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Article
Open AccessEffective methods for bulk RNA-seq deconvolution using scnRNA-seq transcriptomes
RNA profiling technologies at single-cell resolutions, including single-cell and single-nuclei RNA sequencing (scRNA-seq and snRNA-seq, scnRNA-seq for short), can help characterize the composition of tissues a...
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Article
Open AccessSingle cell Hi-C identifies plastic chromosome conformations underlying the gastrulation enhancer landscape
Embryonic development involves massive proliferation and differentiation of cell lineages. This must be supported by chromosome replication and epigenetic reprogramming, but how proliferation and cell fate acq...
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Article
DNA methyltransferases 3A and 3B target specific sequences during mouse gastrulation
In mammalian embryos, DNA methylation is initialized to maximum levels in the epiblast by the de novo DNA methyltransferases DNMT3A and DNMT3B before gastrulation diversifies it across regulatory regions. Here...
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Article
Single-cell transcriptomic analyses provide insights into the developmental origins of neuroblastoma
Neuroblastoma is a pediatric tumor of the develo** sympathetic nervous system. However, the cellular origin of neuroblastoma has yet to be defined. Here we studied the single-cell transcriptomes of neuroblas...
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Article
Single-cell analysis of clonal maintenance of transcriptional and epigenetic states in cancer cells
Propagation of clonal regulatory programs contributes to cancer development. It is poorly understood how epigenetic mechanisms interact with genetic drivers to shape this process. Here, we combine single-cell ...
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Article
Open AccessMetaCell: analysis of single-cell RNA-seq data using K-nn graph partitions
scRNA-seq profiles each represent a highly partial sample of mRNA molecules from a unique cell that can never be resampled, and robust analysis must separate the sampling effect from biological variance. We de...
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Early metazoan cell type diversity and the evolution of multicellular gene regulation
A hallmark of metazoan evolution is the emergence of genomic mechanisms that implement cell-type-specific functions. However, the evolution of metazoan cell types and their underlying gene regulatory programme...
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Transient acquisition of pluripotency during somatic cell transdifferentiation with iPSC reprogramming factors
Methods for direct conversion of fibroblasts to other cell types using pluripotency-associated factors generate a transient pluripotent state.
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Correction: Corrigendum: Derivation of novel human ground state naive pluripotent stem cells
Nature 504, 282–286 (2013); doi:10.1038/nature12745 The reduced representation bisulphite sequencing (RRBS) data generated and analysed in this Letter were not originally uploaded to the Gene Expression Omnibu...
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Correction: Corrigendum: Deterministic direct reprogramming of somatic cells to pluripotency
Nature 502, 65–70 (2013); doi:10.1038/nature12587 In this Article, the reduced representation bisulphite sequencing (RRBS) data obtained and analysed were not initially uploaded to the Gene Expression Omnibus ...
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Article
Dynamic and static maintenance of epigenetic memory in pluripotent and somatic cells
Using a new method to estimate DNA methylation turnover rate, embryonic stem cells are shown to lack clonal transmission of methylation but still maintain a stable epigenetic state, whereas somatic cells trans...
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Article
Derivation of novel human ground state naive pluripotent stem cells
It is known that human embryonic stem (ES) cells are more similar to mouse primed epiblast stem cells than to naive mouse ES cells; here culture conditions are determined that allow human ES and induced plurip...
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Article
Deterministic direct reprogramming of somatic cells to pluripotency
Somatic cells can be inefficiently and stochastically reprogrammed into induced pluripotent stem (iPS) cells by exogenous expression of Oct4 (also called Pou5f1), Sox2, Klf4 and Myc (hereafter referred to as O...
