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Single-cell transcriptomics, scRNA-Seq and C1 CAGE discovered distinct phases of pluripotency during naïve-to-primed conversion in mice
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What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
inferredcites →https://doi.org/10.1007/7651_2015_208openalex-snapshot
From Naive to Primed Pluripotency: In Vitro Conversion of Mouse Embryonic Stem Cells in Epiblast Stem Cells
inferredcites →https://doi.org/10.1007/s00018-017-2703-xopenalex-snapshot
Epigenetic differences between naïve and primed pluripotent stem cells
inferredcites →https://doi.org/10.1016/j.ceb.2017.01.007openalex-snapshot
X chromosome inactivation: silencing, topology and reactivation
inferredcites →https://doi.org/10.1016/j.cell.2010.10.015openalex-snapshot
Epiblast Stem Cell Subpopulations Represent Mouse Embryos of Distinct Pregastrulation Stages
inferredcites →https://doi.org/10.1016/j.cell.2011.06.052openalex-snapshot
Reconstitution of the Mouse Germ Cell Specification Pathway in Culture by Pluripotent Stem Cells
inferredcites →https://doi.org/10.1016/j.cell.2015.05.002openalex-snapshot
Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets
inferredcites →https://doi.org/10.1016/j.cell.2016.03.023openalex-snapshot
Single-Cell RNA-Seq Reveals Lineage and X Chromosome Dynamics in Human Preimplantation Embryos
inferredcites →https://doi.org/10.1016/j.cub.2010.11.010openalex-snapshot
Evidence that Meiotic Sex Chromosome Inactivation Is Essential for Male Fertility
inferredcites →https://doi.org/10.1016/j.jmb.2019.04.045openalex-snapshot
refTSS: A Reference Data Set for Human and Mouse Transcription Start Sites
inferredcites →https://doi.org/10.1016/j.semcdb.2016.04.014openalex-snapshot
Developmental regulation of X-chromosome inactivation
inferredcites →https://doi.org/10.1016/j.stem.2009.04.015openalex-snapshot
Metastable Pluripotent States in NOD-Mouse-Derived ESCs
inferredcites →https://doi.org/10.1016/j.stem.2013.06.002openalex-snapshot
Whole-Genome Bisulfite Sequencing of Two Distinct Interconvertible DNA Methylomes of Mouse Embryonic Stem Cells
inferredcites →https://doi.org/10.1016/j.stem.2014.04.003openalex-snapshot
Reorganization of Enhancer Patterns in Transition from Naive to Primed Pluripotency
inferredcites →https://doi.org/10.1016/j.stem.2014.05.005openalex-snapshot
Epigenomic Comparison Reveals Activation of “Seed” Enhancers during Transition from Naive to Primed Pluripotency
inferredcites →https://doi.org/10.1016/j.stem.2015.10.009openalex-snapshot
Dynamic Pluripotent Stem Cell States and Their Applications
inferredcites →https://doi.org/10.1016/j.stem.2017.02.014openalex-snapshot
Comprehensive Cell Surface Protein Profiling Identifies Specific Markers of Human Naive and Primed Pluripotent States
inferredcites →https://doi.org/10.1016/j.stemcr.2015.02.014openalex-snapshot
A Simple and Robust Method for Establishing Homogeneous Mouse Epiblast Stem Cell Lines by Wnt Inhibition
inferredcites →https://doi.org/10.1016/j.stemcr.2018.01.004openalex-snapshot
RAS Regulates the Transition from Naive to Primed Pluripotent Stem Cells
inferredcites →https://doi.org/10.1038/nature12787openalex-snapshot
An atlas of active enhancers across human cell types and tissues
inferredcites →https://doi.org/10.1038/nature14413openalex-snapshot
An alternative pluripotent state confers interspecies chimaeric competency
inferredcites →https://doi.org/10.1038/nbt.2840openalex-snapshot
Interactive visualization and analysis of large-scale sequencing datasets using ZENBU
inferredcites →https://doi.org/10.1038/nbt.2967openalex-snapshot
Low-coverage single-cell mRNA sequencing reveals cellular heterogeneity and activated signaling pathways in developing cerebral cortex
inferredcites →https://doi.org/10.1038/nbt.3519openalex-snapshot
Near-optimal probabilistic RNA-seq quantification
inferredcites →https://doi.org/10.1038/nbt.4096openalex-snapshot
Integrating single-cell transcriptomic data across different conditions, technologies, and species
