truseq small rna library kit  (Illumina Inc)

 
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    Name:
    TruSeq Small RNA Library Prep Kit Set A
    Description:
    TruSeq Small RNA Library Preparation Kits provide reagents to generate small RNA libraries directly from total RNA MicroRNAs miRNAs generated by Dicer processing are efficiently targeted by the included modified adapters These kits enable multiplexed sequencing with the introduction of 48 unique indexes allowing miRNA and small RNA discovery and profiling throughput to match the unparalleled output of Illumina sequencing Indexes are added in a universal amplification reaction greatly reducing ligation bias and ensuring accurate measurement of miRNA expression Workflow improvements enable streamlined sample preparation allowing economical studies covering all small RNA transcripts in any species Compatible applications include finding novel miRNAs characterizing variation such as isomers with single base resolution and analyzing differential expression without prior assumptions TruSeq Small RNA Sample Datasets The Human Brain Reference RNA HBRR and Universal Human Reference RNA UHRR samples were prepared using the TruSeq Small RNA Library Prep Kit These libraries were sequenced on the MiniSeq System using the MiniSeq High Output Reagent Kit at a 1 x 36 bp read length configuration The total yield was 0 91 Gb with 97 of bases at or above Q30 Browse the Data In BaseSpace Sequence Hub View Run primary analysis and metrics View Project secondary analysis with BaseSpace Apps
    Catalog Number:
    rs-200-0012
    Price:
    None
    Category:
    Library Preparation Kits
    Buy from Supplier


    Structured Review

    Illumina Inc truseq small rna library kit
    TruSeq Small RNA Library Prep Kit Set A
    TruSeq Small RNA Library Preparation Kits provide reagents to generate small RNA libraries directly from total RNA MicroRNAs miRNAs generated by Dicer processing are efficiently targeted by the included modified adapters These kits enable multiplexed sequencing with the introduction of 48 unique indexes allowing miRNA and small RNA discovery and profiling throughput to match the unparalleled output of Illumina sequencing Indexes are added in a universal amplification reaction greatly reducing ligation bias and ensuring accurate measurement of miRNA expression Workflow improvements enable streamlined sample preparation allowing economical studies covering all small RNA transcripts in any species Compatible applications include finding novel miRNAs characterizing variation such as isomers with single base resolution and analyzing differential expression without prior assumptions TruSeq Small RNA Sample Datasets The Human Brain Reference RNA HBRR and Universal Human Reference RNA UHRR samples were prepared using the TruSeq Small RNA Library Prep Kit These libraries were sequenced on the MiniSeq System using the MiniSeq High Output Reagent Kit at a 1 x 36 bp read length configuration The total yield was 0 91 Gb with 97 of bases at or above Q30 Browse the Data In BaseSpace Sequence Hub View Run primary analysis and metrics View Project secondary analysis with BaseSpace Apps
    https://www.bioz.com/result/truseq small rna library kit/product/Illumina Inc
    Average 90 stars, based on 2 article reviews
    Price from $9.99 to $1999.99
    truseq small rna library kit - by Bioz Stars, 2020-02
    90/100 stars

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    Related Articles

    Amplification:

    Article Title: Assessment of microRNA differential expression and detection in multiplexed small RNA sequencing data
    Article Snippet: Briefly, 1 µg of total RNA from each sample was used for library preparation with the TruSeq Small RNA Sample Prep Kit (Illumina). .. The cDNA was then PCR amplified using a common primer and a primer containing one of 12 index sequences.

    Article Title: Evaluation of commercially available small RNASeq library preparation kits using low input RNA
    Article Snippet: Illumina TruSeq small RNA library preparation Small RNA libraries were generated using Illumina TruSeq Small RNA Sample kit (RS-200-0048; Illumina). .. During PCR amplification, the Index primer and RNA PCR primer volumes were reduced by 50% and the volume replaced with water.

    Article Title: Assessing the hodgepodge of non-mapped reads in bacterial transcriptomes: real or artifactual RNA chimeras?
    Article Snippet: Samples were further processed using the TruSeq small RNA Sample Prep Kit (ref. RS-200-0012, Illumina) according to the manufacturer’s protocol. .. Briefly, 3′ adapters and subsequently 5′ adapters were ligated to the RNA. cDNA was synthesized using reverse transcriptase (SuperScript II, ref. 18064–014, Invitrogen) and a specific primer (RNA RT Primer) complementary to the 3′ RNA adapter. cDNA was further amplified by PCR using indexed adapters supplied in the kit.

    Article Title: Small RNA Sequencing of Sporadic Amyotrophic Lateral Sclerosis Cerebrospinal Fluid Reveals Differentially Expressed miRNAs Related to Neural and Glial Activity
    Article Snippet: Small RNA-sequencing RNA was prepared for small RNA-sequencing using the Illumina TruSeq Small RNA library preparation kit following a modified protocol as described in Burgos et al. ( ). .. Adapter-ligated RNA was reverse transcribed to generate a cDNA library and amplified following 15 cycles of PCR (denaturation at 98°C for 30 s the products were amplified following 15 cycles at 98°C for 10 s, 60°C for 30 s, 72°C for 15 s and then 72°C for 10 min) incorporating individual barcodes to each sample to enable the pooling and loading of multiple samples onto the Illumina HiScanSQ.

    Synthesized:

    Article Title: Assessing the hodgepodge of non-mapped reads in bacterial transcriptomes: real or artifactual RNA chimeras?
    Article Snippet: Samples were further processed using the TruSeq small RNA Sample Prep Kit (ref. RS-200-0012, Illumina) according to the manufacturer’s protocol. .. Briefly, 3′ adapters and subsequently 5′ adapters were ligated to the RNA. cDNA was synthesized using reverse transcriptase (SuperScript II, ref. 18064–014, Invitrogen) and a specific primer (RNA RT Primer) complementary to the 3′ RNA adapter. cDNA was further amplified by PCR using indexed adapters supplied in the kit.

    Blocking Assay:

    Article Title: Small RNA Library Preparation Method for Next-Generation Sequencing Using Chemical Modifications to Prevent Adapter Dimer Formation
    Article Snippet: The two most common commercially available kits, TruSeq Small RNA Library Preparation Kit (Illumina) and NEBNext Small RNA Library Prep Set (New England Biolabs), recommend 100 ng total RNA input as the lowest sample amount achievable [ ]. .. We have developed a novel small RNA library preparation method which uses chemically modified adapters to prevent adapter dimer formation by blocking ligation of the 5΄ and 3΄ adapters to one another, while allowing for efficient tagging of adapters onto the small RNA library ( ).

    Microarray:

    Article Title: MicroRNA and mRNA Transcriptome Profiling in Primary Human Astrocytes Infected with Borrelia burgdorferi
    Article Snippet: We isolated microRNAs using two methods based on the Qiagen miRNeasy kit ( ); either the microRNA fraction by itself, which enriches the population of microRNAs, or by purifying total RNA and microRNA, which is recommended by several groups for sequencing or microarray purposes. .. Following isolation of microRNA only fractions from untreated (N = 3), Bb treated (N = 3; 24h) and Bb treated (N = 3; 48h) samples, we prepared pooled libraries using the TruSeq small RNA library preparation kit (Illumina) according to the manufacturer’s instructions, and sequenced the libraries on the MiSeq.

