ArticleBMC genomics2013
Comparison of RNA- or LNA-hybrid oligonucleotides in template-switching reactions for high-speed sequencing library preparation.
Article in BMC genomics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 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
16 citing papers in PubMed.
- Plate-based 10X Genomics-compatible single-cell RNA-sequencing based on Smart-seq3xpress.BMC genomics · 2025Article
- Single-cell mapping of alternative splicing linked to checkpoint immunotherapy response.Nucleic acids research · 2025Article
- Fast and highly sensitive full-length single-cell RNA sequencing using FLASH-seq.Nature biotechnology · 2022Article
- Isoform-resolved mRNA profiling of ribosome load defines interplay of HIF and mTOR dysregulation in kidney cancer.Nature structural & molecular biology · 2022Article
- A versatile 5' RACE-Seq methodology for the accurate identification of the 5' termini of mRNAs.BMC genomics · 2022Article
- TASPERT: Target-Specific Reverse Transcript Pools to Improve HTS Plant Virus Diagnostics.Viruses · 2021Article
- Machine-driven parameter screen of biochemical reactions.Nucleic acids research · 2020Article
- Poly(A)-seq: A method for direct sequencing and analysis of the transcriptomic poly(A)-tails.PloS one · 2020Article
- Single-cell transcriptome analysis of Physcomitrella leaf cells during reprogramming using microcapillary manipulation.Nucleic acids research · 2019Article
- NanoPARE: parallel analysis of RNA 5' ends from low-input RNA.Genome research · 2018Article
- Optimization of single strand DNA incorporation reaction by Moloney murine leukaemia virus reverse transcriptase.DNA research : an international journal for rapid publication of reports on genes and genomes · 2018Article
- Tn5Prime, a Tn5 based 5' capture method for single cell RNA-seq.Nucleic acids research · 2018Article
- A cost effective 5΄ selective single cell transcriptome profiling approach with improved UMI design.Nucleic acids research · 2017Article
- Comprehensive promoter level expression quantitative trait loci analysis of the human frontal lobe.Genome medicine · 2016Article
- C9orf72 is differentially expressed in the central nervous system and myeloid cells and consistently reduced in C9orf72, MAPT and GRN mutation carriers.Acta neuropathologica communications · 2016Article
- Developmental Progression in the Coral Acropora digitifera Is Controlled by Differential Expression of Distinct Regulatory Gene Networks.Genome biology and evolution · 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
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundAnalyzing the RNA pool or transcription start sites requires effective means to convert RNA into cDNA libraries for digital expression counting. With current high-speed sequencers, it is necessary to flank the cDNAs with specific adapters. Adding template-switching oligonucleotides to reverse transcription reactions is the most commonly used approach when working with very small quantities of RNA even from single cells.
resultsHere we compared the performance of DNA-RNA, DNA-LNA and DNA oligonucleotides in template-switching during nanoCAGE library preparation. Test libraries from rat muscle and HeLa cell RNA were prepared in technical triplicates and sequenced for comparison of the gene coverage and distribution of the reads within transcripts. The DNA-RNA oligonucleotide showed the highest specificity for capped 5' ends of mRNA, whereas the DNA-LNA provided similar gene coverage with more reads falling within exons.
conclusionsWhile confirming the cap-specific preference of DNA-RNA oligonucleotides in template-switching reactions, our data indicate that DNA-LNA hybrid oligonucleotides could potentially find other applications in random RNA sequencing.
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.