencing Kit v3 for Illumina® Platforms (Bioo Scientific) and QIAseq miRNA Library Kit (QIAGEN).

    Article Title: Systematic Analysis of Transcriptomic Profile of the Effects of Low Dose Atropine Treatment on Scleral Fibroblasts using Next-Generation Sequencing and Bioinformatics
    Article Snippet: Samples were prepared with the QIAseq miRNA Library Kit (QIAGEN) following the instruction manual. .. Sequencing data was processed by Illumina software.

    Article Title: Transforming Growth Factor-β1 Selectively Recruits microRNAs to the RNA-Induced Silencing Complex and Degrades CFTR mRNA under Permissive Conditions in Human Bronchial Epithelial Cells
    Article Snippet: Cells were treated with TGF-β1 or vehicle for 24 h, total RNA was isolated and used with QIAseqTM miRNA Library Kit (Qiagen), and analyzed on the Illumina platform. .. The miRNA sequencing data were analyzed using the GeneGlobe Data Analysis bioinformatics pipeline from Qiagen.

    Binding Assay:

    Article Title: Transforming Growth Factor-β1 Selectively Recruits microRNAs to the RNA-Induced Silencing Complex and Degrades CFTR mRNA under Permissive Conditions in Human Bronchial Epithelial Cells
    Article Snippet: Cells were treated with TGF-β1 or vehicle for 24 h, total RNA was isolated and used with QIAseqTM miRNA Library Kit (Qiagen), and analyzed on the Illumina platform. .. As shown in A,B, TGF-β1 changed the expression of miRNAs with binding sites in the human CFTR 3’UTR predicted by TargetScan Release 7.2, Diana-TarBase v.8, miRBase, and/or miRmap bioinformatics tools [ , , , ].

    RNA Sequencing Assay:

    Article Title: A comparison of RNA extraction and sequencing protocols for detection of small RNAs in plasma
    Article Snippet: NEXTflex® Small RNA Sequencing Kit v3 (Bioo Scientific) uses randomised adapters to reduce sequencing bias and adapter dimer reduction technology to allow low inputs of RNA [ ]. .. QIAseq miRNA Library Kit (QIAGEN) claims to employ optimised reaction chemistry to reduce bias, minimise adapter dimer formation and contaminating non-miRNAs, facilitating low inputs of RNA.

    Article Title: PIWI proteins contribute to apoptosis during the UPR in human airway epithelial cells
    Article Snippet: .. Small RNA sequencing libraries were prepared using QIAseq miRNA library kit (Qiagen) following the manufacturer’s instructions and followed by sequencing on an Illumina NextSeq instrument. .. Using Qiagen’s Gene Globe Software, sequencing reads were aligned to the human reference genome assembly (hg19) followed by transcript assembly and estimation of the relative abundances.

    Article Title: Inheritance of a Phenotypically Neutral Epimutation Evokes Gene Silencing in Later Generations
    Article Snippet: Paragraph title: Small RNA sequencing and analysis ... Small RNA libraries were prepared with the QIAseq miRNA Library Kit (QIAGEN) according to manufacturer’s instructions and sequenced with an Illumina HiSeq2500.

    Article Title: Bulky DNA adducts, microRNA profiles, and lipid biomarkers in Norwegian tunnel finishing workers occupationally exposed to diesel exhaust
    Article Snippet: .. Small RNA sequencing (sRNA-seq) Libraries for sRNA-seq were prepared using QIAseq miRNA Library kit (Qiagen, Hilden, Germany). .. Briefly, adapters were ligated to the 3' and 5' ends of miRNAs. sRNAs with ligated adapters underwent reverse transcription with unique molecular identifier (UMI) assignment followed by library amplification (16 cycles) on a Mastercycler Nexus (Eppendorf, Hamburg, Germany). sRNA libraries were validated on an Agilent 2100 Bioanalyzer (Agilent, Santa Clara, California, USA) using high-sensitivity DNA chips.