    Expressing:

    Article Title: Small RNA Library Preparation Method for Next-Generation Sequencing Using Chemical Modifications to Prevent Adapter Dimer Formation
    Article Snippet: Furthermore, with low product recovery it is possible to lose RNA sequences that have low expression levels, leading to false negative data. .. The two most common commercially available kits, TruSeq Small RNA Library Preparation Kit (Illumina) and NEBNext Small RNA Library Prep Set (New England Biolabs), recommend 100 ng total RNA input as the lowest sample amount achievable [ ].

    Article Title: A Comprehensive Analysis of Replicating Merkel Cell Polyomavirus Genomes Delineates the Viral Transcription Program and Suggests a Role for mcv-miR-M1 in Episomal Persistence
    Article Snippet: Paragraph title: Small RNA-seq demonstrates high-level expression of mcv-miR-M1 by replicating MCPyV episomes and argues against the existence of tumor-specific miRNA moieties ... To formally investigate this possibility, we re-sequenced the same small RNA material using the standard Illumina TruSeq small RNA library preparation kit.

    Article Title: Integrated analysis of mRNA, microRNA and protein in systemic lupus erythematosus-specific induced pluripotent stem cells from urine
    Article Snippet: The libraries of mRNA and miRNA were constructed by using the Illumina TruSeq RNA Sample Prep Kit v2-Set A and TruSeq Small RNA Sample Prep Kit Set A, respectively, sequenced by the Illumina HiSeq™ 2000 System. .. Differential expression of mRNA and miRNA between SLE-iPSCs and Control-iPSCs were calculated by relative expression analysis.

    Modification:

    Article Title: Small RNA Library Preparation Method for Next-Generation Sequencing Using Chemical Modifications to Prevent Adapter Dimer Formation
    Article Snippet: The two most common commercially available kits, TruSeq Small RNA Library Preparation Kit (Illumina) and NEBNext Small RNA Library Prep Set (New England Biolabs), recommend 100 ng total RNA input as the lowest sample amount achievable [ ]. .. We have developed a novel small RNA library preparation method which uses chemically modified adapters to prevent adapter dimer formation by blocking ligation of the 5΄ and 3΄ adapters to one another, while allowing for efficient tagging of adapters onto the small RNA library ( ).

    Article Title: Small RNA Library Preparation Method for Next-Generation Sequencing Using Chemical Modifications to Prevent Adapter Dimer Formation
    Article Snippet: .. Samples prepared with modified adapters were compared to the TruSeq small RNA Library Preparation Kit (Illumina). .. The TruSeq kit recommends a minimum of 1000 ng RNA input in combination with a gel purification step after library preparation; however, we also tested this kit at lower RNA inputs.

    Article Title: Small RNA Sequencing of Sporadic Amyotrophic Lateral Sclerosis Cerebrospinal Fluid Reveals Differentially Expressed miRNAs Related to Neural and Glial Activity
    Article Snippet: .. Small RNA-sequencing RNA was prepared for small RNA-sequencing using the Illumina TruSeq Small RNA library preparation kit following a modified protocol as described in Burgos et al. ( ). ..

    Gel Purification:

    Article Title: Small RNA Library Preparation Method for Next-Generation Sequencing Using Chemical Modifications to Prevent Adapter Dimer Formation
    Article Snippet: Gel purification significantly limits the ability to automate library preparation for sRNA thus limiting high throughput experiments. .. The two most common commercially available kits, TruSeq Small RNA Library Preparation Kit (Illumina) and NEBNext Small RNA Library Prep Set (New England Biolabs), recommend 100 ng total RNA input as the lowest sample amount achievable [ ].

    Article Title: Small RNA Library Preparation Method for Next-Generation Sequencing Using Chemical Modifications to Prevent Adapter Dimer Formation
    Article Snippet: Samples prepared with modified adapters were compared to the TruSeq small RNA Library Preparation Kit (Illumina). .. The TruSeq kit recommends a minimum of 1000 ng RNA input in combination with a gel purification step after library preparation; however, we also tested this kit at lower RNA inputs.

    Flow Cytometry:

    Article Title: Small RNA Library Preparation Method for Next-Generation Sequencing Using Chemical Modifications to Prevent Adapter Dimer Formation
    Article Snippet: Minimal amounts of adapter dimer contamination will be loaded onto the flow cell along with the tagged library and again preferentially amplify to form clusters and take up valuable sequencing reads that could otherwise be occupied by tagged library. .. The two most common commercially available kits, TruSeq Small RNA Library Preparation Kit (Illumina) and NEBNext Small RNA Library Prep Set (New England Biolabs), recommend 100 ng total RNA input as the lowest sample amount achievable [ ].

    Article Title: Differential expression of urinary exosomal micro RNAs in IgA nephropathy, et al. Differential expression of urinary exosomal microRNAs in IgA nephropathy
    Article Snippet: Resulting PCR products, cDNA, were size‐selected with PAGE gel, according to the protocol of the TruSeq® Small RNA Sample Prep Kit (Illumina, San Diego, TX, USA). .. The purified cDNA library was evaluated using the Agilent 2200 TapeStation, and diluted to 10 pmol/L for cluster generation in situ on the HiSeq2500 (Illumina, USA) single‐end flow cell, followed by sequencing (1×50 bp).

    Ligation:

    Article Title: Small RNA Library Preparation Method for Next-Generation Sequencing Using Chemical Modifications to Prevent Adapter Dimer Formation
    Article Snippet: The two most common commercially available kits, TruSeq Small RNA Library Preparation Kit (Illumina) and NEBNext Small RNA Library Prep Set (New England Biolabs), recommend 100 ng total RNA input as the lowest sample amount achievable [ ]. .. We have developed a novel small RNA library preparation method which uses chemically modified adapters to prevent adapter dimer formation by blocking ligation of the 5΄ and 3΄ adapters to one another, while allowing for efficient tagging of adapters onto the small RNA library ( ).

    Article Title: A Comprehensive Analysis of Replicating Merkel Cell Polyomavirus Genomes Delineates the Viral Transcription Program and Suggests a Role for mcv-miR-M1 in Episomal Persistence
    Article Snippet: It is well documented that biases especially during the ligation step can result in a gross underrepresentation of individual miRNA species between different library preparation methods [ – ]. .. To formally investigate this possibility, we re-sequenced the same small RNA material using the standard Illumina TruSeq small RNA library preparation kit.

    Article Title: Assessing the hodgepodge of non-mapped reads in bacterial transcriptomes: real or artifactual RNA chimeras?
    Article Snippet: Treatments with Antarctic phosphatase (ref. M0289S, NEB) and PNK (ref. M0201S, NEB) were performed in order to make the 5′ and 3′ ends of the RNA available for adapter ligation. .. Samples were further processed using the TruSeq small RNA Sample Prep Kit (ref. RS-200-0012, Illumina) according to the manufacturer’s protocol.

