qiaseq mirna library kit  (Qiagen)

 
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    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
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    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 59 article reviews
    Price from $9.99 to $1999.99
    qiaseq mirna library kit - by Bioz Stars, 2020-09
    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 "Multicenter Evaluation of Independent High-Throughput and RT-qPCR Technologies for the Development of Analytical Workflows for Circulating miRNA Analysis"

    Article Title: Multicenter Evaluation of Independent High-Throughput and RT-qPCR Technologies for the Development of Analytical Workflows for Circulating miRNA Analysis

    Journal: Cancers

    doi: 10.3390/cancers12051166

    QIAseq reveals higher read counts in healthy individuals and NSCLC patients compared to hybridization platforms. Box plot analysis showing comparison of miRNA counts between QIAseq, Toray 3D and nCounter in cfmiRNA and EVmiRNA fractions. The horizontal line in each box represents the median; the whiskers indicate the range; statistical analysis was performed using one-way ANOVA where; ** p
    Figure Legend Snippet: QIAseq reveals higher read counts in healthy individuals and NSCLC patients compared to hybridization platforms. Box plot analysis showing comparison of miRNA counts between QIAseq, Toray 3D and nCounter in cfmiRNA and EVmiRNA fractions. The horizontal line in each box represents the median; the whiskers indicate the range; statistical analysis was performed using one-way ANOVA where; ** p

    Techniques Used: Hybridization

    3) Product Images from "Single-cell lineage analysis reveals genetic and epigenetic interplay in glioblastoma drug resistance"

    Article Title: Single-cell lineage analysis reveals genetic and epigenetic interplay in glioblastoma drug resistance

    Journal: Genome Biology

    doi: 10.1186/s13059-020-02085-1

    Single-cell analyses identify chromosomal amplifications in “jackpot” drug-resistant lineages. a Plot depicts barcode distributions in scRNA-seq data for 1268 individual cells from Experiments #1 and #2 at day 28. Blue circles indicate the number of barcodes (left axis) that were detected in the indicated number of cells ( x -axis). The “jackpot” lineage identified by gDNA analysis of Experiment #2 (e86var) was detected in the largest number of cells ( n = 30). The red line indicates the cumulative fraction of cells (right axis) for which a lineage barcode was detected. b t-SNE plot displays single cells (points) clustered based on their transcriptomes and colored by experiment. c t-SNE plot as in panel b with cells colored by their expression score for cell cycle signature genes. d t-SNE plot as in panel b with cells that correspond to the jackpot lineage e86vac (red) or other lineages (orange) indicated. Gray points indicate cells for which lineage could not be determined. e Barplot depicts fraction of cells positive for the cell cycle signature ( y -axis). Data are shown for cells assigned to the jackpot e86vac or other lineages. f Rank-ordered plot shows chromosomal bands that harbor genes that are higher expressed in the e86vac lineage relative to all others. Chromosome 13 bands are highlighted in red and the three most significant bands are labeled
    Figure Legend Snippet: Single-cell analyses identify chromosomal amplifications in “jackpot” drug-resistant lineages. a Plot depicts barcode distributions in scRNA-seq data for 1268 individual cells from Experiments #1 and #2 at day 28. Blue circles indicate the number of barcodes (left axis) that were detected in the indicated number of cells ( x -axis). The “jackpot” lineage identified by gDNA analysis of Experiment #2 (e86var) was detected in the largest number of cells ( n = 30). The red line indicates the cumulative fraction of cells (right axis) for which a lineage barcode was detected. b t-SNE plot displays single cells (points) clustered based on their transcriptomes and colored by experiment. c t-SNE plot as in panel b with cells colored by their expression score for cell cycle signature genes. d t-SNE plot as in panel b with cells that correspond to the jackpot lineage e86vac (red) or other lineages (orange) indicated. Gray points indicate cells for which lineage could not be determined. e Barplot depicts fraction of cells positive for the cell cycle signature ( y -axis). Data are shown for cells assigned to the jackpot e86vac or other lineages. f Rank-ordered plot shows chromosomal bands that harbor genes that are higher expressed in the e86vac lineage relative to all others. Chromosome 13 bands are highlighted in red and the three most significant bands are labeled

