ArticleBMC research notes2010
RNA isolation method for single embryo transcriptome analysis in zebrafish.
Article in BMC research notes, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed, 47 citations in OpenAlex.
- shox2 is required for vestibular statoacoustic neuron development.Biology open · 2022Article
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- Zebrafish models of alx-linked frontonasal dysplasia reveal a role for Alx1 and Alx3 in the anterior segment and vasculature of the developing eye.Biology open · 2022Article
- Total Nucleic Acid Extraction from Single Zebrafish Embryos for Genotyping and RNA-seq.Bio-protocol · 2022Article
- Evaluation of Metal-Organic Framework MIL-89 nanoparticles toxicity on embryonic zebrafish development.Toxicology reports · 2022Article
- Coagulation Factor IIIa (Frontiers in cell and developmental biology · 2022Article
- Fibroblast Growth Factor Receptors Function Redundantly During Zebrafish Embryonic Development.Genetics · 2019Article
- Article
- Zebrafish Rfx4 controls dorsal and ventral midline formation in the neural tube.Developmental dynamics : an official publication of the American Association of Anatomists · 2018Article
- Multidimensional quantitative analysis of mRNA expression within intact vertebrate embryos.Development (Cambridge, England) · 2018Article
- Article
- Zebrafish zic2 controls formation of periocular neural crest and choroid fissure morphogenesis.Developmental biology · 2017Article
- Transcriptome dynamics in early zebrafish embryogenesis determined by high-resolution time course analysis of 180 successive, individual zebrafish embryos.BMC genomics · 2017Article
- Mother-Specific Signature in the Maternal Transcriptome Composition of Mature, Unfertilized Zebrafish Eggs.PloS one · 2016Article
- De Novo Assembly of Bitter Gourd Transcriptomes: Gene Expression and Sequence Variations in Gynoecious and Monoecious Lines.PloS one · 2015Article
- Possible effects of EXT2 on mesenchymal differentiation--lessons from the zebrafish.Orphanet journal of rare diseases · 2014Article
- Functional analysis of a zebrafish myd88 mutant identifies key transcriptional components of the innate immune system.Disease models & mechanisms · 2013Article
- Nrf2b, novel zebrafish paralog of oxidant-responsive transcription factor NF-E2-related factor 2 (NRF2).The Journal of biological chemistry · 2012Article
- Pathogen recognition and activation of the innate immune response in zebrafish.Advances in hematology · 2012Article
- RNA isolation for transcriptomics of human and mouse small skin biopsies.BMC research notes · 2011Article
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 at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundTranscriptome analysis during embryogenesis usually requires pooling of embryos to obtain sufficient RNA. Hence, the measured levels of gene-expression represent the average mRNA levels of pooled samples and the biological variation among individuals is confounded. This can irreversibly reduce the robustness, resolution, or expressiveness of the experiment. Therefore, we developed a robust method to isolate abundant high-quality RNA from individual embryos to perform single embryo transcriptome analyses using zebrafish as a model organism. Available methods for embryonic zebrafish RNA isolation minimally utilize ten embryos. Further downscaling of these methods to one embryo is practically not feasible.
findingsWe developed a single embryo RNA extraction method based on sample homogenization in liquid nitrogen, RNA extraction with phenol and column purification. Evaluation of this method showed that: the quality of the RNA was very good with an average RIN value of 8.3-8.9; the yield was always >/= 200 ng RNA per embryo; the method was applicable to all stages of zebrafish embryogenesis; the success rate was almost 100%; and the extracted RNA performed excellent in microarray experiments in that the technical variation was much lower than the biological variation.
conclusionsPresented is a high-quality, robust RNA isolation method. Obtaining sufficient RNA from single embryos eliminates the necessity of sample pooling and its associated drawbacks. Although our RNA isolation method has been setup for transcriptome analysis in zebrafish, it can also be used for other model systems and other applications like (q)PCR and transcriptome sequencing.
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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.