Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Sequencing random oligonucleotides using standard GA II protocol

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

ORGANISM(S): synthetic construct

PROVIDER: GSE36540 | GEO | 2012/07/23

SECONDARY ACCESSION(S): PRJNA153413

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

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. Four replicates for N21 (21 random nucleotides), one replicate for N9 (9 random nucleotides), using either standard Illumina protocol or HD protocol

2012-07-23 | E-GEOD-36540 | 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]

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

2015-01-31 | GSE59330 | GEO

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.

2015-01-31 | GSE59331 | GEO

Comparison of sRNA populations obtained using HD or standard Illumina adapters in O sativa

Project description:The sRNA population (sequence identity and distribution of abundances) in O sativa was assessed using High Definition (HD) [Sorefan et al 2012, Xu et al 2015] or standard Illumina adapters; the usage of HD adapters revealed a more diverse population of sRNAs (in particular, it revealed the presence of more unique 24mers)

2019-09-01 | GSE102572 | GEO

Comparison of sRNA populations obtained using HD or standard Illumina adapters in S Lycopersicum without TAP treatment

Project description:The sRNA population (sequence identity and distribution of abundances) in S Lycopersicum was assessed using High Definition (HD) [Sorefan et al 2012, Xu et al 2015] or standard Illumina adapters; the usage of HD adapters revealed a more diverse population of sRNAs (in particular, it revealed the presence of more unique 24mers)

2019-09-01 | GSE102576 | GEO

Comparison of sRNA populations obtained using HD or standard Illumina adapters in M truncatula, with TAP treatment

Project description:The sRNA population (sequence identity and distribution of abundances) in M truncatula was assessed using High Definition (HD) [Sorefan et al 2012, Xu et al 2015] or standard Illumina adapters; the usage of HD adapters revealed a more diverse population of sRNAs (in particular, it revealed the presence of more unique 24mers)

2019-09-01 | GSE102565 | GEO

Comparison of sRNA populations obtained using HD or standard Illumina adapters in M truncatula, without TAP treatment

2018-10-20 | GSE102555 | GEO

Comparison of sRNA populations obtained using HD or standard Illumina adapters in S Lycopersicum with TAP treatment

2018-10-20 | GSE102581 | GEO