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Homo sapiens

ABSTRACT: An improved protocol for small RNA library construction by using High-Definition adapters [cell line]

PROVIDER: PRJNA255088 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR1513328.fastq.gz	Fastqsanger.gz

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Medicago truncatula

Project description:An improved protocol for small RNA library construction by using High-Definition adapters

| PRJNA255087 | ENA

An improved protocol for small RNA library construction by using High-Definition adapters [cell line]

Project description:Most of small RNA library construction methods are based on RNA ligases, which prefer to join the molecules (small RNAs and adapters) that can anneal to each other and form a ligase favoured structure. Different platforms for next generation sequencing use different adapter sequences, causing the cloning bias. Adapters with degenerated nucleotides at the ligating ends (High Definition, HD adapters) were developed to reduce the cloning bias. However, above 90% of the cloning products is adapter dimer when the current available commercial kits and their corresponding protocols are used. Here we adopted and further improved a method demonstrated in a publically available patent (http://www.google.com/patents/WO2011056866A2?cl=en). Using the improved method, we constructed the small RNA libraries by using the total RNA of chondrosarcoma cell line. The adapter dimer was significantly reduced. The small RNA sequences were also analysed. The small RNA libraries of cultured chondrosarcoma cell line were constructed by using an improved protocol where high-definition (HD) adapters were used.

2015-01-31 | E-GEOD-59331 | biostudies-arrayexpress

An improved protocol for small RNA library construction by using High-Definition adapters

Project description:Most of small RNA library construction methods are based on RNA ligases, which prefer to join the molecules (small RNAs and adapters) that can anneal to each other and form a ligase favoured structure. Different platforms for next generation sequencing use different adapter sequences, causing the cloning bias. Adapters with degenerated nucleotides at the ligating ends (High Definition, HD adapters) were developed to reduce the cloning bias. However, above 90% of the cloning products is adapter dimer when the current available commercial kits and their corresponding protocols are used. Here we adopted and further improved a method demonstrated in a publically available patent (http://www.google.com/patents/WO2011056866A2?cl=en). Using the improved method, we constructed the small RNA libraries by using the total RNA of Medicago truncatula leaf tissue. The adapter dimer was significantly reduced. The small RNA sequences were also analysed. The small RNA libraries of medicago truncatula leaves were constructed by using an improved protocol where high-definition (HD) adapters were used.

2015-01-31 | E-GEOD-59330 | biostudies-arrayexpress

An improved protocol for small RNA library construction by using High-Definition adapters [cell line]

2015-01-31 | GSE59331 | GEO

An improved protocol for small RNA library construction by using High-Definition adapters

Project description:Most of small RNA library construction methods are based on RNA ligases, which prefer to join the molecules (small RNAs and adapters) that can anneal to each other and form a ligase favoured structure. Different platforms for next generation sequencing use different adapter sequences, causing the cloning bias. Adapters with degenerated nucleotides at the ligating ends (High Definition, HD adapters) were developed to reduce the cloning bias. However, above 90% of the cloning products is adapter dimer when the current available commercial kits and their corresponding protocols are used. Here we adopted and further improved a method demonstrated in a publically available patent (http://www.google.com/patents/WO2011056866A2?cl=en). Using the improved method, we constructed the small RNA libraries by using the total RNA of Medicago truncatula leaf tissue. The adapter dimer was significantly reduced. The small RNA sequences were also analysed.

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Comparison of mRNA-seq quantification from libraries obtained using either HD or standard Illumina adapters in A thaliana, in wildtype and DCL1 mutants

Project description:One method of directional cloning of fragmented mRNA is based on single strand RNA ligation, for which ligation bias occurrs if the adapters have single sequences. The sequencing bias affects the mRNA quantification and subsequently the differential expression analysis. High definition (HD) adapters [Sorefan et al 2012, Xu et al 2015] can be used to diminish the cloning bias during library construction. HD adapters and standard illumina adapters were used to construct mRNA-seq libraries for a side by side comparison.

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Sequencing random oligonucleotides using standard GA II protocol

Project description:Study on sequencing biases introduced by library preparation step, namely by ligases. Comparison between standard Illumina protocol and improved High Definition (HD) protocol.

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Project description:Study on sequencing biases introduced by library preparation step, namely by ligases. Comparison between standard Illumina protocol and improved High Definition (HD) protocol. Four replicates for N21 (21 random nucleotides), one replicate for N9 (9 random nucleotides), using either standard Illumina protocol or HD protocol

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Comparison of sRNA populations obtained using HD adapters in A thaliana, with NEB RecJ exonuclease or Superscript II enzymes

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