    Infection:

    Article Title: MicroRNA and mRNA Transcriptome Profiling in Primary Human Astrocytes Infected with Borrelia burgdorferi
    Article Snippet: Paragraph title: MicroRNA changes in astrocytes following Bb infection ... Following isolation of microRNA only fractions from untreated (N = 3), Bb treated (N = 3; 24h) and Bb treated (N = 3; 48h) samples, we prepared pooled libraries using the TruSeq small RNA library preparation kit (Illumina) according to the manufacturer’s instructions, and sequenced the libraries on the MiSeq.

    Generated:

    Article Title: Evaluation of commercially available small RNASeq library preparation kits using low input RNA
    Article Snippet: .. Illumina TruSeq small RNA library preparation Small RNA libraries were generated using Illumina TruSeq Small RNA Sample kit (RS-200-0048; Illumina). ..

    Sequencing:

    Article Title: Small RNA Library Preparation Method for Next-Generation Sequencing Using Chemical Modifications to Prevent Adapter Dimer Formation
    Article Snippet: Minimal amounts of adapter dimer contamination will be loaded onto the flow cell along with the tagged library and again preferentially amplify to form clusters and take up valuable sequencing reads that could otherwise be occupied by tagged library. .. The two most common commercially available kits, TruSeq Small RNA Library Preparation Kit (Illumina) and NEBNext Small RNA Library Prep Set (New England Biolabs), recommend 100 ng total RNA input as the lowest sample amount achievable [ ].

    Article Title: Small RNA Library Preparation Method for Next-Generation Sequencing Using Chemical Modifications to Prevent Adapter Dimer Formation
    Article Snippet: Lower inputs With strong suppression of adapter dimer using CleanTag modifications in the library preparation workflow, sequencing from much lower RNA inputs is now possible. .. Samples prepared with modified adapters were compared to the TruSeq small RNA Library Preparation Kit (Illumina).

    Article Title: Quantitative Bias in Illumina TruSeq and a Novel Post Amplification Barcoding Strategy for Multiplexed DNA and Small RNA Deep Sequencing
    Article Snippet: .. TruSeq small RNA and DNA barcoding and sequencing For the TruSeq sample preparation, the Illumina TruSeq Small RNA Sample Prep Kit (RS-200–0012) and the Illumina TruSeq DNA Sample Prep Kit (FC-121–1001) were used. .. Yields and quantification of libraries The PALM barcode ligation step produces several DNA products but only the main product, library products with the barcode adapters ligated to both ends, are able to form clusters and generate sequencing data.

    Article Title: Assessment of microRNA differential expression and detection in multiplexed small RNA sequencing data
    Article Snippet: Paragraph title: Sequencing the small RNA of lung tissue samples ... Briefly, 1 µg of total RNA from each sample was used for library preparation with the TruSeq Small RNA Sample Prep Kit (Illumina).

    Article Title: A Comprehensive Analysis of Replicating Merkel Cell Polyomavirus Genomes Delineates the Viral Transcription Program and Suggests a Role for mcv-miR-M1 in Episomal Persistence
    Article Snippet: However, the relative distribution of seed sequences was very similar to that seen in PFSK-1 MCVSyn cells, with the seed sequence observed by Lee being only marginally abundant at 10 to 14% (red and blue bars in the left panel of ). .. To formally investigate this possibility, we re-sequenced the same small RNA material using the standard Illumina TruSeq small RNA library preparation kit.

    Article Title: Methylmercury exposure increases lipocalin related (lpr) and decreases activated in blocked unfolded protein response (abu) genes and specific miRNAs in Caenorhabditis elegans
    Article Snippet: One µg of isolated small RNAs were used to construct a library using the Small RNA library prep set kit for Illumina (New England Biolabs, Ipswich, MA, USA) using the same conditions as reported previously ( ). .. The sizes of the small RNA sequence libraries were 21.9 million reads for the control and 23.3 million reads for the MeHg treated sample.

    Article Title: Differential expression of urinary exosomal micro RNAs in IgA nephropathy, et al. Differential expression of urinary exosomal microRNAs in IgA nephropathy
    Article Snippet: Paragraph title: 2.8. cDNA library construction and high‐throughput sequencing ... Resulting PCR products, cDNA, were size‐selected with PAGE gel, according to the protocol of the TruSeq® Small RNA Sample Prep Kit (Illumina, San Diego, TX, USA).

    Article Title: A Comprehensive Analysis of Replicating Merkel Cell Polyomavirus Genomes Delineates the Viral Transcription Program and Suggests a Role for mcv-miR-M1 in Episomal Persistence
    Article Snippet: .. Small RNA sequencing For sequencing of small RNA moieties, RNA from MCVSyn transfected cells and MCC cell lines was subjected to library preparation using the TruSeq Small RNA Sample Preparation Kit (Illumina) or the NEBNext Small RNA Library Prep Set for Illumina. .. Small RNA libraries were sequenced on the Illumina HiSeq platform.

    Article Title: MicroRNA and mRNA Transcriptome Profiling in Primary Human Astrocytes Infected with Borrelia burgdorferi
    Article Snippet: Therefore, we used the microRNA only fraction to make libraries and perform the microRNA sequencing for the experiments described here. .. Following isolation of microRNA only fractions from untreated (N = 3), Bb treated (N = 3; 24h) and Bb treated (N = 3; 48h) samples, we prepared pooled libraries using the TruSeq small RNA library preparation kit (Illumina) according to the manufacturer’s instructions, and sequenced the libraries on the MiSeq.

    Article Title: Assessing the hodgepodge of non-mapped reads in bacterial transcriptomes: real or artifactual RNA chimeras?
    Article Snippet: Paragraph title: Directional RNA-seq library preparation and sequencing ... Samples were further processed using the TruSeq small RNA Sample Prep Kit (ref. RS-200-0012, Illumina) according to the manufacturer’s protocol.

    Article Title: Integrated analysis of mRNA, microRNA and protein in systemic lupus erythematosus-specific induced pluripotent stem cells from urine
    Article Snippet: Paragraph title: Sequencing of mRNA and miRNA ... The libraries of mRNA and miRNA were constructed by using the Illumina TruSeq RNA Sample Prep Kit v2-Set A and TruSeq Small RNA Sample Prep Kit Set A, respectively, sequenced by the Illumina HiSeq™ 2000 System.

    Nucleic Acid Electrophoresis:

    Article Title: Integrated analysis of mRNA, microRNA and protein in systemic lupus erythematosus-specific induced pluripotent stem cells from urine
    Article Snippet: The concentration and quality of total RNA were measured by the UV absorbance at 260 nm and 280 nm (A260/280) and checked by gel electrophoresis. .. The libraries of mRNA and miRNA were constructed by using the Illumina TruSeq RNA Sample Prep Kit v2-Set A and TruSeq Small RNA Sample Prep Kit Set A, respectively, sequenced by the Illumina HiSeq™ 2000 System.

    RNA Sequencing Assay:

    Article Title: Assessment of microRNA differential expression and detection in multiplexed small RNA sequencing data
    Article Snippet: Multiplexed small RNA sequencing was conducted on the Illumina HiSeq 2000 sequencer according to the manufacturer's protocol. .. Briefly, 1 µg of total RNA from each sample was used for library preparation with the TruSeq Small RNA Sample Prep Kit (Illumina).

