ArticleScientific reports2017
High resolution temporal transcriptomics of mouse embryoid body development reveals complex expression dynamics of coding and noncoding loci.
Article in Scientific reports, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
What it found
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Who cites it
10 citing papers in PubMed, 12 citations in OpenAlex.
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- Dynamics in zebrafish development define transcriptomic specificity after angiogenesis inhibitor exposure.Archives of toxicology · 2025Article
- CCIVR2 facilitates comprehensive identification of both overlapping and non-overlapping antisense transcripts within specified regions.Scientific reports · 2023Article
- Experimental Design for Time-Series RNA-Seq Analysis of Gene Expression and Alternative Splicing.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Deciphering the Nature ofCancers · 2021Article
- Three Lessons from Accelerating Scientific Insight Discovery via Visual Querying.Patterns (New York, N.Y.) · 2020Article
- Automated minute scale RNA-seq of pluripotent stem cell differentiation reveals early divergence of human and mouse gene expression kinetics.PLoS computational biology · 2019Article
- Time-resolved transcriptomics in neural stem cells identifies a v-ATPase/Notch regulatory loop.The Journal of cell biology · 2018Article
- Rapid and Dynamic Alternative Splicing Impacts the Arabidopsis Cold Response Transcriptome.The Plant cell · 2018Article
- Intergenic disease-associated regions are abundant in novel transcripts.Genome biology · 2017Article
Corrections and comments
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Authors and funding
7 authors at 4 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Cellular responses to stimuli are rapid and continuous and yet the vast majority of investigations of transcriptional responses during developmental transitions typically use long interval time courses; limiting the available interpretive power. Moreover, such experiments typically focus on protein-coding transcripts, ignoring the important impact of long noncoding RNAs. We therefore evaluated coding and noncoding expression dynamics at unprecedented temporal resolution (6-hourly) in differentiating mouse embryonic stem cells and report new insight into molecular processes and genome organization. We present a highly resolved differentiation cascade that exhibits coding and noncoding transcriptional alterations, transcription factor network interactions and alternative splicing events, little of which can be resolved by long-interval developmental time-courses. We describe novel short lived and cycling patterns of gene expression and dissect temporally ordered gene expression changes in response to transcription factors. We elucidate patterns in gene co-expression across the genome, describe asynchronous transcription at bidirectional promoters and functionally annotate known and novel regulatory lncRNAs. These findings highlight the complex and dynamic molecular events underlying mammalian differentiation that can only be observed though a temporally resolved time course.
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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.