Dataset Information

Multiple freeze-thaw cycles lead to a loss of consistency in poly(A)-enriched RNA sequencing.

ABSTRACT:

Background

Both RNA-Seq and sample freeze-thaw are ubiquitous. However, knowledge about the impact of freeze-thaw on downstream analyses is limited. The lack of common quality metrics that are sufficiently sensitive to freeze-thaw and RNA degradation, e.g. the RNA Integrity Score, makes such assessments challenging.

Results

Here we quantify the impact of repeated freeze-thaw cycles on the reliability of RNA-Seq by examining poly(A)-enriched and ribosomal RNA depleted RNA-seq from frozen leukocytes drawn from a toddler Autism cohort. To do so, we estimate the relative noise, or percentage of random counts, separating technical replicates. Using this approach we measured noise associated with RIN and freeze-thaw cycles. As expected, RIN does not fully capture sample degradation due to freeze-thaw. We further examined differential expression results and found that three freeze-thaws should extinguish the differential expression reproducibility of similar experiments. Freeze-thaw also resulted in a 3' shift in the read coverage distribution along the gene body of poly(A)-enriched samples compared to ribosomal RNA depleted samples, suggesting that library preparation may exacerbate freeze-thaw-induced sample degradation.

Conclusion

The use of poly(A)-enrichment for RNA sequencing is pervasive in library preparation of frozen tissue, and thus, it is important during experimental design and data analysis to consider the impact of repeated freeze-thaw cycles on reproducibility.

SUBMITTER: Kellman BP

PROVIDER: S-EPMC7818915 | biostudies-literature | 2021 Jan

REPOSITORIES: biostudies-literature

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Publications

Multiple freeze-thaw cycles lead to a loss of consistency in poly(A)-enriched RNA sequencing.

Kellman Benjamin P BP Baghdassarian Hratch M HM Pramparo Tiziano T Shamie Isaac I Gazestani Vahid V Begzati Arjana A Li Shangzhong S Nalabolu Srinivasa S Murray Sarah S Lopez Linda L Pierce Karen K Courchesne Eric E Lewis Nathan E NE

BMC genomics 20210121 1

<h4>Background</h4>Both RNA-Seq and sample freeze-thaw are ubiquitous. However, knowledge about the impact of freeze-thaw on downstream analyses is limited. The lack of common quality metrics that are sufficiently sensitive to freeze-thaw and RNA degradation, e.g. the RNA Integrity Score, makes such assessments challenging.<h4>Results</h4>Here we quantify the impact of repeated freeze-thaw cycles on the reliability of RNA-Seq by examining poly(A)-enriched and ribosomal RNA depleted RNA-seq from ...[more]

PMID: 33478392

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Dataset Information

Multiple freeze-thaw cycles lead to a loss of consistency in poly(A)-enriched RNA sequencing.

Background

Results

Conclusion

Publications

Multiple freeze-thaw cycles lead to a loss of consistency in poly(A)-enriched RNA sequencing.

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