    Article Title: A Comprehensive Analysis of Replicating Merkel Cell Polyomavirus Genomes Delineates the Viral Transcription Program and Suggests a Role for mcv-miR-M1 in Episomal Persistence
    Article Snippet: Paragraph title: Small RNA-seq demonstrates high-level expression of mcv-miR-M1 by replicating MCPyV episomes and argues against the existence of tumor-specific miRNA moieties ... To formally investigate this possibility, we re-sequenced the same small RNA material using the standard Illumina TruSeq small RNA library preparation kit.

    Article Title: A Comprehensive Analysis of Replicating Merkel Cell Polyomavirus Genomes Delineates the Viral Transcription Program and Suggests a Role for mcv-miR-M1 in Episomal Persistence
    Article Snippet: .. Small RNA sequencing For sequencing of small RNA moieties, RNA from MCVSyn transfected cells and MCC cell lines was subjected to library preparation using the TruSeq Small RNA Sample Preparation Kit (Illumina) or the NEBNext Small RNA Library Prep Set for Illumina. .. Small RNA libraries were sequenced on the Illumina HiSeq platform.

    Article Title: Assessing the hodgepodge of non-mapped reads in bacterial transcriptomes: real or artifactual RNA chimeras?
    Article Snippet: Paragraph title: Directional RNA-seq library preparation and sequencing ... Samples were further processed using the TruSeq small RNA Sample Prep Kit (ref. RS-200-0012, Illumina) according to the manufacturer’s protocol.

    Article Title: Small RNA Sequencing of Sporadic Amyotrophic Lateral Sclerosis Cerebrospinal Fluid Reveals Differentially Expressed miRNAs Related to Neural and Glial Activity
    Article Snippet: .. Small RNA-sequencing RNA was prepared for small RNA-sequencing using the Illumina TruSeq Small RNA library preparation kit following a modified protocol as described in Burgos et al. ( ). ..

    Isolation:

    Article Title: Methylmercury exposure increases lipocalin related (lpr) and decreases activated in blocked unfolded protein response (abu) genes and specific miRNAs in Caenorhabditis elegans
    Article Snippet: .. One µg of isolated small RNAs were used to construct a library using the Small RNA library prep set kit for Illumina (New England Biolabs, Ipswich, MA, USA) using the same conditions as reported previously ( ). .. Library products were sequenced on Illumina GAIIx instrument in single read 38nt mode.

    Article Title: MicroRNA and mRNA Transcriptome Profiling in Primary Human Astrocytes Infected with Borrelia burgdorferi
    Article Snippet: .. Following isolation of microRNA only fractions from untreated (N = 3), Bb treated (N = 3; 24h) and Bb treated (N = 3; 48h) samples, we prepared pooled libraries using the TruSeq small RNA library preparation kit (Illumina) according to the manufacturer’s instructions, and sequenced the libraries on the MiSeq. .. A small subset of microRNAs were found to change significantly following 24h (2 microRNAs) and 48h (38 microRNAs) of infection ( and ).

    Article Title: Integrated analysis of mRNA, microRNA and protein in systemic lupus erythematosus-specific induced pluripotent stem cells from urine
    Article Snippet: Total mRNA and miRNA isolated from three independent cultures were, respectively, pooled for subsequent library construction and sequence analysis. .. The libraries of mRNA and miRNA were constructed by using the Illumina TruSeq RNA Sample Prep Kit v2-Set A and TruSeq Small RNA Sample Prep Kit Set A, respectively, sequenced by the Illumina HiSeq™ 2000 System.

    Article Title: Small RNA Sequencing of Sporadic Amyotrophic Lateral Sclerosis Cerebrospinal Fluid Reveals Differentially Expressed miRNAs Related to Neural and Glial Activity
    Article Snippet: Small RNA-sequencing RNA was prepared for small RNA-sequencing using the Illumina TruSeq Small RNA library preparation kit following a modified protocol as described in Burgos et al. ( ). .. Individual cDNA library products of 140–160 bp were isolated on a 6% TBE PAGE gel (Supplementary Figure ).

    Transfection:

    Article Title: A Comprehensive Analysis of Replicating Merkel Cell Polyomavirus Genomes Delineates the Viral Transcription Program and Suggests a Role for mcv-miR-M1 in Episomal Persistence
    Article Snippet: .. Small RNA sequencing For sequencing of small RNA moieties, RNA from MCVSyn transfected cells and MCC cell lines was subjected to library preparation using the TruSeq Small RNA Sample Preparation Kit (Illumina) or the NEBNext Small RNA Library Prep Set for Illumina. .. Small RNA libraries were sequenced on the Illumina HiSeq platform.

    Purification:

    Article Title: Differential expression of urinary exosomal micro RNAs in IgA nephropathy, et al. Differential expression of urinary exosomal microRNAs in IgA nephropathy
    Article Snippet: Resulting PCR products, cDNA, were size‐selected with PAGE gel, according to the protocol of the TruSeq® Small RNA Sample Prep Kit (Illumina, San Diego, TX, USA). .. The purified cDNA library was evaluated using the Agilent 2200 TapeStation, and diluted to 10 pmol/L for cluster generation in situ on the HiSeq2500 (Illumina, USA) single‐end flow cell, followed by sequencing (1×50 bp).

    Article Title: Integrated analysis of mRNA, microRNA and protein in systemic lupus erythematosus-specific induced pluripotent stem cells from urine
    Article Snippet: The polyA mRNAs were selected by RNA Purification Beads (Illumina, SanDiego, CA). .. The libraries of mRNA and miRNA were constructed by using the Illumina TruSeq RNA Sample Prep Kit v2-Set A and TruSeq Small RNA Sample Prep Kit Set A, respectively, sequenced by the Illumina HiSeq™ 2000 System.

    Polymerase Chain Reaction:

    Article Title: Small RNA Library Preparation Method for Next-Generation Sequencing Using Chemical Modifications to Prevent Adapter Dimer Formation
    Article Snippet: Adapters were diluted to optimized concentrations for each amount of total RNA input and PCR cycles were increased accordingly ( , Sample Preparation Section). .. Samples prepared with modified adapters were compared to the TruSeq small RNA Library Preparation Kit (Illumina).

    Article Title: Assessment of microRNA differential expression and detection in multiplexed small RNA sequencing data
    Article Snippet: Briefly, 1 µg of total RNA from each sample was used for library preparation with the TruSeq Small RNA Sample Prep Kit (Illumina). .. The cDNA was then PCR amplified using a common primer and a primer containing one of 12 index sequences.

    Article Title: Differential expression of urinary exosomal micro RNAs in IgA nephropathy, et al. Differential expression of urinary exosomal microRNAs in IgA nephropathy
    Article Snippet: .. Resulting PCR products, cDNA, were size‐selected with PAGE gel, according to the protocol of the TruSeq® Small RNA Sample Prep Kit (Illumina, San Diego, TX, USA). .. The purified cDNA library was evaluated using the Agilent 2200 TapeStation, and diluted to 10 pmol/L for cluster generation in situ on the HiSeq2500 (Illumina, USA) single‐end flow cell, followed by sequencing (1×50 bp).