    Techniques Used: Expressing, Labeling

    4) Product Images from "STAT1-induced upregulation of lncRNA KTN1-AS1 predicts poor prognosis and facilitates non-small cell lung cancer progression via miR-23b/DEPDC1 axis"

    Article Title: STAT1-induced upregulation of lncRNA KTN1-AS1 predicts poor prognosis and facilitates non-small cell lung cancer progression via miR-23b/DEPDC1 axis

    Journal: Aging (Albany NY)

    doi: 10.18632/aging.103191

    miR-23b was directly targeted by KTN1-AS1. ( A ) The subcellular localization of KTN1-AS1 was predicted by lncATLAS and lncLocator. ( B ) Subcellular fractionation assays. ( C ) The ceRNA network of KTN1-AS1 was analyzed by lnCAR. ( D ) starBase program analyzed the expressing correlation between KTN1-AS1 and miRNAs. ( E ) qPCR analysis detected the expression of miR-23b and miR-23c. ( F ) The intersection of the results from miRDB, TargetScan, starBase and miRWalk prediction. The commonly predicting genes were also used fo GO and KEGG analysis. ( G ) The predicting binding site between KTN1-AS1 and miR-23b. (H) qPCR assessed the miR-23b levels in 127 NSCLC tissues. ( I ) Relative luciferase activity detection. ( J ) RNA-pull down. ( K , L ) qPCR analysis detected the levels of KTN1-AS1 and miR-23b, respectively. * P
    Figure Legend Snippet: miR-23b was directly targeted by KTN1-AS1. ( A ) The subcellular localization of KTN1-AS1 was predicted by lncATLAS and lncLocator. ( B ) Subcellular fractionation assays. ( C ) The ceRNA network of KTN1-AS1 was analyzed by lnCAR. ( D ) starBase program analyzed the expressing correlation between KTN1-AS1 and miRNAs. ( E ) qPCR analysis detected the expression of miR-23b and miR-23c. ( F ) The intersection of the results from miRDB, TargetScan, starBase and miRWalk prediction. The commonly predicting genes were also used fo GO and KEGG analysis. ( G ) The predicting binding site between KTN1-AS1 and miR-23b. (H) qPCR assessed the miR-23b levels in 127 NSCLC tissues. ( I ) Relative luciferase activity detection. ( J ) RNA-pull down. ( K , L ) qPCR analysis detected the levels of KTN1-AS1 and miR-23b, respectively. * P

    Techniques Used: Fractionation, Expressing, Real-time Polymerase Chain Reaction, Binding Assay, Luciferase, Activity Assay

    5) Product Images from "Multicenter Evaluation of Independent High-Throughput and RT-qPCR Technologies for the Development of Analytical Workflows for Circulating miRNA Analysis"

    Article Title: Multicenter Evaluation of Independent High-Throughput and RT-qPCR Technologies for the Development of Analytical Workflows for Circulating miRNA Analysis

    Journal: Cancers

    doi: 10.3390/cancers12051166

    QIAseq reveals higher read counts in healthy individuals and NSCLC patients compared to hybridization platforms. Box plot analysis showing comparison of miRNA counts between QIAseq, Toray 3D and nCounter in cfmiRNA and EVmiRNA fractions. The horizontal line in each box represents the median; the whiskers indicate the range; statistical analysis was performed using one-way ANOVA where; ** p
    Figure Legend Snippet: QIAseq reveals higher read counts in healthy individuals and NSCLC patients compared to hybridization platforms. Box plot analysis showing comparison of miRNA counts between QIAseq, Toray 3D and nCounter in cfmiRNA and EVmiRNA fractions. The horizontal line in each box represents the median; the whiskers indicate the range; statistical analysis was performed using one-way ANOVA where; ** p

    Techniques Used: Hybridization

    6) Product Images from "microRNA Expression Profile in the Vitreous of Proliferative Diabetic Retinopathy Patients and Differences from Patients Treated with Anti-VEGF Therapy"

    Article Title: microRNA Expression Profile in the Vitreous of Proliferative Diabetic Retinopathy Patients and Differences from Patients Treated with Anti-VEGF Therapy