    Article Title: Evaluation of methodologies for microRNA biomarker detection by next generation sequencing
    Article Snippet: .. In this study, we have benchmarked four commercial kits intended for Illumina sequencing: Nextflex Small RNA-Seq Kit v3, Bioo Scientific (BSC); SMARTer smRNA-Seq Kit, Clontech/Takara (CLT); NEBNext Small RNA Library Prep Set, New England Biolabs (NEB) and QIAseq miRNA Library Kit, Qiagen (QIA). .. All methodologies can generate miRNA sequencing libraries from low input amounts (1–100 ng) and are therefore suitable to process RNA derived from biofluids.

    Article Title: Multisite Evaluation of Next-Generation Methods for Small RNA Quantification
    Article Snippet: .. Most of the kits tested, including Illumina TruSeq Small RNA Library Prep Kit, Lexogen Small RNA-Seq Library Prep Kit, New England Biolabs NEBNext Small RNA Library Prep Set, PerkinElmer (formerly Bioo Scientific) NextFlex Small RNA-Seq Kit v.3, Qiagen QIAseq miRNA Library Kit, and Trilink CleanTag Small RNA Library Prep Kit all use variants of this methodology. .. The Takara SMARTer smRNA Kit and the Diagenode CATS Small RNA-Seq Kit both begin by polyadenylation of the 3′ nucleotide of the smRNA followed by reverse transcription and template switching.

    Article Title: A comparison of RNA extraction and sequencing protocols for detection of small RNAs in plasma
    Article Snippet: .. Library preparation and sequencing Libraries were prepared from 5 μl of miRNeasy RNA using NEXTflex® Small RNA Sequencing Kit v3 for Illumina® Platforms (Bioo Scientific) and QIAseq miRNA Library Kit (QIAGEN) and from 2 μl miRNeasy RNA using CleanTag™ Small RNA Library Prep Kit (TriLink), following each of the manufacturers’ instructions. .. Additionally, libraries were prepared from 5 μl MagnaZol RNA using NEXTflex® Small RNA Sequencing Kit v3 for Illumina® Platforms (Bioo Scientific) and QIAseq miRNA Library Kit (QIAGEN).

    Article Title: Transforming Growth Factor-β1 Selectively Recruits microRNAs to the RNA-Induced Silencing Complex and Degrades CFTR mRNA under Permissive Conditions in Human Bronchial Epithelial Cells
    Article Snippet: F508del-CFTR Modulates TGF-β1-Induced Changes in miRNA Landscape We used small RNA-seq to examine TGF-β1 effects on the entire miRNA landscape. .. Cells were treated with TGF-β1 or vehicle for 24 h, total RNA was isolated and used with QIAseqTM miRNA Library Kit (Qiagen), and analyzed on the Illumina platform.

    Isolation:

    Article Title: A comparison of RNA extraction and sequencing protocols for detection of small RNAs in plasma
    Article Snippet: QIAseq miRNA Library Kit (QIAGEN) claims to employ optimised reaction chemistry to reduce bias, minimise adapter dimer formation and contaminating non-miRNAs, facilitating low inputs of RNA. .. The MagnaZol™ cfRNA Isolation Reagent (Bioo Scientific) and miRNeasy Serum/Plasma kit (QIAGEN) are RNA extraction kits for the extraction of small RNAs from biofluids, specifically designed to work with low input volumes of plasma.

    Article Title: PIWI proteins contribute to apoptosis during the UPR in human airway epithelial cells
    Article Snippet: Next generation small RNAs sequencing analyses 16HBE14o- cells were used for the RNA isolation and analyses. .. Small RNA sequencing libraries were prepared using QIAseq miRNA library kit (Qiagen) following the manufacturer’s instructions and followed by sequencing on an Illumina NextSeq instrument.

    Article Title: HNRNPA2/B1 is upregulated in endocrine-resistant LCC9 breast cancer cells and alters the miRNA transcriptome when overexpressed in MCF-7 cells
    Article Snippet: For miRNA-seq miRNA was isolated from six separate, biological replicate experiments for each sample group (Control, HNRNPA2/B1 48 h, HNRNPA2/B172 h) using the miRNeasy mini kit from Qiagen (Hilden, Germany) following the manufacturer’s directions. .. Libraries were prepared using QIAseq miRNA Library Kit (Qiagen). cDNA samples were barcoded with QIAseq miRNA NGS ILM IP primers.