    Article Title: Evaluation of commercially available small RNASeq library preparation kits using low input RNA
    Article Snippet: Illumina TruSeq small RNA library preparation Small RNA libraries were generated using Illumina TruSeq Small RNA Sample kit (RS-200-0048; Illumina). .. During PCR amplification, the Index primer and RNA PCR primer volumes were reduced by 50% and the volume replaced with water.

    Article Title: Assessing the hodgepodge of non-mapped reads in bacterial transcriptomes: real or artifactual RNA chimeras?
    Article Snippet: Samples were further processed using the TruSeq small RNA Sample Prep Kit (ref. RS-200-0012, Illumina) according to the manufacturer’s protocol. .. Briefly, 3′ adapters and subsequently 5′ adapters were ligated to the RNA. cDNA was synthesized using reverse transcriptase (SuperScript II, ref. 18064–014, Invitrogen) and a specific primer (RNA RT Primer) complementary to the 3′ RNA adapter. cDNA was further amplified by PCR using indexed adapters supplied in the kit.

    Article Title: Small RNA Sequencing of Sporadic Amyotrophic Lateral Sclerosis Cerebrospinal Fluid Reveals Differentially Expressed miRNAs Related to Neural and Glial Activity
    Article Snippet: Small RNA-sequencing RNA was prepared for small RNA-sequencing using the Illumina TruSeq Small RNA library preparation kit following a modified protocol as described in Burgos et al. ( ). .. Adapter-ligated RNA was reverse transcribed to generate a cDNA library and amplified following 15 cycles of PCR (denaturation at 98°C for 30 s the products were amplified following 15 cycles at 98°C for 10 s, 60°C for 30 s, 72°C for 15 s and then 72°C for 10 min) incorporating individual barcodes to each sample to enable the pooling and loading of multiple samples onto the Illumina HiScanSQ.

    Construct:

    Article Title: Methylmercury exposure increases lipocalin related (lpr) and decreases activated in blocked unfolded protein response (abu) genes and specific miRNAs in Caenorhabditis elegans
    Article Snippet: .. One µg of isolated small RNAs were used to construct a library using the Small RNA library prep set kit for Illumina (New England Biolabs, Ipswich, MA, USA) using the same conditions as reported previously ( ). .. Library products were sequenced on Illumina GAIIx instrument in single read 38nt mode.

    Article Title: Integrated analysis of mRNA, microRNA and protein in systemic lupus erythematosus-specific induced pluripotent stem cells from urine
    Article Snippet: .. The libraries of mRNA and miRNA were constructed by using the Illumina TruSeq RNA Sample Prep Kit v2-Set A and TruSeq Small RNA Sample Prep Kit Set A, respectively, sequenced by the Illumina HiSeq™ 2000 System. ..

    Polyacrylamide Gel Electrophoresis:

    Article Title: Differential expression of urinary exosomal micro RNAs in IgA nephropathy, et al. Differential expression of urinary exosomal microRNAs in IgA nephropathy
    Article Snippet: .. Resulting PCR products, cDNA, were size‐selected with PAGE gel, according to the protocol of the TruSeq® Small RNA Sample Prep Kit (Illumina, San Diego, TX, USA). .. The purified cDNA library was evaluated using the Agilent 2200 TapeStation, and diluted to 10 pmol/L for cluster generation in situ on the HiSeq2500 (Illumina, USA) single‐end flow cell, followed by sequencing (1×50 bp).

    Article Title: Assessment of methods for serum extracellular vesicle small RNA sequencing to support biomarker development
    Article Snippet: 10 ng of RNA was used for input into the TruSeq Small RNA Library Prep kit (Illumina). .. Indexed samples were pooled and run on 6% TBE PAGE gels.

    Article Title: Small RNA Sequencing of Sporadic Amyotrophic Lateral Sclerosis Cerebrospinal Fluid Reveals Differentially Expressed miRNAs Related to Neural and Glial Activity
    Article Snippet: Small RNA-sequencing RNA was prepared for small RNA-sequencing using the Illumina TruSeq Small RNA library preparation kit following a modified protocol as described in Burgos et al. ( ). .. Individual cDNA library products of 140–160 bp were isolated on a 6% TBE PAGE gel (Supplementary Figure ).

    cDNA Library Assay:

    Article Title: Differential expression of urinary exosomal micro RNAs in IgA nephropathy, et al. Differential expression of urinary exosomal microRNAs in IgA nephropathy
    Article Snippet: Paragraph title: 2.8. cDNA library construction and high‐throughput sequencing ... Resulting PCR products, cDNA, were size‐selected with PAGE gel, according to the protocol of the TruSeq® Small RNA Sample Prep Kit (Illumina, San Diego, TX, USA).

    Article Title: Small RNA Sequencing of Sporadic Amyotrophic Lateral Sclerosis Cerebrospinal Fluid Reveals Differentially Expressed miRNAs Related to Neural and Glial Activity
    Article Snippet: Small RNA-sequencing RNA was prepared for small RNA-sequencing using the Illumina TruSeq Small RNA library preparation kit following a modified protocol as described in Burgos et al. ( ). .. Adapter-ligated RNA was reverse transcribed to generate a cDNA library and amplified following 15 cycles of PCR (denaturation at 98°C for 30 s the products were amplified following 15 cycles at 98°C for 10 s, 60°C for 30 s, 72°C for 15 s and then 72°C for 10 min) incorporating individual barcodes to each sample to enable the pooling and loading of multiple samples onto the Illumina HiScanSQ.

    Software:

    Article Title: Integrated analysis of mRNA, microRNA and protein in systemic lupus erythematosus-specific induced pluripotent stem cells from urine
    Article Snippet: The libraries of mRNA and miRNA were constructed by using the Illumina TruSeq RNA Sample Prep Kit v2-Set A and TruSeq Small RNA Sample Prep Kit Set A, respectively, sequenced by the Illumina HiSeq™ 2000 System. .. The high-quality clean reads were mapped to the reference human genome using the SOAP (version 2.0) software.

    Selection:

    Article Title: Assessing the hodgepodge of non-mapped reads in bacterial transcriptomes: real or artifactual RNA chimeras?
    Article Snippet: Samples were further processed using the TruSeq small RNA Sample Prep Kit (ref. RS-200-0012, Illumina) according to the manufacturer’s protocol. .. Finally, size selection of the libraries pas performed using 6% Novex® TBE Gels (ref. EC6265BOX, Life Technologies).

    Sample Prep:

    Article Title: Small RNA Library Preparation Method for Next-Generation Sequencing Using Chemical Modifications to Prevent Adapter Dimer Formation
    Article Snippet: Adapters were diluted to optimized concentrations for each amount of total RNA input and PCR cycles were increased accordingly ( , Sample Preparation Section). .. Samples prepared with modified adapters were compared to the TruSeq small RNA Library Preparation Kit (Illumina).

    Article Title: Quantitative Bias in Illumina TruSeq and a Novel Post Amplification Barcoding Strategy for Multiplexed DNA and Small RNA Deep Sequencing
    Article Snippet: .. TruSeq small RNA and DNA barcoding and sequencing For the TruSeq sample preparation, the Illumina TruSeq Small RNA Sample Prep Kit (RS-200–0012) and the Illumina TruSeq DNA Sample Prep Kit (FC-121–1001) were used. .. Yields and quantification of libraries The PALM barcode ligation step produces several DNA products but only the main product, library products with the barcode adapters ligated to both ends, are able to form clusters and generate sequencing data.