inferredcites →https://doi.org/10.1038/nbt0816-888dopenalex-snapshot
Erratum: Near-optimal probabilistic RNA-seq quantification
inferredcites →https://doi.org/10.1038/ncb3264openalex-snapshot
The metabolome regulates the epigenetic landscape during naive-to-primed human embryonic stem cell transition
inferredcites →https://doi.org/10.1038/ncomms6125openalex-snapshot
Assessing technical performance in differential gene expression experiments with external spike-in RNA control ratio mixtures
inferredcites →https://doi.org/10.1038/ng.2965openalex-snapshot
Deep transcriptome profiling of mammalian stem cells supports a regulatory role for retrotransposons in pluripotency maintenance
inferredcites →https://doi.org/10.1038/nmeth.2967openalex-snapshot
Bayesian approach to single-cell differential expression analysis
inferredcites →https://doi.org/10.1038/s41467-018-08126-5openalex-snapshot
C1 CAGE detects transcription start sites and enhancer activity at single-cell resolution
inferredcites →https://doi.org/10.1038/s41556-020-0508-xopenalex-snapshot
In vitro capture and characterization of embryonic rosette-stage pluripotency between naive and primed states
inferredcites →https://doi.org/10.1038/s41598-018-24051-5openalex-snapshot
Comparative analysis of naive, primed and ground state pluripotency in mouse embryonic stem cells originating from the same genetic background
inferredcites →https://doi.org/10.1038/s41598-019-38807-0openalex-snapshot
Xist/Tsix expression dynamics during mouse peri-implantation development revealed by whole-mount 3D RNA-FISH
inferredcites →https://doi.org/10.1038/srep39921openalex-snapshot
Batch effects and the effective design of single-cell gene expression studies
inferredcites →https://doi.org/10.1089/scd.2018.0199openalex-snapshot
WNT Inhibition and Increased FGF Signaling Promotes Derivation of Less Heterogeneous Primed Human Embryonic Stem Cells, Compatible with Differentiation
inferredcites →https://doi.org/10.1091/mbc.02-02-0030openalex-snapshot
Identification of Genes Periodically Expressed in the Human Cell Cycle and Their Expression in Tumors
inferredcites →https://doi.org/10.1091/mbc.e10-02-0105openalex-snapshot
Nuclear Organization and Dynamics of 7SK RNA in Regulating Gene Expression
inferredcites →https://doi.org/10.1093/bioinformatics/btp352openalex-snapshot
The Sequence Alignment/Map format and SAMtools
inferredcites →https://doi.org/10.1093/bioinformatics/btp527openalex-snapshot
TagDust—a program to eliminate artifacts from next generation sequencing data
inferredcites →https://doi.org/10.1093/bioinformatics/bts635openalex-snapshot
STAR: ultrafast universal RNA-seq aligner
inferredcites →https://doi.org/10.1093/bioinformatics/btt730openalex-snapshot
CrossMap: a versatile tool for coordinate conversion between genome assemblies
inferredcites →https://doi.org/10.1093/nar/gkv054openalex-snapshot
CAGEr: precise TSS data retrieval and high-resolution promoterome mining for integrative analyses
inferredcites →https://doi.org/10.1093/nar/gkw377openalex-snapshot
Enrichr: a comprehensive gene set enrichment analysis web server 2016 update
inferredcites →https://doi.org/10.1093/nar/gkw430openalex-snapshot
TSCAN: Pseudo-time reconstruction and evaluation in single-cell RNA-seq analysis
inferredcites →https://doi.org/10.1093/nar/gkw620openalex-snapshot
A subset of replication-dependent histone mRNAs are expressed as polyadenylated RNAs in terminally differentiated tissues
inferredcites →https://doi.org/10.1093/nar/gkx949openalex-snapshot
SCPortalen: human and mouse single-cell centric database
inferredcites →https://doi.org/10.1101/088500openalex-snapshot
Single-cell transcriptomes of fluorescent, ubiquitination-based cell cycle indicator cells
inferredcites →https://doi.org/10.1101/gr.099796.109openalex-snapshot
Genome-wide dynamics of replication timing revealed by in vitro models of mouse embryogenesis
inferredcites →https://doi.org/10.1101/gr.107524.110openalex-snapshot
The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data
inferredcites →https://doi.org/10.1101/gr.2899304openalex-snapshot