    Article Title: Transforming Growth Factor-β1 Selectively Recruits microRNAs to the RNA-Induced Silencing Complex and Degrades CFTR mRNA under Permissive Conditions in Human Bronchial Epithelial Cells
    Article Snippet: .. Cells were treated with TGF-β1 or vehicle for 24 h, total RNA was isolated and used with QIAseqTM miRNA Library Kit (Qiagen), and analyzed on the Illumina platform. .. The miRNA sequencing data were analyzed using the GeneGlobe Data Analysis bioinformatics pipeline from Qiagen.

    RNA Extraction:

    Article Title: A comparison of RNA extraction and sequencing protocols for detection of small RNAs in plasma
    Article Snippet: QIAseq miRNA Library Kit (QIAGEN) claims to employ optimised reaction chemistry to reduce bias, minimise adapter dimer formation and contaminating non-miRNAs, facilitating low inputs of RNA. .. RNA extraction methods have been reported to affect the profile of miRNAs detected [ , , , ].

    Purification:

    Article Title: Inheritance of a Phenotypically Neutral Epimutation Evokes Gene Silencing in Later Generations
    Article Snippet: Total RNA from exponentially growing cultures was extracted with the MasterPure Yeast RNA Purification Kit (Epicenter). .. Small RNA libraries were prepared with the QIAseq miRNA Library Kit (QIAGEN) according to manufacturer’s instructions and sequenced with an Illumina HiSeq2500.

    Article Title: Systematic Analysis of Transcriptomic Profile of the Effects of Low Dose Atropine Treatment on Scleral Fibroblasts using Next-Generation Sequencing and Bioinformatics
    Article Snippet: Purified RNA was quantified at an optical density of 260nm with a ND-1000 spectrophotometer (Nanodrop Technologies, Wilmington, DE, USA). .. Samples were prepared with the QIAseq miRNA Library Kit (QIAGEN) following the instruction manual.

    Polymerase Chain Reaction:

    Article Title: A comparison of RNA extraction and sequencing protocols for detection of small RNAs in plasma
    Article Snippet: QIAseq miRNA Library Kit (QIAGEN) claims to employ optimised reaction chemistry to reduce bias, minimise adapter dimer formation and contaminating non-miRNAs, facilitating low inputs of RNA. .. QIAseq is the only kit to incorporate unique molecular indices (UMIs) into each cDNA to enable correction for PCR bias.

    Article Title: Evaluation of methodologies for microRNA biomarker detection by next generation sequencing
    Article Snippet: As such, certain adapter-miRNA pairs or sequence compositions may be favoured over others during ligation and PCR amplification, and thereby result in over- or underrepresentation of these miRNAs in the sequencing library [ , ]. .. In this study, we have benchmarked four commercial kits intended for Illumina sequencing: Nextflex Small RNA-Seq Kit v3, Bioo Scientific (BSC); SMARTer smRNA-Seq Kit, Clontech/Takara (CLT); NEBNext Small RNA Library Prep Set, New England Biolabs (NEB) and QIAseq miRNA Library Kit, Qiagen (QIA).

    Software:

    Article Title: PIWI proteins contribute to apoptosis during the UPR in human airway epithelial cells
    Article Snippet: Small RNA sequencing libraries were prepared using QIAseq miRNA library kit (Qiagen) following the manufacturer’s instructions and followed by sequencing on an Illumina NextSeq instrument. .. Using Qiagen’s Gene Globe Software, sequencing reads were aligned to the human reference genome assembly (hg19) followed by transcript assembly and estimation of the relative abundances.

