Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

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

ABSTRACT: 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.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE102510 | GEO | 2019/10/01

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Comparison of sRNA populations obtained using HD or standard Illumina adapters in A thaliana, with or without TAP treatment

Project description:The sRNA population (sequence identity and distribution of abundances) in A thaliana 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)

2020-06-30 | GSE102545 | GEO

Comparison of sRNA populations obtained using HD or standard Illumina adapters in S Lycopersicum (rdr6 mutant) 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)

2019-10-01 | GSE102579 | GEO

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

2018-10-20 | GSE102581 | GEO

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

2019-09-01 | GSE102576 | 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 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

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

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

Project description:Multiple companies produce RecJ exonuclease and RNA dependent DNA polymerase for making cDNA. Our standard protocol was developed based on the enzymes from Epicenter (epicenter was recently bought by the Illumina company). As an alternative for the enzymes from EPicenter, we tested the RecJ exonuclease from NEB and Superperscript II from Invitrogen in sRNA library construction using HD adapters [Sorefan et al 2012, Xu et al 2015].

2018-12-20 | GSE102509 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data