    Journal: Translational Vision Science & Technology

    doi: 10.1167/tvst.9.6.16

    Expression levels of miRNAs in the vitreous with and without anti-VEGF therapy. The expression levels of miRNAs were measured in the vitreous of patients with PDR who had not received anti-VEGF treatment, PDR(–) and in the vitreous of patients who had received anti-VEGF treatment, PDR(+). For hsa-miR-23b-3p, the expression levels are shown as absolute amounts on a log10 scale relative to the PDR(–) group. Box plots indicate median, minimum, and maximum and first and third quartiles. ( A ) The symbol on the x -axis represents one individual without detectable expression. ( B ) For hsa-miR-20a-5p, hsa-miR-142-3p, hsa-miR-185-5p, hsa-miR-326, and hsa-miR-362-5p, the expression levels are shown as the means of absolute amounts with standard deviations as compared with the PDR(–) group on a log10 scale. * P = 0.03.
    Figure Legend Snippet: Expression levels of miRNAs in the vitreous with and without anti-VEGF therapy. The expression levels of miRNAs were measured in the vitreous of patients with PDR who had not received anti-VEGF treatment, PDR(–) and in the vitreous of patients who had received anti-VEGF treatment, PDR(+). For hsa-miR-23b-3p, the expression levels are shown as absolute amounts on a log10 scale relative to the PDR(–) group. Box plots indicate median, minimum, and maximum and first and third quartiles. ( A ) The symbol on the x -axis represents one individual without detectable expression. ( B ) For hsa-miR-20a-5p, hsa-miR-142-3p, hsa-miR-185-5p, hsa-miR-326, and hsa-miR-362-5p, the expression levels are shown as the means of absolute amounts with standard deviations as compared with the PDR(–) group on a log10 scale. * P = 0.03.

    Techniques Used: Expressing

    Expression levels of miRNAs in the vitreous that were significantly different between control and PDR patients. The expression levels of miRNAs in the screening cohort consisted of control and PDR samples (control, n = 10; PDR, n = 10). The expression levels are shown as the means of absolute amounts with standard deviations as compared with controls on a log10 scale. The expression levels of hsa-miR-20a-5p, hsa-miR-23b-3p, hsa-miR-142-3p, hsa-miR-185-5p, hsa-miR-199a-5p, hsa-miR-223-3p, hsa-miR-326, and hsa-miR-362-5p are relative to the control group. The expression levels of hsa-miR-662 were calculated as absolute amounts (2 −Ct × 1E 12 ). * P
    Figure Legend Snippet: Expression levels of miRNAs in the vitreous that were significantly different between control and PDR patients. The expression levels of miRNAs in the screening cohort consisted of control and PDR samples (control, n = 10; PDR, n = 10). The expression levels are shown as the means of absolute amounts with standard deviations as compared with controls on a log10 scale. The expression levels of hsa-miR-20a-5p, hsa-miR-23b-3p, hsa-miR-142-3p, hsa-miR-185-5p, hsa-miR-199a-5p, hsa-miR-223-3p, hsa-miR-326, and hsa-miR-362-5p are relative to the control group. The expression levels of hsa-miR-662 were calculated as absolute amounts (2 −Ct × 1E 12 ). * P

    Techniques Used: Expressing

    Expression levels of miRNAs in the vitreous of the confirmation cohort. The expression levels of miRNAs with a significant difference in the screening cohort were measured in control and PDR samples of a second, larger cohort. The expression levels are shown as absolute amounts on a log10 scale relative to the control group. Box plots indicate median, minimum, and maximum and first and third quartiles. Symbols on the x -axis represent individuals without detectable expression. * P
    Figure Legend Snippet: Expression levels of miRNAs in the vitreous of the confirmation cohort. The expression levels of miRNAs with a significant difference in the screening cohort were measured in control and PDR samples of a second, larger cohort. The expression levels are shown as absolute amounts on a log10 scale relative to the control group. Box plots indicate median, minimum, and maximum and first and third quartiles. Symbols on the x -axis represent individuals without detectable expression. * P

    Techniques Used: Expressing

    7) Product Images from "Multicenter Evaluation of Independent High-Throughput and RT-qPCR Technologies for the Development of Analytical Workflows for Circulating miRNA Analysis"

    Article Title: Multicenter Evaluation of Independent High-Throughput and RT-qPCR Technologies for the Development of Analytical Workflows for Circulating miRNA Analysis