    Article Title: Cigarette Smoke Condensate Exposure Changes RNA Content of Extracellular Vesicles Released from Small Airway Epithelial Cells
    Article Snippet: Small RNA libraries were made using the QIAseq® miRNA Library Kit (QIAGEN) following the manufacturer’s protocol. .. The miRDeep2 software package, version 2.0.0.8, was used to trim adapter sequences from the reads and quantify miRNA read counts using the miRBase database, release 22. piRNAs were counted by mapping the trimmed reads to piRNA sequences downloaded from the DASHR database [ ] using Bowtie version 1.2.2 with parameters -v2 -l18 -a -M10 -best -strata.

    Article Title: Systematic Analysis of Transcriptomic Profile of the Effects of Low Dose Atropine Treatment on Scleral Fibroblasts using Next-Generation Sequencing and Bioinformatics
    Article Snippet: Samples were prepared with the QIAseq miRNA Library Kit (QIAGEN) following the instruction manual. .. Sequencing data was processed by Illumina software.

    Functional Assay:

    Article Title: Immunophenotyping and transcriptional profiling of in vitro cultured human adipose tissue derived stem cells
    Article Snippet: Differentially expressed genes were grouped in functional pathways using Ingenuity Pathway Analysis (IPA Spring Release 2017, Redwood City, USA) on gene level using RefSeq annotation. .. 2 combination (Supplementary Table ). miRNA-seq was performed for the same set of five biological replicate experiments using QIAseq miRNA Library Kit (Qiagen, Hilden, Germany) following the manufacturer protocol, starting with 500 ng of input RNA for each sample.

    Selection:

    Article Title: Evaluation of methodologies for microRNA biomarker detection by next generation sequencing
    Article Snippet: In order to generate small RNA sequencing (sRNA-seq) libraries, adapters are ligated to both ends of the miRNA, followed by reverse transcription, template amplification by PCR and size selection of small RNA species. .. In this study, we have benchmarked four commercial kits intended for Illumina sequencing: Nextflex Small RNA-Seq Kit v3, Bioo Scientific (BSC); SMARTer smRNA-Seq Kit, Clontech/Takara (CLT); NEBNext Small RNA Library Prep Set, New England Biolabs (NEB) and QIAseq miRNA Library Kit, Qiagen (QIA).

    Next-Generation Sequencing:

    Article Title: Cigarette Smoke Condensate Exposure Changes RNA Content of Extracellular Vesicles Released from Small Airway Epithelial Cells
    Article Snippet: Paragraph title: 2.5. Extraction of EVs RNA and Next Generation Sequencing (NGS) ... Small RNA libraries were made using the QIAseq® miRNA Library Kit (QIAGEN) following the manufacturer’s protocol.

    Article Title: HNRNPA2/B1 is upregulated in endocrine-resistant LCC9 breast cancer cells and alters the miRNA transcriptome when overexpressed in MCF-7 cells
    Article Snippet: .. Libraries were prepared using QIAseq miRNA Library Kit (Qiagen). cDNA samples were barcoded with QIAseq miRNA NGS ILM IP primers. .. Adaptor dimers were removed from amplified libraries using QIAseq miRNA NGS beads.

    Article Title: Systematic Analysis of Transcriptomic Profile of the Effects of Low Dose Atropine Treatment on Scleral Fibroblasts using Next-Generation Sequencing and Bioinformatics
    Article Snippet: Paragraph title: Next-Generation Sequencing (NGS) for miRNA and mRNA Expression Profiling ... Samples were prepared with the QIAseq miRNA Library Kit (QIAGEN) following the instruction manual.

    Spectrophotometry:

    Article Title: Systematic Analysis of Transcriptomic Profile of the Effects of Low Dose Atropine Treatment on Scleral Fibroblasts using Next-Generation Sequencing and Bioinformatics
    Article Snippet: Purified RNA was quantified at an optical density of 260nm with a ND-1000 spectrophotometer (Nanodrop Technologies, Wilmington, DE, USA). .. Samples were prepared with the QIAseq miRNA Library Kit (QIAGEN) following the instruction manual.