    Article Title: Assessment of microRNA differential expression and detection in multiplexed small RNA sequencing data
    Article Snippet: .. Briefly, 1 µg of total RNA from each sample was used for library preparation with the TruSeq Small RNA Sample Prep Kit (Illumina). ..

    Article Title: Differential expression of urinary exosomal micro RNAs in IgA nephropathy, et al. Differential expression of urinary exosomal microRNAs in IgA nephropathy
    Article Snippet: .. Resulting PCR products, cDNA, were size‐selected with PAGE gel, according to the protocol of the TruSeq® Small RNA Sample Prep Kit (Illumina, San Diego, TX, USA). .. The purified cDNA library was evaluated using the Agilent 2200 TapeStation, and diluted to 10 pmol/L for cluster generation in situ on the HiSeq2500 (Illumina, USA) single‐end flow cell, followed by sequencing (1×50 bp).

    Article Title: A Comprehensive Analysis of Replicating Merkel Cell Polyomavirus Genomes Delineates the Viral Transcription Program and Suggests a Role for mcv-miR-M1 in Episomal Persistence
    Article Snippet: .. Small RNA sequencing For sequencing of small RNA moieties, RNA from MCVSyn transfected cells and MCC cell lines was subjected to library preparation using the TruSeq Small RNA Sample Preparation Kit (Illumina) or the NEBNext Small RNA Library Prep Set for Illumina. .. Small RNA libraries were sequenced on the Illumina HiSeq platform.

    Article Title: Assessing the hodgepodge of non-mapped reads in bacterial transcriptomes: real or artifactual RNA chimeras?
    Article Snippet: .. Samples were further processed using the TruSeq small RNA Sample Prep Kit (ref. RS-200-0012, Illumina) according to the manufacturer’s protocol. .. Briefly, 3′ adapters and subsequently 5′ adapters were ligated to the RNA. cDNA was synthesized using reverse transcriptase (SuperScript II, ref. 18064–014, Invitrogen) and a specific primer (RNA RT Primer) complementary to the 3′ RNA adapter. cDNA was further amplified by PCR using indexed adapters supplied in the kit.

    Article Title: Integrated analysis of mRNA, microRNA and protein in systemic lupus erythematosus-specific induced pluripotent stem cells from urine
    Article Snippet: .. The libraries of mRNA and miRNA were constructed by using the Illumina TruSeq RNA Sample Prep Kit v2-Set A and TruSeq Small RNA Sample Prep Kit Set A, respectively, sequenced by the Illumina HiSeq™ 2000 System. ..

    In Situ:

    Article Title: Differential expression of urinary exosomal micro RNAs in IgA nephropathy, et al. Differential expression of urinary exosomal microRNAs in IgA nephropathy
    Article Snippet: Resulting PCR products, cDNA, were size‐selected with PAGE gel, according to the protocol of the TruSeq® Small RNA Sample Prep Kit (Illumina, San Diego, TX, USA). .. The purified cDNA library was evaluated using the Agilent 2200 TapeStation, and diluted to 10 pmol/L for cluster generation in situ on the HiSeq2500 (Illumina, USA) single‐end flow cell, followed by sequencing (1×50 bp).

    Concentration Assay:

    Article Title: Assessment of methods for serum extracellular vesicle small RNA sequencing to support biomarker development
    Article Snippet: 10 ng of RNA was used for input into the TruSeq Small RNA Library Prep kit (Illumina). .. Twelve uniquely indexed libraries were pooled in equimolar ratio based on concentration between 145–160 bp as was determined by Agilent Bioanalyzer.

    Article Title: Integrated analysis of mRNA, microRNA and protein in systemic lupus erythematosus-specific induced pluripotent stem cells from urine
    Article Snippet: The concentration and quality of total RNA were measured by the UV absorbance at 260 nm and 280 nm (A260/280) and checked by gel electrophoresis. .. The libraries of mRNA and miRNA were constructed by using the Illumina TruSeq RNA Sample Prep Kit v2-Set A and TruSeq Small RNA Sample Prep Kit Set A, respectively, sequenced by the Illumina HiSeq™ 2000 System.

    High Throughput Screening Assay:

    Article Title: Small RNA Library Preparation Method for Next-Generation Sequencing Using Chemical Modifications to Prevent Adapter Dimer Formation
    Article Snippet: Gel purification significantly limits the ability to automate library preparation for sRNA thus limiting high throughput experiments. .. The two most common commercially available kits, TruSeq Small RNA Library Preparation Kit (Illumina) and NEBNext Small RNA Library Prep Set (New England Biolabs), recommend 100 ng total RNA input as the lowest sample amount achievable [ ].

    Article Title: Differential expression of urinary exosomal micro RNAs in IgA nephropathy, et al. Differential expression of urinary exosomal microRNAs in IgA nephropathy
    Article Snippet: Paragraph title: 2.8. cDNA library construction and high‐throughput sequencing ... Resulting PCR products, cDNA, were size‐selected with PAGE gel, according to the protocol of the TruSeq® Small RNA Sample Prep Kit (Illumina, San Diego, TX, USA).

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  • 90
    Illumina Inc truseq small rna kit
    Bias in miRNA detection using various <t>small-RNA</t> library preparation kits. For each kit, sequencing libraries were prepared from the miRXplore™ pool and sequenced; the sequence data were then used to calculate fold-deviations from the equimolar input and plotted as log 2 values. Densities of miRNAs within a two-fold deviation from the expected values (between vertical lines ) are considered unbiased according to [ 8 ]. Under-represented, over-represented, and accurately quantified percentages of miRNAs are shown in red font . Results for two-adapter schemes are a <t>TruSeq®</t> Small RNA, b NEBNext®, and c QIAseq. d NEXTFlex™, a scheme using two adapters with randomized sequences. e SMARTer, which uses template switching. f RealSeq®-AC, which uses a single-adapter and circularization (* p value vs other kits
    Truseq Small Rna Kit, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 90/100, based on 43 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/truseq small rna kit/product/Illumina Inc
    Average 90 stars, based on 43 article reviews
    Price from $9.99 to $1999.99
    truseq small rna kit - by Bioz Stars, 2020-02
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    90
    Illumina Inc truseq small rna sample kit
    a Average percentage of reads mapped to the human transcriptome to <t>RNA</t> biotypes for Illumina <t>TruSeq</t> and BiooScientific NEXTFlex for the plasma samples. The percentages presented here are averaged over the 6 different volumes for each kit respectively. b PCA plot of the plasma samples show clustering of the samples by kit-type and not by input volume. c Number of miRNAs detected at three expression thresholds: > 1 read per million mapped to the genome (RPM), > 10 RPM and > 100 RPM for all the plasma samples for Illumina TruSeq and BiooScientific NEXTFlex
    Truseq Small Rna Sample Kit, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 90/100, based on 5 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/truseq small rna sample kit/product/Illumina Inc
    Average 90 stars, based on 5 article reviews
    Price from $9.99 to $1999.99
    truseq small rna sample kit - by Bioz Stars, 2020-02
    90/100 stars
      Buy from Supplier

