ArticleSilence2011
Experimental design, preprocessing, normalization and differential expression analysis of small RNA sequencing experiments.
Article in Silence, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 51 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.
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
51 citing papers in PubMed.
- A method of comprehensive sequencing analysis of the small RNA fragmentome (RiboMarker).RNA (New York, N.Y.) · 2026Article
- Small RNA sequencing provides insights into molecular mechanism of flower development in Rhododendron pulchrum Sweet.Scientific reports · 2023Article
- DNA methylation in transposable elements buffers the connection between three-dimensional chromatin organization and gene transcription upon rice genome duplication.Journal of advanced research · 2022Article
- Quality control and evaluation of plant epigenomics data.The Plant cell · 2022Article
- Profile of Small RNAs, vDNA Forms and Viral Integrations in Late Chikungunya Virus Infection ofViruses · 2021Article
- Oxidative Phosphorylation Is Dysregulated Within the Basocortical Circuit in a 6-month old Mouse Model of Down Syndrome and Alzheimer's Disease.Frontiers in aging neuroscience · 2021Article
- Decreasing miRNA sequencing bias using a single adapter and circularization approach.Genome biology · 2018Article
- Identification of novel ΔNp63α-regulated miRNAs using an optimized small RNA-Seq analysis pipeline.Scientific reports · 2018Article
- Threshold-dependent repression of SPL gene expression by miR156/miR157 controls vegetative phase change in Arabidopsis thaliana.PLoS genetics · 2018Article
- miRCat2: accurate prediction of plant and animal microRNAs from next-generation sequencing datasets.Bioinformatics (Oxford, England) · 2017Article
- Comprehensive processing of high-throughput small RNA sequencing data including quality checking, normalization, and differential expression analysis using the UEA sRNA Workbench.RNA (New York, N.Y.) · 2017Article
- MicroRNAs Associated with Caste Determination and Differentiation in a Primitively Eusocial Insect.Scientific reports · 2017Article
- Considerations and complications of mapping small RNA high-throughput data to transposable elements.Mobile DNA · 2017Article
- Toward reliable biomarker signatures in the age of liquid biopsies - how to standardize the small RNA-Seq workflow.Nucleic acids research · 2016Article
- Small RNA and PARE sequencing in flower bud reveal the involvement of sRNAs in endodormancy release of Japanese pear (Pyrus pyrifolia 'Kosui').BMC genomics · 2016Article
- Mobile small RNAs regulate genome-wide DNA methylation.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
- Article
- The Influence of Genotype and Environment on Small RNA Profiles in Grapevine Berry.Frontiers in plant science · 2016Article
- Screening for the optimal gene and functional gene sets related to breast cancer using differential co-expression and differential expression analysis.Cancer biomarkers : section A of Disease markers · 2016Article
- Autotetraploid rice methylome analysis reveals methylation variation of transposable elements and their effects on gene expression.Proceedings of the National Academy of Sciences of the United States of America · 2015Article
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.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Prior to the advent of new, deep sequencing methods, small RNA (sRNA) discovery was dependent on Sanger sequencing, which was time-consuming and limited knowledge to only the most abundant sRNA. The innovation of large-scale, next-generation sequencing has exponentially increased knowledge of the biology, diversity and abundance of sRNA populations. In this review, we discuss issues involved in the design of sRNA sequencing experiments, including choosing a sequencing platform, inherent biases that affect sRNA measurements and replication. We outline the steps involved in preprocessing sRNA sequencing data and review both the principles behind and the current options for normalization. Finally, we discuss differential expression analysis in the absence and presence of biological replicates. While our focus is on sRNA sequencing experiments, many of the principles discussed are applicable to the sequencing of other RNA populations.
Identifiers
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.