    Concentration Assay:

    Article Title: A comparison of RNA extraction and sequencing protocols for detection of small RNAs in plasma
    Article Snippet: Library preparation and sequencing Libraries were prepared from 5 μl of miRNeasy RNA using NEXTflex® Small RNA Sequencing Kit v3 for Illumina® Platforms (Bioo Scientific) and QIAseq miRNA Library Kit (QIAGEN) and from 2 μl miRNeasy RNA using CleanTag™ Small RNA Library Prep Kit (TriLink), following each of the manufacturers’ instructions. .. Quality and concentration of libraries were determined by Fragment Analyzer (Advanced Analytical).

    Variant Assay:

    Article Title: Transforming Growth Factor-β1 Selectively Recruits microRNAs to the RNA-Induced Silencing Complex and Degrades CFTR mRNA under Permissive Conditions in Human Bronchial Epithelial Cells
    Article Snippet: Cells were treated with TGF-β1 or vehicle for 24 h, total RNA was isolated and used with QIAseqTM miRNA Library Kit (Qiagen), and analyzed on the Illumina platform. .. The F508del variant significantly affected the TGF-β1-induced changes in the miRNA landscape ( and A,B).

    Similar Products

  • Logo
  • About
  • News
  • Press Release
  • Team
  • Advisors
  • Partners
  • Contact
  • Bioz Stars
  • Bioz vStars
  • 99
    Qiagen qiaseq mirna library kit
    Overview of the small RNA sequencing workflow, compared methodologies for library preparation and computational analysis pipeline. (a) Schematic illustration of small RNA sequencing (sRNA-seq) library preparation. With exception of the SMARTer smRNA-Seq kit, all kits employed a ligation-based approach to attach 3′ and 5′ adapter to the <t>miRNA.</t> In the <t>QIAseq</t> protocol, a unique barcode is attached at the RT stage (orange dotted line), so-called unique molecular indices (UMI). Illumina adapter (purple and blue) and sequencing index (light purple) for multiplexing are added during the PCR amplification. Several steps of the protocol may introduce bias to the sequencing libraries as indicated by the yellow warning triangles. (b) Table summary of the key features of the four assessed sRNA-seq kits. (c) Small RNA sequencing data analysis pipeline. In the case of QIAseq, UMIs were trimmed alongside the adapters to allow side-by-side comparison by a single computational pipeline. Abbreviations: Nextflex Small RNA-Seq Kit v3 (Nextflex), NEBNext Small RNA Library Prep Set (NEBNext) and QIAseq miRNA Library Kit (QIAseq).
    Qiaseq Mirna Library Kit, supplied by Qiagen, used in various techniques. Bioz Stars score: 99/100, based on 2 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/qiaseq mirna library kit/product/Qiagen
    Average 99 stars, based on 2 article reviews
    Price from $9.99 to $1999.99
    qiaseq mirna library kit - by Bioz Stars, 2020-04
    99/100 stars
      Buy from Supplier

    Image Search Results


    Overview of the small RNA sequencing workflow, compared methodologies for library preparation and computational analysis pipeline. (a) Schematic illustration of small RNA sequencing (sRNA-seq) library preparation. With exception of the SMARTer smRNA-Seq kit, all kits employed a ligation-based approach to attach 3′ and 5′ adapter to the miRNA. In the QIAseq protocol, a unique barcode is attached at the RT stage (orange dotted line), so-called unique molecular indices (UMI). Illumina adapter (purple and blue) and sequencing index (light purple) for multiplexing are added during the PCR amplification. Several steps of the protocol may introduce bias to the sequencing libraries as indicated by the yellow warning triangles. (b) Table summary of the key features of the four assessed sRNA-seq kits. (c) Small RNA sequencing data analysis pipeline. In the case of QIAseq, UMIs were trimmed alongside the adapters to allow side-by-side comparison by a single computational pipeline. Abbreviations: Nextflex Small RNA-Seq Kit v3 (Nextflex), NEBNext Small RNA Library Prep Set (NEBNext) and QIAseq miRNA Library Kit (QIAseq).

