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Illumina NovaSeq 6000 sequencing: WGS of rattus norvegicus: whole blood of of the BXH6/Cub strain

ABSTRACT: Illumina NovaSeq 6000 sequencing: WGS of rattus norvegicus: whole blood of of the BXH6/Cub strain

PROVIDER: PRJEB67504 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR12131691_1.fastq.gz	Fastqsanger.gz
	ERR12131691_2.fastq.gz	Fastqsanger.gz
	ERR12131692_1.fastq.gz	Fastqsanger.gz
	ERR12131692_2.fastq.gz	Fastqsanger.gz

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Project description:Gene expression profiles generated with RNA sequencing can be biased by RNA amount and methods utilised for cDNA library generation. Polymerase chain reaction (PCR) amplification can generate high PCR duplicate proportions and introduce bias in transcript counts. In this study, we investigate the impact of input amount and PCR cycle number on the PCR duplication rate and on the RNA-seq data quality. We used a range of inputs (1 ng - 1,000 ng) and assessed the PCR duplication rate using unique molecular identifiers (UMIs). For broader applicability, we sequenced the data on four different short-read sequencing platforms: Illumina NovaSeq 6000, Illumina NovaSeq X, Element Biosciences AVITI, and Singular Genomics G4. We highlight the limitations of using input amounts below 125 ng and the advantages for using UMIs for deduplication. We contrast the data obtained from different sequencers and discuss the benefits and drawbacks of using Illumina library conversion kits.

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Project description:In this study, we examined the consequences of the early stress (ES) of maternal separation on hippocampal gene expression in young adulthood. Young adult (2 months old) ES animals exhibit hippocampal transcriptome changes with a significant regulation of genes associated with intracellular signaling, MAP kinase signaling, plasma membrane function, neurotransmitter and neuropeptide receptors and cytoskeletal components. Agilent one-color experiment, Agilent-024724 Genotypic-designed Custom Rattus Norvegicus 8x15k; Organism: Rattus norvegicus; Labeling kit: Agilent Quick-Amp labeling Kit (p/n5190-0442); Biological replicates: 4 per treatment group.

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To examine the influence of the early stress of maternal separation on the hippocampal transcriptome in middle-aged life

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