    Journal: Cancers

    doi: 10.3390/cancers12051166

    QIAseq reveals higher read counts in healthy individuals and NSCLC patients compared to hybridization platforms. Box plot analysis showing comparison of miRNA counts between QIAseq, Toray 3D and nCounter in cfmiRNA and EVmiRNA fractions. The horizontal line in each box represents the median; the whiskers indicate the range; statistical analysis was performed using one-way ANOVA where; ** p
    Figure Legend Snippet: QIAseq reveals higher read counts in healthy individuals and NSCLC patients compared to hybridization platforms. Box plot analysis showing comparison of miRNA counts between QIAseq, Toray 3D and nCounter in cfmiRNA and EVmiRNA fractions. The horizontal line in each box represents the median; the whiskers indicate the range; statistical analysis was performed using one-way ANOVA where; ** p

    Techniques Used: Hybridization

    8) Product Images from "Citrus aurantium L. Dry Extracts Ameliorate Adipocyte Differentiation of 3T3-L1 Cells Exposed to TNFα by Down-Regulating miR-155 Expression"

    Article Title: Citrus aurantium L. Dry Extracts Ameliorate Adipocyte Differentiation of 3T3-L1 Cells Exposed to TNFα by Down-Regulating miR-155 Expression

    Journal: Nutrients

    doi: 10.3390/nu12061587

    Effect of CA de on the expression of miR-155 and its target genes, C/Ebpβ and Creb , during the early stage of adipogenesis in 3T3-L1 cells exposed to TNFα. 3T3-L1 pre-adipocytes were cultured for 0.25, 0.5, 1, 2, and 4 h with AS (Ctrl) or AS supplemented with TNFα (1 ng/mL) ± CA de (100 μg/mL). The miRNA and gene expressions were evaluated by quantitative real-time PCR. Time course of miR-155 ( a ), C/Ebpβ ( b ), and Creb ( c ) levels in Ctrl, TNFα-, and TNFα + CA de-treated cells are shown relative to untreated 3T3-L1 cells at time 0. Values are means ± SEM of three independent experiments. Control value at time 0 was set as 1.00. Statistical significances among groups were tested by one-way ANOVA followed by Bonferroni correction post-hoc test (* p
    Figure Legend Snippet: Effect of CA de on the expression of miR-155 and its target genes, C/Ebpβ and Creb , during the early stage of adipogenesis in 3T3-L1 cells exposed to TNFα. 3T3-L1 pre-adipocytes were cultured for 0.25, 0.5, 1, 2, and 4 h with AS (Ctrl) or AS supplemented with TNFα (1 ng/mL) ± CA de (100 μg/mL). The miRNA and gene expressions were evaluated by quantitative real-time PCR. Time course of miR-155 ( a ), C/Ebpβ ( b ), and Creb ( c ) levels in Ctrl, TNFα-, and TNFα + CA de-treated cells are shown relative to untreated 3T3-L1 cells at time 0. Values are means ± SEM of three independent experiments. Control value at time 0 was set as 1.00. Statistical significances among groups were tested by one-way ANOVA followed by Bonferroni correction post-hoc test (* p

    Techniques Used: Expressing, Cell Culture, Real-time Polymerase Chain Reaction

    9) 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

    Sequencing:

    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: 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.

    other:

    Article Title: Multicenter Evaluation of Independent High-Throughput and RT-qPCR Technologies for the Development of Analytical Workflows for Circulating miRNA Analysis
    Article Snippet: The following are available online at https://www.mdpi.com/2072-6694/12/5/1166/s1 , Figure S1: Mapping distribution of different small RNAs measured with the QIAseq miRNA library kit.

    RNA Sequencing Assay:

    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: 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: 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.

