Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Systematic assessment of next-generation sequencing for quantitative small RNA profiling: a multiple protocol study across multiple laboratories

ABSTRACT: Systematic assessment of next-generation sequencing for quantitative small RNA profiling: a multiple protocol study across multiple laboratories

PROVIDER: PRJNA371516 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Similar Datasets

Systematic assessment of next-generation sequencing for quantitative small RNA profiling: a multiple protocol study across multiple laboratories

Project description:Small RNA-seq is increasingly being used for profiling of small RNAs. Quantitative characteristics of long RNA-seq have been extensively described, but small RNA-seq involves fundamentally different methods for library preparation, with distinct protocols and technical variations that have not been fully and systematically studied. We report here the results of a study using common references (synthetic RNA pools of defined composition, as well as plasma-derived RNA) to evaluate the accuracy, reproducibility and bias of small RNA-seq library preparation for five distinct protocols and across nine different laboratories. We observed protocol-specific and sequence-specific bias, which was ameliorated using adapters for ligation with randomized end-nucleotides, and computational correction factors. Despite this technical bias, relative quantification using small RNA-seq was remarkably accurate and reproducible, even across multiple laboratories using different methods. These results provide strong evidence for the feasibility of reproducible cross-laboratory small RNA-seq studies, even those involving analysis of data generated using different protocols. This SuperSeries is composed of the SubSeries listed below.

2018-07-09 | GSE94586 | GEO

Systematic evaluation of RNA-Seq preparation protocol performance

Project description:Systematic evaluation of RNA-Seq preparation protocol performance

| PRJNA543480 | ENA

Systematic evaluation of RNA-Seq preparation protocol performance (RNASeq: TruSeq)

Project description:Systematic evaluation of RNA-Seq preparation protocol performance (RNASeq: TruSeq)

| PRJNA543482 | ENA

Systematic evaluation of RNA-Seq preparation protocol performance (RNASeq: SMARTer)

Project description:Systematic evaluation of RNA-Seq preparation protocol performance (RNASeq: SMARTer)

| PRJNA543483 | ENA

Protocol matters – reproducibility and rigor of DNA methylation data sets [BiSulfite-seq]

Project description:While epigenetics continues to be a burgeoning research area in neuroscience, unaddressed issues related to data reproducibility across laboratories remain. Indeed, separating meaningful experimental changes from background variability is a challenge in epigenomic studies. Genome-wide DNA methylation analysis of hippocampal tissues from wild-type rats across three independent laboratories revealed that seemingly minor protocol differences resulted in significant epigenome profile changes, even in the absence of experimental intervention. Difficult-to-match factors such as animal vendors and a subset of husbandry and tissue extraction procedures produced quantifiable variations between wild-type animals across the three laboratories. To enhance scientific rigor, we conclude that strict adherence to protocols is necessary for the execution and interpretation of epigenetic studies and that protocol-sensitive epigenetic changes, amongst naive animals, may confound experimental results.

2022-01-12 | GSE164831 | GEO

Protocol matters – reproducibility and rigor of DNA methylation data sets [RNA-seq]

2022-01-12 | GSE164800 | GEO

Systematic assessment of commercially available low-input miRNA library preparation kits

Project description:Systematic assessment of commercially available low-input miRNA library preparation kits

| PRJNA552326 | ENA

Systematic assessment of next-generation sequencing for quantitative small RNA profiling: human plasma pool

Project description:Small RNA-seq is increasingly being used for profiling of small RNAs. Quantitative characteristics of long RNA-seq have been extensively described, but small RNA-seq involves fundamentally different methods for library preparation, with distinct protocols and technical variations that have not been fully and systematically studied. Using common sets of reference samples, we evaluated the accuracy, reproducibility and bias of small RNA-seq library preparation for five distinct protocols and across nine different laboratories. As part of this larger study, we assessed reproducibility and diversity of sequencing of mature miRNAs, generating libraries from RNA extracted from human plasma that was pooled from 11 healthy individuals. We find that protocol-specific biases are largely recapitulated in the biological samples, and that inter-protocol bias correction factors estimated from the more comprehensive equimolar synthetic pools can be applied to the biological samples to get more comparable, and in some cases, more accurate estimates of miRNA abundance.

2018-07-09 | GSE94582 | GEO

Systematic assessment of next-generation sequencing for quantitative small RNA profiling: synthetic equimolar pool

Project description:Small RNA-seq is increasingly being used for profiling of small RNAs. Quantitative characteristics of long RNA-seq have been extensively described, but small RNA-seq involves fundamentally different methods for library preparation, with distinct protocols and technical variations that have not been fully and systematically studied. Using common sets of reference samples, we evaluated the accuracy, reproducibility and bias of small RNA-seq library preparation for five distinct protocols and across nine different laboratories. As part of this larger study, we assessed sequencing bias and reproducibility using an equimolar pool of 1,152 small RNA sequences ranging from 15-90 nt, and primarily comprised of annotated human microRNAs. We observed extensive protocol-specific and sequence-specific bias that was largely mitigated in protocols employing sequencing adapters with randomized end-nucleotides. We find that sequencing bias is highly reproducible across labs using the same library preparation technologies, and use the data to calculate inter-protocol bias correction factors. These results provide strong evidence for the feasibility of reproducible cross-laboratory small RNA-seq studies, even those involving analysis of data generated using different protocols.

2018-07-09 | GSE94584 | GEO

Ebola virus sequencing Dutch Mobile Laboratories

Project description:Ebola virus sequencing Dutch Mobile Laboratories

| PRJEB10265 | ENA