ArticleCurrent protocols in human genetics2014
RNA-seq Data: Challenges in and Recommendations for Experimental Design and Analysis.
Article in Current protocols in human genetics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 52 papers, 1 of them a synthesis that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
The trial behind it
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
52 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Transcriptomic Profile of Glioblastoma Cells Infected with Zika Virus: A Systematic Review and Pathway Analysis.Viruses · 2026Pooled it
- Response to geographic song variation predicts differential gene expression in the blood of a songbird.iScience · 2026Article
- Genomic diversification between aposematic and cryptic phenotypes of Oophaga granulifera (Anura: Dendrobatidae).Scientific reports · 2026Article
- Nanopore direct RNA sequencing and the epitranscriptome: Advances in mapping native RNA landscapes.iMeta · 2026Review
- The transcriptomics and differential gene expression of freezing and thawing in a freeze-tolerant vertebrate.BMC genomics · 2026Article
- BIOGEN: evidence-grounded multi-agent reasoning framework for transcriptomic interpretation in antimicrobial resistance.Frontiers in bioinformatics · 2026Article
- Designing RNA sequencing experiments: A practical guide to reproducible gene expression analysis.Computational and structural biotechnology journal · 2026Review
- Article
- Self-organizing maps for allele specific expression data reconstruction and identification of anomalous genomic regions.Frontiers in bioinformatics · 2026Article
- Technical considerations and review of urinary microRNAs as biomarkers for chronic kidney disease in dogs and cats.Veterinary clinical pathology · 2025Review
- Exploring Alternative Splicing in Response to Salinity: A Tissue-Level Comparative Analysis UsingPlants (Basel, Switzerland) · 2025Article
- Differential Expression of Small Non-Coding RNAs in Uterine Leiomyomas.International journal of molecular sciences · 2025Article
- Prostaglandin D2 receptor 2 downstream signaling and modulation of type 2 innate lymphoid cells from patients with asthma.PloS one · 2024Article
- Integrative analysis of Iso-Seq and RNA-seq reveals dynamic changes of alternative promoter, alternative splicing and alternative polyadenylation during Angiotensin II-induced senescence in rat primary aortic endothelial cells.Frontiers in genetics · 2023Article
- Design, execution, and interpretation of plant RNA-seq analyses.Frontiers in plant science · 2023Review
- Article
- Article
- Powerful eQTL mapping through low-coverage RNA sequencing.HGG advances · 2022Article
- Transcriptomic Profile of Canine DH82 Macrophages Infected byInternational journal of molecular sciences · 2022Article
- Comment on 'SARS-CoV-2 suppresses anticoagulant and fibrinolytic gene expression in the lung'.eLife · 2022Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
Abstract
RNA-seq is widely used to determine differential expression of genes or transcripts as well as identify novel transcripts, identify allele-specific expression, and precisely measure translation of transcripts. Thoughtful experimental design and choice of analysis tools are critical to ensure high-quality data and interpretable results. Important considerations for experimental design include number of replicates, whether to collect paired-end or single-end reads, sequence length, and sequencing depth. Common analysis steps in all RNA-seq experiments include quality control, read alignment, assigning reads to genes or transcripts, and estimating gene or transcript abundance. Our aims are two-fold: to make recommendations for common components of experimental design and assess tool capabilities for each of these steps. We also test tools designed to detect differential expression, since this is the most widespread application of RNA-seq. We hope that these analyses will help guide those who are new to RNA-seq and will generate discussion about remaining needs for tool improvement and development.
Indexed as
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What OpenQuestion holds
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.