ArticlePloS one2011
An RNA-Seq strategy to detect the complete coding and non-coding transcriptome including full-length imprinted macro ncRNAs.
Article in PloS one, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 69 papers.
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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
69 citing papers in PubMed, 118 citations in OpenAlex.
- The lncRNA PACER Regulates Lung Adenocarcinoma Phenotypes via COX-2 Signaling and RNA Structural Dynamics.bioRxiv : the preprint server for biology · 2025Article
- Isogenic comparison of Airn and Xist reveals core principles of Polycomb recruitment by lncRNAs.Molecular cell · 2025Article
- EFFICIENT RIBOSOMAL RNA DEPLETION FROMWellcome open research · 2025Article
- RAG-seq: NSR-primed and Transposase Tagmentation-mediated Strand-specific Total RNA Sequencing in Single Cells.Genomics, proteomics & bioinformatics · 2024Article
- Single-cell RNA sequencing of nc886, a non-coding RNA transcribed by RNA polymerase III, with a primer spike-in strategy.PloS one · 2024Article
- Imprinted Long Non-Coding RNAs in Mammalian Development and Disease.International journal of molecular sciences · 2023Review
- Proximity-dependent recruitment of Polycomb repressive complexes by the lncRNA Airn.Cell reports · 2023Article
- Human placental microRNAs dysregulated by cadmium exposure predict neurobehavioral outcomes at birth.Pediatric research · 2023Article
- A method for simultaneous detection of small and long RNA biotypes by ribodepleted RNA-Seq.Scientific reports · 2022Article
- Perspectives on Bulk-Tissue RNA Sequencing and Single-Cell RNA Sequencing for Cardiac Transcriptomics.Frontiers in molecular medicine · 2022Review
- The control of polycomb repressive complexes by long noncoding RNAs.Wiley interdisciplinary reviews. RNA · 2021Review
- Bias in RNA-seq Library Preparation: Current Challenges and Solutions.BioMed research international · 2021Review
- Article
- Review
- Long noncoding RNA functionality in imprinted domain regulation.PLoS genetics · 2020Review
- A reverse transcriptase-mediated ribosomal RNA depletion (RTR2D) strategy for the cost-effective construction of RNA sequencing libraries.Journal of advanced research · 2020Article
- Common gene expression signatures in Parkinson's disease are driven by changes in cell composition.Acta neuropathologica communications · 2020Article
- Copper associates with differential methylation in placentae from two US birth cohorts.Epigenetics · 2020Article
- Article
- Placental lncRNA expression associated with placental cadmium concentrations and birth weight.Environmental epigenetics · 2020Article
9 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
12 authors at 4 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Imprinted macro non-protein-coding (nc) RNAs are cis-repressor transcripts that silence multiple genes in at least three imprinted gene clusters in the mouse genome. Similar macro or long ncRNAs are abundant in the mammalian genome. Here we present the full coding and non-coding transcriptome of two mouse tissues: differentiated ES cells and fetal head using an optimized RNA-Seq strategy. The data produced is highly reproducible in different sequencing locations and is able to detect the full length of imprinted macro ncRNAs such as Airn and Kcnq1ot1, whose length ranges between 80-118 kb. Transcripts show a more uniform read coverage when RNA is fragmented with RNA hydrolysis compared with cDNA fragmentation by shearing. Irrespective of the fragmentation method, all coding and non-coding transcripts longer than 8 kb show a gradual loss of sequencing tags towards the 3' end. Comparisons to published RNA-Seq datasets show that the strategy presented here is more efficient in detecting known functional imprinted macro ncRNAs and also indicate that standardization of RNA preparation protocols would increase the comparability of the transcriptome between different RNA-Seq datasets.
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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.