ArticleBMC genomics2022
Quantitative analysis of transcriptome dynamics provides novel insights into developmental state transitions.
Article in BMC genomics, 2022. 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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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
10 citing papers in PubMed, 12 citations in OpenAlex.
- Analyzing Co-expression Networks with Network Skeleton Extraction.Research square · 2026Article
- Dynamic and non-uniform expression of key transcription factors provides insights into the emergence of neural crest cells at the neural plate border.Development (Cambridge, England) · 2026Article
- Wdr5 and Myc cooperate to regulate formation of neural crest stem cells.Development (Cambridge, England) · 2026Article
- Krüppel-like factors play essential roles in regulating pluripotency and the formation of neural crest stem cells.Development (Cambridge, England) · 2025Article
- Basal Xenobot transcriptomics reveals changes and novel control modality in cells freed from organismal influence.Communications biology · 2025Article
- Shared features of blastula and neural crest stem cells evolved at the base of vertebrates.Nature ecology & evolution · 2024Article
- SoxB1 transcription factors are essential for initiating and maintaining neural plate border gene expression.Development (Cambridge, England) · 2024Article
- BET activity plays an essential role in control of stem cell attributes in Xenopus.Development (Cambridge, England) · 2024Article
- Small molecule-mediated reprogramming of Xenopus blastula stem cells to a neural crest state.Developmental biology · 2024Article
- Article
Corrections and comments
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Authors and funding
4 authors at 2 institutions in 2 countries.
Funding
Abstract
backgroundDuring embryogenesis, the developmental potential of initially pluripotent cells becomes progressively restricted as they transit to lineage restricted states. The pluripotent cells of Xenopus blastula-stage embryos are an ideal system in which to study cell state transitions during developmental decision-making, as gene expression dynamics can be followed at high temporal resolution.
resultsHere we use transcriptomics to interrogate the process by which pluripotent cells transit to four different lineage-restricted states: neural progenitors, epidermis, endoderm and ventral mesoderm, providing quantitative insights into the dynamics of Waddington's landscape. Our findings provide novel insights into why the neural progenitor state is the default lineage state for pluripotent cells and uncover novel components of lineage-specific gene regulation. These data reveal an unexpected overlap in the transcriptional responses to BMP4/7 and Activin signaling and provide mechanistic insight into how the timing of signaling inputs such as BMP are temporally controlled to ensure correct lineage decisions.
conclusionsTogether these analyses provide quantitative insights into the logic and dynamics of developmental decision making in early embryos. They also provide valuable lineage-specific time series data following the acquisition of specific lineage states during development.
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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 Socratic graph.