    90
    Illumina Inc truseq small rna sample preparation kit
    Adapter-tRNA ligation efficiencies with a conventional method and YAMAT-seq. ( A ) Schematic representation of the adapter ligation reactions used in the conventional and YAMAT-seq methods. In the conventional method, tRNA was subjected to 3΄-adapter (3΄-AD) and 5΄-adapter (5΄-AD) ligations catalyzed by truncated Rnl2 and Rnl1, respectively, using the Illumina <t>TruSeq</t> Small <t>RNA</t> Sample Preparation Kit. In contrast, in the YAMAT-seq method, a Y-shaped adapter (Y-AD) is ligated to a tRNA by Rnl2. ( B ) Ligation products of synthetic human cyto tRNA AspGUC and 5΄-AD or 3΄-AD were quantified by real-time qRT-PCR. The amounts of ligation products were determined based on standard curves, and ligation efficiencies were calculated as percentages of ligated tRNA versus input tRNA (set as 100%). Each data set represents the average of three independent experiments with bars showing the SD. ( C ) Ligation products of the indicated native cyto tRNAs in BT-474 total RNA and 5΄-AD or 3΄-AD were quantified by real-time qRT-PCR. Each data set represents the average Ct values of three independent experiments with bars showing the SD. ( D ) Image of 8% native polyacrylamide gel electrophoresis (PAGE) of amplified cDNAs resulting from BT-474 total RNA sequencing by conventional and YAMAT-seq procedures. The total adapter lengths of the conventional and YAMAT-seq procedures are 118 and 140 bp, respectively. The YAMAT-seq-derived cDNAs in the designated Bands 1–3 regions were gel-purified and subjected to cloning; the identified sequences are shown in Supplementary Table S1 . The cDNAs in regions designated with gray lines are expected to contain tRNA fraction.
    Truseq Small Rna Sample Preparation Kit, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 90/100, based on 12 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/truseq small rna sample preparation kit/product/Illumina Inc
    Average 90 stars, based on 12 article reviews
    Price from $9.99 to $1999.99
    truseq small rna sample preparation kit - by Bioz Stars, 2020-02
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    Bias in miRNA detection using various small-RNA library preparation kits. For each kit, sequencing libraries were prepared from the miRXplore™ pool and sequenced; the sequence data were then used to calculate fold-deviations from the equimolar input and plotted as log 2 values. Densities of miRNAs within a two-fold deviation from the expected values (between vertical lines ) are considered unbiased according to [ 8 ]. Under-represented, over-represented, and accurately quantified percentages of miRNAs are shown in red font . Results for two-adapter schemes are a TruSeq® Small RNA, b NEBNext®, and c QIAseq. d NEXTFlex™, a scheme using two adapters with randomized sequences. e SMARTer, which uses template switching. f RealSeq®-AC, which uses a single-adapter and circularization (* p value vs other kits

    Journal: Genome Biology

    Article Title: Decreasing miRNA sequencing bias using a single adapter and circularization approach

    doi: 10.1186/s13059-018-1488-z

    Figure Lengend Snippet: Bias in miRNA detection using various small-RNA library preparation kits. For each kit, sequencing libraries were prepared from the miRXplore™ pool and sequenced; the sequence data were then used to calculate fold-deviations from the equimolar input and plotted as log 2 values. Densities of miRNAs within a two-fold deviation from the expected values (between vertical lines ) are considered unbiased according to [ 8 ]. Under-represented, over-represented, and accurately quantified percentages of miRNAs are shown in red font . Results for two-adapter schemes are a TruSeq® Small RNA, b NEBNext®, and c QIAseq. d NEXTFlex™, a scheme using two adapters with randomized sequences. e SMARTer, which uses template switching. f RealSeq®-AC, which uses a single-adapter and circularization (* p value vs other kits

    Article Snippet: Sequencing results of a library prepared using the TruSeq® Small RNA kit (Illumina) with 1 pmol of synthetic miRNAs (miRXplore™ Universal Pool) as input.

    Techniques: Sequencing

    Differential quantification of brain samples between different small RNA library preparation kits. Data obtained with either a TruSeq®, b NEBNext®, c NEXTFlex™, d QIAseq, or e SMARTer kits were compared with data obtained with RealSeq®-AC to obtain differential quantification (log 2 ) values for 276 high-confidence miRNAs. These values were plotted against the accuracy of detection of that miRNA when profiling the equimolar pool of synthetic miRNAs (Fig. 2 a–c). f–j The reverse comparison, with the differential quantification of RealSeq®-AC versus each of the other kits plotted against the accuracy of RealSeq®-AC when quantifying the synthetic pool of miRNAs. FN false negative, FP false positive. See Methods for more details

    Journal: Genome Biology

    Article Title: Decreasing miRNA sequencing bias using a single adapter and circularization approach

    doi: 10.1186/s13059-018-1488-z

    Figure Lengend Snippet: Differential quantification of brain samples between different small RNA library preparation kits. Data obtained with either a TruSeq®, b NEBNext®, c NEXTFlex™, d QIAseq, or e SMARTer kits were compared with data obtained with RealSeq®-AC to obtain differential quantification (log 2 ) values for 276 high-confidence miRNAs. These values were plotted against the accuracy of detection of that miRNA when profiling the equimolar pool of synthetic miRNAs (Fig. 2 a–c). f–j The reverse comparison, with the differential quantification of RealSeq®-AC versus each of the other kits plotted against the accuracy of RealSeq®-AC when quantifying the synthetic pool of miRNAs. FN false negative, FP false positive. See Methods for more details

    Article Snippet: Sequencing results of a library prepared using the TruSeq® Small RNA kit (Illumina) with 1 pmol of synthetic miRNAs (miRXplore™ Universal Pool) as input.

    Techniques:

    Small RNA analysis performed by using the Agilent 2100 Bioanalyzer and and the sequencing library preparation using Illumina TruSeq Small RNA kit: a miRNA/sRNA ratio: Ratio of miRNA molecules expressed as a portion of all small RNA molecules (%) detected with the Agilent 2100 Bioanalyzer. b Electronic gel image of small RNA library obtained using Illumina TruSeq Small RNA kit for the unpooled samples where carrier was added to the TRIzol extraction procedure

    Journal: Molecular Biology Reports

    Article Title: Identification of extracellular miRNA in archived serum samples by next-generation sequencing from RNA extracted using multiple methods

    doi: 10.1007/s11033-016-4043-6

    Figure Lengend Snippet: Small RNA analysis performed by using the Agilent 2100 Bioanalyzer and and the sequencing library preparation using Illumina TruSeq Small RNA kit: a miRNA/sRNA ratio: Ratio of miRNA molecules expressed as a portion of all small RNA molecules (%) detected with the Agilent 2100 Bioanalyzer. b Electronic gel image of small RNA library obtained using Illumina TruSeq Small RNA kit for the unpooled samples where carrier was added to the TRIzol extraction procedure

    Article Snippet: The small RNA library preparation was carried out using Illumina TruSeq small RNA kit and sequencing was carried out using Illumina platform.

