ArticleGenome research2018
Single-cell RNA-seq of human induced pluripotent stem cells reveals cellular heterogeneity and cell state transitions between subpopulations.
Article in Genome research, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 74 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
The trial behind it
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
74 citing papers in PubMed.
- Molecular profiling of the single-cell proteome via gel electrophoresis and 3D single-molecule imaging.Nature communications · 2026Article
- Article
- Article
- Single cell transcriptional perturbome in pluripotent stem cell models.Molecular systems biology · 2026Article
- Single nuclei and spatial profiling of sacrococcygeal teratomas reveals cellular composition and X inactivation heterogeneity.NPJ precision oncology · 2026Article
- A novel paradigm for single-cell annotation in stem cell research.Stem cell reports · 2025Review
- Unveiling and stratifying cell cycle-dependent drug efficacy using a single-cell PLOM-CON approach with correlation anomaly and presage protein signals.Communications biology · 2025Article
- Deterministic cell pairing with simultaneous microfluidic merging and sorting of droplets.Lab on a chip · 2025Article
- Review
- Functional phenotyping of genomic variants using joint multiomic single-cell DNA-RNA sequencing.Nature methods · 2025Article
- Protein Marker-Dependent Drug Discovery Targeting Breast Cancer Stem Cells.International journal of molecular sciences · 2025Review
- Refate identifies chemical compounds to target trans-regulatory networks for cellular conversion.bioRxiv : the preprint server for biology · 2025Article
- Deterministic Cell Pairing with Simultaneous Microfluidic Merging and Sorting of Droplets.bioRxiv : the preprint server for biology · 2025Article
- Examination of an iPSC model of human eye development reveals progressive emergence of critical embryonic cell types.Scientific reports · 2025Article
- DNA Methylation, Aging, and Cancer.Epigenomes · 2025Review
- Identification of Critical States in Complex Biological Systems Using Cell-Specific Causal Network Entropy.Research (Washington, D.C.) · 2025Article
- FGF2 supports NANOG expression via pyruvate dehydrogenase-dependent histone acetylation under low oxygen conditions.Frontiers in cell and developmental biology · 2025Article
- Evaluating Strategies to Assess the Differentiation Potential of Human Pluripotent Stem Cells: A Review, Analysis and Call for Innovation.Stem cell reviews and reports · 2025Review
- MetaPhenotype: A Transferable Meta-Learning Model for Single-Cell Mass Spectrometry-Based Cell Phenotype Prediction Using Limited Number of Cells.Analytical chemistry · 2024Article
- Article
14 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
8 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Heterogeneity of cell states represented in pluripotent cultures has not been described at the transcriptional level. Since gene expression is highly heterogeneous between cells, single-cell RNA sequencing can be used to identify how individual pluripotent cells function. Here, we present results from the analysis of single-cell RNA sequencing data from 18,787 individual WTC-CRISPRi human induced pluripotent stem cells. We developed an unsupervised clustering method and, through this, identified four subpopulations distinguishable on the basis of their pluripotent state, including a core pluripotent population (48.3%), proliferative (47.8%), early primed for differentiation (2.8%), and late primed for differentiation (1.1%). For each subpopulation, we were able to identify the genes and pathways that define differences in pluripotent cell states. Our method identified four transcriptionally distinct predictor gene sets composed of 165 unique genes that denote the specific pluripotency states; using these sets, we developed a multigenic machine learning prediction method to accurately classify single cells into each of the subpopulations. Compared against a set of established pluripotency markers, our method increases prediction accuracy by 10%, specificity by 20%, and explains a substantially larger proportion of deviance (up to threefold) from the prediction model. Finally, we developed an innovative method to predict cells transitioning between subpopulations and support our conclusions with results from two orthogonal pseudotime trajectory methods.
Indexed as
Identifiers
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.