    Journal: RNA Biology

    Article Title: Evaluation of methodologies for microRNA biomarker detection by next generation sequencing

    doi: 10.1080/15476286.2018.1514236

    Figure Lengend Snippet: Overview of the small RNA sequencing workflow, compared methodologies for library preparation and computational analysis pipeline. (a) Schematic illustration of small RNA sequencing (sRNA-seq) library preparation. With exception of the SMARTer smRNA-Seq kit, all kits employed a ligation-based approach to attach 3′ and 5′ adapter to the miRNA. In the QIAseq protocol, a unique barcode is attached at the RT stage (orange dotted line), so-called unique molecular indices (UMI). Illumina adapter (purple and blue) and sequencing index (light purple) for multiplexing are added during the PCR amplification. Several steps of the protocol may introduce bias to the sequencing libraries as indicated by the yellow warning triangles. (b) Table summary of the key features of the four assessed sRNA-seq kits. (c) Small RNA sequencing data analysis pipeline. In the case of QIAseq, UMIs were trimmed alongside the adapters to allow side-by-side comparison by a single computational pipeline. Abbreviations: Nextflex Small RNA-Seq Kit v3 (Nextflex), NEBNext Small RNA Library Prep Set (NEBNext) and QIAseq miRNA Library Kit (QIAseq).

    Article Snippet: In this study, we have benchmarked four commercial kits intended for Illumina sequencing: Nextflex Small RNA-Seq Kit v3, Bioo Scientific (BSC); SMARTer smRNA-Seq Kit, Clontech/Takara (CLT); NEBNext Small RNA Library Prep Set, New England Biolabs (NEB) and QIAseq miRNA Library Kit, Qiagen (QIA).

    Techniques: RNA Sequencing Assay, Ligation, Sequencing, Multiplexing, Polymerase Chain Reaction, Amplification, Introduce

    miRNA detection and bias. Percentages of Miltenyi Biotec miRXplore miRNA detected above 5 CPM in MUR ( A ) and in MUR-D ( B ) are shown. Percentages and amplitude of Miltenyi Biotec miRXplore miRNA detected that deviated from the median are shown in MUR ( C ) or MUR-D ( D ). The darkest shade is within 2-fold of the median; the medium shade is 2–10-fold either up or down vs. the expected value; the lightest shade is > 10× either increased or decreased. Percentages of reads increased > 10× from median in MUR ( E ) or MUR-D ( F ). CLO-S and C, Takara Bio (Clontech) SMARTer smRNA-Seq Kit; DIA and D, Diagenode CATS Small RNA-Seq Kit; ILMN and I, Illumina TruSeq Small RNA Library Prep Kit; LEX and L, Lexogen Small RNA-Seq Library Prep Kit; Nano, NanoString nCounter miRNA Expression Assay; NEB and N, New England Biolabs NEBNext Small RNA Library Prep Set; PEB and P, PerkinElmer NextFlex Small RNA-Seq Kit v.3; QIA and Q, Qiagen QIAseq miRNA Library Kit; SOM and S, Somagenics RealSeq-AC miRNA Library Kit; TRI and T, Trilink CleanTag Small RNA Library Prep Kit.

    Journal: Journal of Biomolecular Techniques : JBT

    Article Title: Multisite Evaluation of Next-Generation Methods for Small RNA Quantification

    doi: 10.7171/jbt.20-3102-001

    Figure Lengend Snippet: miRNA detection and bias. Percentages of Miltenyi Biotec miRXplore miRNA detected above 5 CPM in MUR ( A ) and in MUR-D ( B ) are shown. Percentages and amplitude of Miltenyi Biotec miRXplore miRNA detected that deviated from the median are shown in MUR ( C ) or MUR-D ( D ). The darkest shade is within 2-fold of the median; the medium shade is 2–10-fold either up or down vs. the expected value; the lightest shade is > 10× either increased or decreased. Percentages of reads increased > 10× from median in MUR ( E ) or MUR-D ( F ). CLO-S and C, Takara Bio (Clontech) SMARTer smRNA-Seq Kit; DIA and D, Diagenode CATS Small RNA-Seq Kit; ILMN and I, Illumina TruSeq Small RNA Library Prep Kit; LEX and L, Lexogen Small RNA-Seq Library Prep Kit; Nano, NanoString nCounter miRNA Expression Assay; NEB and N, New England Biolabs NEBNext Small RNA Library Prep Set; PEB and P, PerkinElmer NextFlex Small RNA-Seq Kit v.3; QIA and Q, Qiagen QIAseq miRNA Library Kit; SOM and S, Somagenics RealSeq-AC miRNA Library Kit; TRI and T, Trilink CleanTag Small RNA Library Prep Kit.