    Techniques: Sequencing

    a Average percentage of reads mapped to the human transcriptome to RNA biotypes for Illumina TruSeq and BiooScientific NEXTFlex for the plasma samples. The percentages presented here are averaged over the 6 different volumes for each kit respectively. b PCA plot of the plasma samples show clustering of the samples by kit-type and not by input volume. c Number of miRNAs detected at three expression thresholds: > 1 read per million mapped to the genome (RPM), > 10 RPM and > 100 RPM for all the plasma samples for Illumina TruSeq and BiooScientific NEXTFlex

    Journal: BMC Genomics

    Article Title: Evaluation of commercially available small RNASeq library preparation kits using low input RNA

    doi: 10.1186/s12864-018-4726-6

    Figure Lengend Snippet: a Average percentage of reads mapped to the human transcriptome to RNA biotypes for Illumina TruSeq and BiooScientific NEXTFlex for the plasma samples. The percentages presented here are averaged over the 6 different volumes for each kit respectively. b PCA plot of the plasma samples show clustering of the samples by kit-type and not by input volume. c Number of miRNAs detected at three expression thresholds: > 1 read per million mapped to the genome (RPM), > 10 RPM and > 100 RPM for all the plasma samples for Illumina TruSeq and BiooScientific NEXTFlex

    Article Snippet: Illumina TruSeq small RNA library preparation Small RNA libraries were generated using Illumina TruSeq Small RNA Sample kit (RS-200-0048; Illumina).

    Techniques: Expressing

    Schematic of study design. Tissue RNA from brain, liver and placenta were sequenced at two sites at two input amounts (1 μg and 10 ng) using three different RNA sequencing kits (Illumina TruSeq, NEB Next and BiooScientific NEXTFlex). RNA from plasma samples at 5 different input volumes (200 μL – 5 mL) were sequenced at Site 1 using only TruSeq and BiooScientific. The green arrow depicts the flow of one of the tissue samples – brain using NEB Next and the red arrows, the plasma samples. The RNASeq results from the tissue samples were then validated using three different platforms (qPCR, EdgeSeq performed by Site1 and Fireplex performed by Site2). For a full list of samples sequenced, please refer to Additional file 1 : Table S1

    Journal: BMC Genomics

    Article Title: Evaluation of commercially available small RNASeq library preparation kits using low input RNA

    doi: 10.1186/s12864-018-4726-6

    Figure Lengend Snippet: Schematic of study design. Tissue RNA from brain, liver and placenta were sequenced at two sites at two input amounts (1 μg and 10 ng) using three different RNA sequencing kits (Illumina TruSeq, NEB Next and BiooScientific NEXTFlex). RNA from plasma samples at 5 different input volumes (200 μL – 5 mL) were sequenced at Site 1 using only TruSeq and BiooScientific. The green arrow depicts the flow of one of the tissue samples – brain using NEB Next and the red arrows, the plasma samples. The RNASeq results from the tissue samples were then validated using three different platforms (qPCR, EdgeSeq performed by Site1 and Fireplex performed by Site2). For a full list of samples sequenced, please refer to Additional file 1 : Table S1

    Article Snippet: Illumina TruSeq small RNA library preparation Small RNA libraries were generated using Illumina TruSeq Small RNA Sample kit (RS-200-0048; Illumina).

    Techniques: RNA Sequencing Assay, Flow Cytometry, Real-time Polymerase Chain Reaction

    Adapter-tRNA ligation efficiencies with a conventional method and YAMAT-seq. ( A ) Schematic representation of the adapter ligation reactions used in the conventional and YAMAT-seq methods. In the conventional method, tRNA was subjected to 3΄-adapter (3΄-AD) and 5΄-adapter (5΄-AD) ligations catalyzed by truncated Rnl2 and Rnl1, respectively, using the Illumina TruSeq Small RNA Sample Preparation Kit. In contrast, in the YAMAT-seq method, a Y-shaped adapter (Y-AD) is ligated to a tRNA by Rnl2. ( B ) Ligation products of synthetic human cyto tRNA AspGUC and 5΄-AD or 3΄-AD were quantified by real-time qRT-PCR. The amounts of ligation products were determined based on standard curves, and ligation efficiencies were calculated as percentages of ligated tRNA versus input tRNA (set as 100%). Each data set represents the average of three independent experiments with bars showing the SD. ( C ) Ligation products of the indicated native cyto tRNAs in BT-474 total RNA and 5΄-AD or 3΄-AD were quantified by real-time qRT-PCR. Each data set represents the average Ct values of three independent experiments with bars showing the SD. ( D ) Image of 8% native polyacrylamide gel electrophoresis (PAGE) of amplified cDNAs resulting from BT-474 total RNA sequencing by conventional and YAMAT-seq procedures. The total adapter lengths of the conventional and YAMAT-seq procedures are 118 and 140 bp, respectively. The YAMAT-seq-derived cDNAs in the designated Bands 1–3 regions were gel-purified and subjected to cloning; the identified sequences are shown in Supplementary Table S1 . The cDNAs in regions designated with gray lines are expected to contain tRNA fraction.

    Journal: Nucleic Acids Research

    Article Title: YAMAT-seq: an efficient method for high-throughput sequencing of mature transfer RNAs

    doi: 10.1093/nar/gkx005

    Figure Lengend Snippet: Adapter-tRNA ligation efficiencies with a conventional method and YAMAT-seq. ( A ) Schematic representation of the adapter ligation reactions used in the conventional and YAMAT-seq methods. In the conventional method, tRNA was subjected to 3΄-adapter (3΄-AD) and 5΄-adapter (5΄-AD) ligations catalyzed by truncated Rnl2 and Rnl1, respectively, using the Illumina TruSeq Small RNA Sample Preparation Kit. In contrast, in the YAMAT-seq method, a Y-shaped adapter (Y-AD) is ligated to a tRNA by Rnl2. ( B ) Ligation products of synthetic human cyto tRNA AspGUC and 5΄-AD or 3΄-AD were quantified by real-time qRT-PCR. The amounts of ligation products were determined based on standard curves, and ligation efficiencies were calculated as percentages of ligated tRNA versus input tRNA (set as 100%). Each data set represents the average of three independent experiments with bars showing the SD. ( C ) Ligation products of the indicated native cyto tRNAs in BT-474 total RNA and 5΄-AD or 3΄-AD were quantified by real-time qRT-PCR. Each data set represents the average Ct values of three independent experiments with bars showing the SD. ( D ) Image of 8% native polyacrylamide gel electrophoresis (PAGE) of amplified cDNAs resulting from BT-474 total RNA sequencing by conventional and YAMAT-seq procedures. The total adapter lengths of the conventional and YAMAT-seq procedures are 118 and 140 bp, respectively. The YAMAT-seq-derived cDNAs in the designated Bands 1–3 regions were gel-purified and subjected to cloning; the identified sequences are shown in Supplementary Table S1 . The cDNAs in regions designated with gray lines are expected to contain tRNA fraction.

    Article Snippet: cDNA amplification and Illumina sequencing cDNA amplification was performed using the TruSeq Small RNA Sample Preparation Kit (Illumina) according to the manufacturer's protocol.

    Techniques: Ligation, Sample Prep, Quantitative RT-PCR, Polyacrylamide Gel Electrophoresis, Amplification, RNA Sequencing Assay, Derivative Assay, Purification, Clone Assay