Contribution of Asian mouse subspeciesMus musculus molossinusto genomic constitution of strain C57BL/6J, as defined by BAC-end sequence–SNP analysis
inferredcites →https://doi.org/10.1111/j.1365-2184.2004.00298.xopenalex-snapshot
Embryonic stem cells
inferredcites →https://doi.org/10.1146/annurev-cellbio-092910-154020openalex-snapshot
The Coupling of X-Chromosome Inactivation to Pluripotency
inferredcites →https://doi.org/10.1186/1471-2105-14-128openalex-snapshot
Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool
inferredcites →https://doi.org/10.1186/1471-2105-15-144openalex-snapshot
MOIRAI: a compact workflow system for CAGE analysis
inferredcites →https://doi.org/10.1186/gb-2013-14-9-r98openalex-snapshot
The non-coding snRNA 7SKcontrols transcriptional termination, poising, and bidirectionality in embryonic stem cells
inferredcites →https://doi.org/10.1186/s12864-018-4772-0openalex-snapshot
Slingshot: cell lineage and pseudotime inference for single-cell transcriptomics
inferredcites →https://doi.org/10.1186/s13059-016-0970-8openalex-snapshot
Fast and accurate single-cell RNA-seq analysis by clustering of transcript-compatibility counts
inferredcites →https://doi.org/10.1242/dev.000018openalex-snapshot
Meiotic sex chromosome inactivation
inferredcites →https://doi.org/10.1242/dev.005611openalex-snapshot
Cellular dynamics associated with the genome-wide epigenetic reprogramming in migrating primordial germ cells in mice
inferredcites →https://doi.org/10.1242/dev.102.1.3openalex-snapshot
Teratocarcinomas and Embryonic Stem Cells: A Practical Approach
inferredcites →https://doi.org/10.1242/dev.122.3.881openalex-snapshot
Germline regulatory element of Oct-4 specific for the totipotent cycle of embryonal cells
inferredcites →https://doi.org/10.1242/dev.142679openalex-snapshot
Formative pluripotency: the executive phase in a developmental continuum
inferredcites →https://doi.org/10.1242/dev.172916openalex-snapshot
Capacitation of human naïve pluripotent stem cells for multi-lineage differentiation
inferredcites →https://doi.org/10.1242/jcs.146720openalex-snapshot
Role of cell–cell adhesion complexes in embryonic stem cell biology
inferredcites →https://doi.org/10.12688/f1000research.10707.1openalex-snapshot
X chromosome inactivation: new players in the initiation of gene silencing
inferredcites →https://doi.org/10.1371/journal.pone.0045220openalex-snapshot
E-Cadherin Promotes Incorporation of Mouse Epiblast Stem Cells into Normal Development
inferredcites →https://doi.org/10.1371/journal.pone.0095329openalex-snapshot
A Modified EpiSC Culture Condition Containing a GSK3 Inhibitor Can Support Germline-Competent Pluripotency in Mice
inferredcites →https://doi.org/10.1371/journal.pone.0116109openalex-snapshot
Live Cell Imaging of the Nascent Inactive X Chromosome during the Early Differentiation Process of Naive ES Cells towards Epiblast Stem Cells
inferredcites →https://doi.org/10.1371/journal.pone.0163962openalex-snapshot
SeqKit: A Cross-Platform and Ultrafast Toolkit for FASTA/Q File Manipulation
inferredcites →https://doi.org/10.4161/fly.19695openalex-snapshot
A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff
What points at this work
Incoming claims: where this work appears in other papers’ reference lists and arguments.
inferred← citeshttps://doi.org/10.1007/978-1-0716-2281-0_11openalex-snapshot
Complete Transcriptome Analysis by 5′-End Single-Cell RNA-Seq with Random Priming
inferred← citeshttps://doi.org/10.15748/jasse.11.147openalex-snapshot
Effects of pseudobulk and Gaussian noise on the application of the dynamical network biomarker theory to single-cell RNA-seq data
inferred← citeshttps://doi.org/10.2142/biophysico.bppb-v21.s016openalex-snapshot
Yuragi biomarker concept for evaluating human induced pluripotent stem cells using heterogeneity-based Raman finger-printing
inferred← citeshttps://doi.org/10.64898/2026.04.24.720575openalex-snapshot
Evolutionary origins and chromatin state shape X-chromosome upregulation pattern during eutherian and metatherian embryogenesis
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