ArticleFrontiers in genetics2013
Comparison of Analysis Tools for miRNA High Throughput Sequencing Using Nerve Crush as a Model.
Article in Frontiers in genetics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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
27 citing papers in PubMed.
- Trial
- miR-193-5p, miR-1307-5p, and miR-671-5p: Potential biomarkers for chemoresistance in diffuse large B-cell lymphoma.The Indian journal of medical research · 2026Review
- Standardization of preclinical methodologies for discovery and validation of circulating microRNA biomarkers for post-traumatic epileptogenesis - Lessons learned from the EpiBioS4Rx Project 1.Epilepsy research · 2025Article
- Beyond CSF and Neuroimaging Assessment: Evaluating Plasma miR-145-5p as a Potential Biomarker for Mild Cognitive Impairment and Alzheimer's Disease.ACS chemical neuroscience · 2024Article
- Revised Annotation and Characterization of NovelBiology · 2022Article
- A Pilot Study of miRNA Expression Profile as a Liquid Biopsy for Full-Marathon Participants.Sports (Basel, Switzerland) · 2021Article
- A Set of 17 microRNAs Common for Brain and Cerebrospinal Fluid Differentiates Primary Central Nervous System Lymphoma from Non-Malignant Brain Tumors.Biomolecules · 2021Article
- Circulating exosomal microRNA expression patterns distinguish cardiac sarcoidosis from myocardial ischemia.PloS one · 2021Article
- A mouse tissue atlas of small noncoding RNA.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Bringing MicroRNAs to Light: Methods for MicroRNA Quantification and Visualization in Live Cells.Frontiers in bioengineering and biotechnology · 2020Review
- HNRNPA2/B1 is upregulated in endocrine-resistant LCC9 breast cancer cells and alters the miRNA transcriptome when overexpressed in MCF-7 cells.Scientific reports · 2019Article
- Circulating microRNA and automated motion analysis as novel methods of assessing chemotherapy-induced peripheral neuropathy in mice.PloS one · 2019Article
- Identification of key differentially expressed MicroRNAs in cancer patients through pan-cancer analysis.Computers in biology and medicine · 2018Article
- The microRNA miR-192/215 family is upregulated in mucinous ovarian carcinomas.Scientific reports · 2018Article
- Evaluation of Bioinformatics Approaches for Next-Generation Sequencing Analysis of microRNAs with a Toxicogenomics Study Design.Frontiers in genetics · 2018Article
- A comprehensive, cell specific microRNA catalogue of human peripheral blood.Nucleic acids research · 2017Article
- Enhancing identification of cancer types via lowly-expressed microRNAs.Nucleic acids research · 2017Article
- Small RNA Sequencing of Sporadic Amyotrophic Lateral Sclerosis Cerebrospinal Fluid Reveals Differentially Expressed miRNAs Related to Neural and Glial Activity.Frontiers in neuroscience · 2017Article
- Identification of drought-responsive microRNAs and their targets in Ammopiptanthus mongolicus by using high-throughput sequencing.Scientific reports · 2016Article
- Toward reliable biomarker signatures in the age of liquid biopsies - how to standardize the small RNA-Seq workflow.Nucleic acids research · 2016Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
9 authors.
Funding
Abstract
Recent advances in sample preparation and analysis for next generation sequencing have made it possible to profile and discover new miRNAs in a high throughput manner. In the case of neurological disease and injury, these types of experiments have been more limited. Possibly because tissues such as the brain and spinal cord are inaccessible for direct sampling in living patients, and indirect sampling of blood and cerebrospinal fluid are affected by low amounts of RNA. We used a mouse model to examine changes in miRNA expression in response to acute nerve crush. We assayed miRNA from both muscle tissue and blood plasma. We examined how the depth of coverage (the number of mapped reads) changed the number of detectable miRNAs in each sample type. We also found that samples with very low starting amounts of RNA (mouse plasma) made high depth of mature miRNA coverage more difficult to obtain. Each tissue must be assessed independently for the depth of coverage required to adequately power detection of differential expression, weighed against the cost of sequencing that sample to the adequate depth. We explored the changes in total mapped reads and differential expression results generated by three different software packages: miRDeep2, miRNAKey, and miRExpress and two different analysis packages, DESeq and EdgeR. We also examine the accuracy of using miRDeep2 to predict novel miRNAs and subsequently detect them in the samples using qRT-PCR.
Indexed as
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.