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Common cell lysis procedures distort ribosome profiling analyses of gene expression

ABSTRACT: Common cell lysis procedures distort ribosome profiling analyses of gene expression

PROVIDER: PRJNA1148174 | ENA |

REPOSITORIES: ENA

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			Action	DRS
		Other
	SRR30244812_1.fastq.gz	Fastqsanger.gz
	SRR30244812_2.fastq.gz	Fastqsanger.gz
	SRR30244814.fastq.gz	Fastqsanger.gz
	SRR30244816_1.fastq.gz	Fastqsanger.gz

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Common cell lysis procedures distort ribosome profiling analyses of gene expression

Project description:Ribosome profiling is a powerful technique used to study gene expression on a transcriptome-wide scale. It involves sequencing of mRNA fragments protected by ribosomes from ribonuclease digestion. The initial steps commonly involve cell lysis followed by centrifugation and ribonuclease digestion. We find that centrifugation depletes 329 translated mRNAs in HEK293T cells. Many of these mRNAs encode cytoskeleton proteins. This suggests that the expression of a subset of mRNAs may be significantly underestimated in most ribosome profiling experiments. We show that omitting the centrifugation step after cell lysis can resolve this issue.

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Humans and other commonly used model organisms are resistant to cycloheximide-mediated biases in ribosome profiling experiments

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