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    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 26 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/qiaseq mirna library kit/product/Qiagen
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    Qiagen library barcodes
    Single-cell analyses identify chromosomal amplifications in “jackpot” drug-resistant lineages. a Plot depicts barcode distributions in scRNA-seq data for 1268 individual cells from Experiments #1 and #2 at day 28. Blue circles indicate the number of <t>barcodes</t> (left axis) that were detected in the indicated number of cells ( x -axis). The “jackpot” lineage identified by gDNA analysis of Experiment #2 (e86var) was detected in the largest number of cells ( n = 30). The red line indicates the cumulative fraction of cells (right axis) for which a lineage barcode was detected. b t-SNE plot displays single cells (points) clustered based on their transcriptomes and colored by experiment. c t-SNE plot as in panel b with cells colored by their expression score for cell cycle signature genes. d t-SNE plot as in panel b with cells that correspond to the jackpot lineage e86vac (red) or other lineages (orange) indicated. Gray points indicate cells for which lineage could not be determined. e Barplot depicts fraction of cells positive for the cell cycle signature ( y -axis). Data are shown for cells assigned to the jackpot e86vac or other lineages. f Rank-ordered plot shows chromosomal bands that harbor genes that are higher expressed in the e86vac lineage relative to all others. Chromosome 13 bands are highlighted in red and the three most significant bands are labeled
    Library Barcodes, supplied by Qiagen, used in various techniques. Bioz Stars score: 80/100, based on 0 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Qiagen mirna expression
    miR-23b was directly targeted by KTN1-AS1. ( A ) The subcellular localization of KTN1-AS1 was predicted by lncATLAS and lncLocator. ( B ) Subcellular fractionation assays. ( C ) The ceRNA network of KTN1-AS1 was analyzed by lnCAR. ( D ) starBase program analyzed the expressing correlation between KTN1-AS1 and <t>miRNAs.</t> ( E ) qPCR analysis detected the expression of miR-23b and miR-23c. ( F ) The intersection of the results from miRDB, TargetScan, starBase and miRWalk prediction. The commonly predicting genes were also used fo GO and KEGG analysis. ( G ) The predicting binding site between KTN1-AS1 and miR-23b. (H) qPCR assessed the miR-23b levels in 127 NSCLC tissues. ( I ) Relative luciferase activity detection. ( J ) <t>RNA-pull</t> down. ( K , L ) qPCR analysis detected the levels of KTN1-AS1 and miR-23b, respectively. * P
    Mirna Expression, supplied by Qiagen, used in various techniques. Bioz Stars score: 93/100, based on 26 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    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

    QIAseq reveals higher read counts in healthy individuals and NSCLC patients compared to hybridization platforms. Box plot analysis showing comparison of miRNA counts between QIAseq, Toray 3D and nCounter in cfmiRNA and EVmiRNA fractions. The horizontal line in each box represents the median; the whiskers indicate the range; statistical analysis was performed using one-way ANOVA where; ** p

    Journal: Cancers

    Article Title: Multicenter Evaluation of Independent High-Throughput and RT-qPCR Technologies for the Development of Analytical Workflows for Circulating miRNA Analysis

    doi: 10.3390/cancers12051166

    Figure Lengend Snippet: QIAseq reveals higher read counts in healthy individuals and NSCLC patients compared to hybridization platforms. Box plot analysis showing comparison of miRNA counts between QIAseq, Toray 3D and nCounter in cfmiRNA and EVmiRNA fractions. The horizontal line in each box represents the median; the whiskers indicate the range; statistical analysis was performed using one-way ANOVA where; ** p

    Article Snippet: QIAseq miRNA Library KitNGS libraries were prepared from 5 µL aliquots using the QIAseq miRNA Library kit (QIAGEN).

    Techniques: Hybridization

    Single-cell analyses identify chromosomal amplifications in “jackpot” drug-resistant lineages. a Plot depicts barcode distributions in scRNA-seq data for 1268 individual cells from Experiments #1 and #2 at day 28. Blue circles indicate the number of barcodes (left axis) that were detected in the indicated number of cells ( x -axis). The “jackpot” lineage identified by gDNA analysis of Experiment #2 (e86var) was detected in the largest number of cells ( n = 30). The red line indicates the cumulative fraction of cells (right axis) for which a lineage barcode was detected. b t-SNE plot displays single cells (points) clustered based on their transcriptomes and colored by experiment. c t-SNE plot as in panel b with cells colored by their expression score for cell cycle signature genes. d t-SNE plot as in panel b with cells that correspond to the jackpot lineage e86vac (red) or other lineages (orange) indicated. Gray points indicate cells for which lineage could not be determined. e Barplot depicts fraction of cells positive for the cell cycle signature ( y -axis). Data are shown for cells assigned to the jackpot e86vac or other lineages. f Rank-ordered plot shows chromosomal bands that harbor genes that are higher expressed in the e86vac lineage relative to all others. Chromosome 13 bands are highlighted in red and the three most significant bands are labeled

