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Drosophila melanogaster

ABSTRACT: The effect of sample splitting and technical replication on mRNA-seq and sRNA-seq quantification

PROVIDER: PRJNA339435 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR4041321.fastq.gz	Fastqsanger.gz
	SRR4041322.fastq.gz	Fastqsanger.gz
	SRR4041323.fastq.gz	Fastqsanger.gz
	SRR4041324.fastq.gz	Fastqsanger.gz
	SRR4041325.fastq.gz	Fastqsanger.gz

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The effect of sample splitting and technical replication on mRNA-seq and sRNA-seq quantification

Project description:RNA sequencing (RNA-seq) is a widely used method for quantifying RNA levels across the environmental, biological and medical sciences. The accuracy of the output from an RNA-seq experiment is known to vary due to sequencing biases or errors in quantification. These have the potential to lead to false calls of differential expression (DE), and hence, to affect the accuracy of the biological inference. A proposed solution to reduce the number of false positives and increase confidence in the quality of results from such experiments is to increase the number of biological replicates. In addition, more recent suggestions are to create additional technical replicates within biological replicates (i.e. to split samples across sequencing lanes). The optimal strategy for analysing and normalizing such data, and for maximising accuracy as a function of cost, biological and technical replication is important to understand, yet currently unclear. The aim of this study was to test the effect of technical replication and sample splitting on the overall outcome of gene expression profiling for RNA-seq data.

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Project description:We sequenced mRNA and small RNA (sRNA) profiles in the interaction between Brachypodium distachyon (Bd) and Serendipita indica (Si; syn. Piriformospora indica), at four (4) days post inoculation (DPI). sRNA sequencing reads of Si-colonized and non-colonized roots, as well as axenic fungal cultures were generated. Three biological samples of each were sequenced, with two technical replicates per sample (SE). Raw reads from sRNA sequencing were submitted to technical adapter trimming (Cutadapt) before upload.

2021-07-15 | E-MTAB-10650 | biostudies-arrayexpress

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