    Article Snippet: Most of the kits tested, including Illumina TruSeq Small RNA Library Prep Kit, Lexogen Small RNA-Seq Library Prep Kit, New England Biolabs NEBNext Small RNA Library Prep Set, PerkinElmer (formerly Bioo Scientific) NextFlex Small RNA-Seq Kit v.3, Qiagen QIAseq miRNA Library Kit, and Trilink CleanTag Small RNA Library Prep Kit all use variants of this methodology.

    Techniques: RNA Sequencing Assay, Expressing

    Study design and workflow metrics. A ) Schematic of study design is shown. MUR, MUR-D, and HBR were processed using 9 different smRNA profiling methods at 4 sites each. The general methodologies included sequential ligation (Illumina, TriLink, Qiagen, NEB, PerkinElmer, Lexogen), template switching (Takara, Diagenode), circularization (Somagenics), and NanoString probe-based hybridization. B ) Total start-to-finish preparation time for each kit as reported by sites. C ) Mean “ease of use” reported by each site (scale: 1 = uncomfortable, 5 = comfortable). D ) Library preparation success rates. Light color blocks are successfully produced libraries. Dark colors are failed libraries. CLO and CLO-S, Takara Bio (Clontech) SMARTer smRNA-Seq Kit; DIA, Diagenode CATS Small RNA-Seq Kit; ILL and ILMN, Illumina TruSeq Small RNA Library Prep Kit; LEX, Lexogen Small RNA-Seq Library Prep Kit; NANO, NanoString nCounter miRNA Expression Assay; NEB, New England Biolabs NEBNext Small RNA Library Prep Set; PEB, PerkinElmer NextFlex Small RNA-Seq Kit v.3; QIA, Qiagen QIAseq miRNA Library Kit; SOM, Somagenics RealSeq-AC miRNA Library Kit; TRI, Trilink CleanTag Small RNA Library Prep Kit.

    Journal: Journal of Biomolecular Techniques : JBT

    Article Title: Multisite Evaluation of Next-Generation Methods for Small RNA Quantification

    doi: 10.7171/jbt.20-3102-001

    Figure Lengend Snippet: Study design and workflow metrics. A ) Schematic of study design is shown. MUR, MUR-D, and HBR were processed using 9 different smRNA profiling methods at 4 sites each. The general methodologies included sequential ligation (Illumina, TriLink, Qiagen, NEB, PerkinElmer, Lexogen), template switching (Takara, Diagenode), circularization (Somagenics), and NanoString probe-based hybridization. B ) Total start-to-finish preparation time for each kit as reported by sites. C ) Mean “ease of use” reported by each site (scale: 1 = uncomfortable, 5 = comfortable). D ) Library preparation success rates. Light color blocks are successfully produced libraries. Dark colors are failed libraries. CLO and CLO-S, Takara Bio (Clontech) SMARTer smRNA-Seq Kit; DIA, Diagenode CATS Small RNA-Seq Kit; ILL and ILMN, Illumina TruSeq Small RNA Library Prep Kit; LEX, Lexogen Small RNA-Seq Library Prep Kit; NANO, NanoString nCounter miRNA Expression Assay; NEB, New England Biolabs NEBNext Small RNA Library Prep Set; PEB, PerkinElmer NextFlex Small RNA-Seq Kit v.3; QIA, Qiagen QIAseq miRNA Library Kit; SOM, Somagenics RealSeq-AC miRNA Library Kit; TRI, Trilink CleanTag Small RNA Library Prep Kit.

