ArticleCell stem cell2015
Single Cell RNA-Sequencing of Pluripotent States Unlocks Modular Transcriptional Variation.
Article in Cell stem cell, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 287 papers, 1 of them a synthesis that pooled it.
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
287 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Guidelines for bioinformatics of single-cell sequencing data analysis in Alzheimer's disease: review, recommendation, implementation and application.Molecular neurodegeneration · 2022Pooled it
- Developmental and tissue expression breadth define distinct but overlapping classes of housekeeping genes.PLoS computational biology · 2026Article
- Single-cell marker gene clustering: A unified deep learning framework for marker gene-based clustering of single-cell RNA-sequencing data.Quantitative biology (Beijing, China) · 2026Article
- scFANCL: Dual contrastive learning with false-negative correction at cell level for single-cell RNA-seq clustering.BMC genomics · 2026Article
- CycleVI: isolating cell cycle variation with an interpretable deep generative model.Bioinformatics (Oxford, England) · 2026Article
- Joint Low Rank Representation with Symmetric Orthogonal Decomposition for Clustering of scRNA-seq Data.Interdisciplinary sciences, computational life sciences · 2026Article
- Serum coating enables feeder-free culture of naive human pluripotent stem cells preserving developmental potential.The EMBO journal · 2026Article
- Compact and informative representation learning for scRNA-seq data clustering with masked information bottleneck.BMC biology · 2026Article
- Gateway analysis reveals transient molecular programs at cell-fate transitions.bioRxiv : the preprint server for biology · 2026Article
- scSCCNIA: similarity matrix based contrastive clustering with neighbor information aggregation for single-cell RNA sequencing data.Briefings in bioinformatics · 2026Article
- Distinct roles for SETα and SETβ in early cell fate decisions.Nucleic acids research · 2026Article
- Landscape of microRNA and target expression variation and covariation in single mouse embryonic stem cells.Genome research · 2026Article
- Optimization of Gastruloid Pre-culture Conditions for Reproducible Germ Layer Composition.Methods in molecular biology (Clifton, N.J.) · 2026Article
- CycleMix: Gaussian mixture modeling of the cell cycle.Bioinformatics advances · 2026Article
- Development and comparison of evaluation metrics for batch correction reveals performance differences.Bioinformatics advances · 2026Article
- Single-cell dynamics of genome-nucleolus interactions captured by nucleolar laser microdissection (NoLMseq).Nature communications · 2025Article
- Natural variation in regulatory code revealed through Bayesian analysis of plant pan-genomes and pan-transcriptomes.bioRxiv : the preprint server for biology · 2025Article
- A novel gene expression stability metric to unveil homeostasis and regulation.Genome biology · 2025Article
- Network based simultaneous embedding of cells and marker genes from scRNA-seq studies.Briefings in bioinformatics · 2025Article
- USP17L promotes the 2-cell-like program through deubiquitination of H2AK119ub1 and ZSCAN4.Nature communications · 2025Article
227 more citing papers are in PubMed but not listed here.
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Authors and funding
12 authors.
Funding
Abstract
Embryonic stem cell (ESC) culture conditions are important for maintaining long-term self-renewal, and they influence cellular pluripotency state. Here, we report single cell RNA-sequencing of mESCs cultured in three different conditions: serum, 2i, and the alternative ground state a2i. We find that the cellular transcriptomes of cells grown in these conditions are distinct, with 2i being the most similar to blastocyst cells and including a subpopulation resembling the two-cell embryo state. Overall levels of intercellular gene expression heterogeneity are comparable across the three conditions. However, this masks variable expression of pluripotency genes in serum cells and homogeneous expression in 2i and a2i cells. Additionally, genes related to the cell cycle are more variably expressed in the 2i and a2i conditions. Mining of our dataset for correlations in gene expression allowed us to identify additional components of the pluripotency network, including Ptma and Zfp640, illustrating its value as a resource for future discovery.
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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.