    Journal: Genome Biology

    Article Title: Single-cell lineage analysis reveals genetic and epigenetic interplay in glioblastoma drug resistance

    doi: 10.1186/s13059-020-02085-1

    Figure Lengend Snippet: Single-cell analyses identify chromosomal amplifications in “jackpot” drug-resistant lineages. a Plot depicts barcode distributions in scRNA-seq data for 1268 individual cells from Experiments #1 and #2 at day 28. Blue circles indicate the number of barcodes (left axis) that were detected in the indicated number of cells ( x -axis). The “jackpot” lineage identified by gDNA analysis of Experiment #2 (e86var) was detected in the largest number of cells ( n = 30). The red line indicates the cumulative fraction of cells (right axis) for which a lineage barcode was detected. b t-SNE plot displays single cells (points) clustered based on their transcriptomes and colored by experiment. c t-SNE plot as in panel b with cells colored by their expression score for cell cycle signature genes. d t-SNE plot as in panel b with cells that correspond to the jackpot lineage e86vac (red) or other lineages (orange) indicated. Gray points indicate cells for which lineage could not be determined. e Barplot depicts fraction of cells positive for the cell cycle signature ( y -axis). Data are shown for cells assigned to the jackpot e86vac or other lineages. f Rank-ordered plot shows chromosomal bands that harbor genes that are higher expressed in the e86vac lineage relative to all others. Chromosome 13 bands are highlighted in red and the three most significant bands are labeled

    Article Snippet: Fastq files for each library were generated using bcl2fastq allowing for up to one mismatch to expected library barcodes.

    Techniques: Expressing, Labeling

    miR-23b was directly targeted by KTN1-AS1. ( A ) The subcellular localization of KTN1-AS1 was predicted by lncATLAS and lncLocator. ( B ) Subcellular fractionation assays. ( C ) The ceRNA network of KTN1-AS1 was analyzed by lnCAR. ( D ) starBase program analyzed the expressing correlation between KTN1-AS1 and miRNAs. ( E ) qPCR analysis detected the expression of miR-23b and miR-23c. ( F ) The intersection of the results from miRDB, TargetScan, starBase and miRWalk prediction. The commonly predicting genes were also used fo GO and KEGG analysis. ( G ) The predicting binding site between KTN1-AS1 and miR-23b. (H) qPCR assessed the miR-23b levels in 127 NSCLC tissues. ( I ) Relative luciferase activity detection. ( J ) RNA-pull down. ( K , L ) qPCR analysis detected the levels of KTN1-AS1 and miR-23b, respectively. * P

    Journal: Aging (Albany NY)

    Article Title: STAT1-induced upregulation of lncRNA KTN1-AS1 predicts poor prognosis and facilitates non-small cell lung cancer progression via miR-23b/DEPDC1 axis

    doi: 10.18632/aging.103191

    Figure Lengend Snippet: miR-23b was directly targeted by KTN1-AS1. ( A ) The subcellular localization of KTN1-AS1 was predicted by lncATLAS and lncLocator. ( B ) Subcellular fractionation assays. ( C ) The ceRNA network of KTN1-AS1 was analyzed by lnCAR. ( D ) starBase program analyzed the expressing correlation between KTN1-AS1 and miRNAs. ( E ) qPCR analysis detected the expression of miR-23b and miR-23c. ( F ) The intersection of the results from miRDB, TargetScan, starBase and miRWalk prediction. The commonly predicting genes were also used fo GO and KEGG analysis. ( G ) The predicting binding site between KTN1-AS1 and miR-23b. (H) qPCR assessed the miR-23b levels in 127 NSCLC tissues. ( I ) Relative luciferase activity detection. ( J ) RNA-pull down. ( K , L ) qPCR analysis detected the levels of KTN1-AS1 and miR-23b, respectively. * P

    Article Snippet: The miRNA expression was normalized to U6 small nuclear RNA.

    Techniques: Fractionation, Expressing, Real-time Polymerase Chain Reaction, Binding Assay, Luciferase, Activity Assay