    Article Snippet: Most of the kits tested, including Illumina TruSeq Small RNA Library Prep Kit, Lexogen Small RNA-Seq Library Prep Kit, New England Biolabs NEBNext Small RNA Library Prep Set, PerkinElmer (formerly Bioo Scientific) NextFlex Small RNA-Seq Kit v.3, Qiagen QIAseq miRNA Library Kit, and Trilink CleanTag Small RNA Library Prep Kit all use variants of this methodology.

    Techniques: Ligation, Hybridization, Produced, RNA Sequencing Assay, Expressing

    Relative expression of miRNAs. A ) Correlation scatter plots of miRNAs detected in MUR and MUR-D for the QIA method, with miRNAs scored in log2 mapped reads per million. B ) Correlation scatter plot of miRNAs detected in MUR-D using LEX vs. ILL kits, with miRNAs scored in log2 mapped reads per million. C ) Unsupervised hierarchical clustering heatmap of log2 transformed CPM across all methods. C (prep kit), Takara Bio (Clontech) SMARTer smRNA-Seq Kit; C (prep type), circularization; D, Diagenode CATS Small RNA-Seq Kit; ILL and I, Illumina TruSeq Small RNA Library Prep Kit; L (prep type), sequential ligation; LEX and L (prep kit), Lexogen Small RNA-Seq Library Prep Kit; N, New England Biolabs NEBNext Small RNA Library Prep Set; Nano, NanoString nCounter miRNA Expression Assay; NO, No size selection; P, PerkinElmer NextFlex Small RNA-Seq Kit v.3; QIA and Q, Qiagen QIAseq miRNA Library Kit; S, Somagenics RealSeq-AC miRNA Library Kit; SAGE, pippin prep; SPRI, solid phase reversible immobilization; T (prep kit), Trilink CleanTag Small Library Prep Kit; T (prep type), template switching.

    Journal: Journal of Biomolecular Techniques : JBT

    Article Title: Multisite Evaluation of Next-Generation Methods for Small RNA Quantification

    doi: 10.7171/jbt.20-3102-001

    Figure Lengend Snippet: Relative expression of miRNAs. A ) Correlation scatter plots of miRNAs detected in MUR and MUR-D for the QIA method, with miRNAs scored in log2 mapped reads per million. B ) Correlation scatter plot of miRNAs detected in MUR-D using LEX vs. ILL kits, with miRNAs scored in log2 mapped reads per million. C ) Unsupervised hierarchical clustering heatmap of log2 transformed CPM across all methods. C (prep kit), Takara Bio (Clontech) SMARTer smRNA-Seq Kit; C (prep type), circularization; D, Diagenode CATS Small RNA-Seq Kit; ILL and I, Illumina TruSeq Small RNA Library Prep Kit; L (prep type), sequential ligation; LEX and L (prep kit), Lexogen Small RNA-Seq Library Prep Kit; N, New England Biolabs NEBNext Small RNA Library Prep Set; Nano, NanoString nCounter miRNA Expression Assay; NO, No size selection; P, PerkinElmer NextFlex Small RNA-Seq Kit v.3; QIA and Q, Qiagen QIAseq miRNA Library Kit; S, Somagenics RealSeq-AC miRNA Library Kit; SAGE, pippin prep; SPRI, solid phase reversible immobilization; T (prep kit), Trilink CleanTag Small Library Prep Kit; T (prep type), template switching.

    Article Snippet: Most of the kits tested, including Illumina TruSeq Small RNA Library Prep Kit, Lexogen Small RNA-Seq Library Prep Kit, New England Biolabs NEBNext Small RNA Library Prep Set, PerkinElmer (formerly Bioo Scientific) NextFlex Small RNA-Seq Kit v.3, Qiagen QIAseq miRNA Library Kit, and Trilink CleanTag Small RNA Library Prep Kit all use variants of this methodology.

    Techniques: Expressing, Transformation Assay, RNA Sequencing Assay, Ligation, Selection