ArticlePloS one2014
Sequencing degraded RNA addressed by 3' tag counting.
Article in PloS one, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 64 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
64 citing papers in PubMed, 113 citations in OpenAlex.
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- Enhanced RNA Preservation in Mouse Brain Tissue: A Strategy Combining Cardiac Perfusion with Hypersaline Immersion.ACS omega · 2025Article
- The effects of space radiation on the transcriptome of heart right ventricle tissue.NPJ microgravity · 2025Article
- Your Blood is Out for Delivery: Considerations of Shipping Time and Temperature on Degradation of RNA from Stabilized Whole Blood.Analytical chemistry · 2025Article
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- Your Blood is Out for Delivery: Considerations of Shipping Time and Temperature on Degradation of RNA from Stabilized Whole Blood.bioRxiv : the preprint server for biology · 2024Article
- The hidden RNA viruses inMicrobial genomics · 2024Article
- Spitting in the wind?-The challenges of RNA sequencing for biomarker discovery from saliva.International journal of legal medicine · 2024Article
- CRISPR activation to characterize splice-altering variants in easily accessible cells.American journal of human genetics · 2024Article
- Transcriptomic Analysis of the Effect of Torin-2 on the Central Nervous System ofInternational journal of molecular sciences · 2023Article
- Transcriptome Analysis of Redox Systems and Polyamine Metabolic Pathway in Hepatoma and Non-Tumor Hepatocyte-like Cells.Biomolecules · 2023Article
- Integrated transcriptome landscape of ALS identifies genome instability linked to TDP-43 pathology.Nature communications · 2023Article
- Article
- 3' RNA-seq is superior to standard RNA-seq in cases of sparse data but inferior at identifying toxicity pathways in a model organism.Frontiers in bioinformatics · 2023Article
- An optimized method for high-quality RNA extraction from distinctive intrinsic laryngeal muscles in the rat model.Scientific reports · 2022Article
- Generalized nuclear localization of retroelement transcripts.Mobile DNA · 2022Article
- Optimization of RNA extraction for bacterial whole transcriptome studies of low-biomass samples.iScience · 2022Article
4 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
RNA sequencing has become widely used in gene expression profiling experiments. Prior to any RNA sequencing experiment the quality of the RNA must be measured to assess whether or not it can be used for further downstream analysis. The RNA integrity number (RIN) is a scale used to measure the quality of RNA that runs from 1 (completely degraded) to 10 (intact). Ideally, samples with high RIN (> 8) are used in RNA sequencing experiments. RNA, however, is a fragile molecule which is susceptible to degradation and obtaining high quality RNA is often hard, or even impossible when extracting RNA from certain clinical tissues. Thus, occasionally, working with low quality RNA is the only option the researcher has. Here we investigate the effects of RIN on RNA sequencing and suggest a computational method to handle data from samples with low quality RNA which also enables reanalysis of published datasets. Using RNA from a human cell line we generated and sequenced samples with varying RINs and illustrate what effect the RIN has on the basic procedure of RNA sequencing; both quality aspects and differential expression. We show that the RIN has systematic effects on gene coverage, false positives in differential expression and the quantification of duplicate reads. We introduce 3' tag counting (3TC) as a computational approach to reliably estimate differential expression for samples with low RIN. We show that using the 3TC method in differential expression analysis significantly reduces false positives when comparing samples with different RIN, while retaining reasonable sensitivity.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.