Simultaneous profiling of transcriptome and DNA methylome from a single cell

Hu, Youjin; Huang, Kevin; An, Qin; Du, Guizhen; Hu, Ganlu; Xue, Jinfeng; Zhu, Xianmin; Wang, Cun‐Yu; Xue, Zhigang; Fan, Guoping

doi:10.1186/s13059-016-0950-z

Cited by 253 publications

(177 citation statements)

References 32 publications

(37 reference statements)

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“…Single-cell triple omics sequencing method, including genome, DNA methylome, and transcriptome, is another innovation [117]. A complete circuit of a single cell can be detected by the integration of genomics, epigenomics, transcriptomics, and proteomics.…”

Section: Discussionmentioning

confidence: 99%

Studying hematopoiesis using single-cell technologies

Huang

Guo

2017

J Hematol Oncol

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Hematopoiesis is probably the best-understood stem cell differentiation system; hematopoietic stem cell (HSC) transplantation represents the most widely used regenerative therapy. The classical view of lineage hierarchy in hematopoiesis is built on cell type definition system by a group of cell surface markers. However, the traditional model is facing increasing challenges, as many classical cell types are proved to be heterogeneous. Recently, the developments of new technologies allow genome, transcriptome, proteome, and epigenome analysis at the single-cell level. For the first time, we can study hematopoietic system at single-cell resolution on a multi-omic scale. Here, we review recent technical advances in single-cell analysis technology, as well as their current applications. We will also discuss the impact of single-cell technologies on both basic research and clinical application in hematology.

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Section: Discussionmentioning

confidence: 99%

Studying hematopoiesis using single-cell technologies

Huang

Guo

2017

J Hematol Oncol

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“…The results showed that the connection strength between methylome and transcriptome varies from cell to cell. Another similar method called scMT-seq applied Smartseq 2 and scRRBS for single-cell transcriptome sequencing and methylome sequencing, respectively [103]. Compared to scM&T-seq, scMT-seq provides similar CpG islands overlap in a more cost-effective way.…”

Section: Exemplary Applicationsmentioning

confidence: 99%

Using single‐cell multiple omics approaches to resolve tumor heterogeneity

Ortega

Poirion

Zhu

et al. 2017

Clinical & Translational Med

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It has become increasingly clear that both normal and cancer tissues are composed of heterogeneous populations. Genetic variation can be attributed to the downstream effects of inherited mutations, environmental factors, or inaccurately resolved errors in transcription and replication. When lesions occur in regions that confer a proliferative advantage, it can support clonal expansion, subclonal variation, and neoplastic progression. In this manner, the complex heterogeneous microenvironment of a tumour promotes the likelihood of angiogenesis and metastasis. Recent advances in next-generation sequencing and computational biology have utilized single-cell applications to build deep profiles of individual cells that are otherwise masked in bulk profiling. In addition, the development of new techniques for combining single-cell multi-omic strategies is providing a more precise understanding of factors contributing to cellular identity, function, and growth. Continuing advancements in single-cell technology and computational deconvolution of data will be critical for reconstructing patient specific intra-tumour features and developing more personalized cancer treatments.

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“…The most critical step of simultaneously sequencing RNA and DNA is to separate RNA from DNA. The most common way is to partially lyse single cells without breaking the nucleic membrane 115,116 . The cytoplasmic mRNA is released and genomic DNA is still contained in the nuclei.…”

Section: Simultaneous Sequencing Of Dna and Rnamentioning

confidence: 99%

Microfluidics for genome-wide studies involving next generation sequencing

Murphy

2017

Biomicrofluidics

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Next-generation sequencing (NGS) has revolutionized how molecular biology studies are conducted. Its decreasing cost and increasing throughput permit profiling of genomic, transcriptomic, and epigenomic features for a wide range of applications. Microfluidics has been proven to be highly complementary to NGS technology with its unique capabilities for handling small volumes of samples and providing platforms for automation, integration, and multiplexing. In this article, we review recent progress on applying microfluidics to facilitate genome-wide studies. We emphasize on several technical aspects of NGS and how they benefit from coupling with microfluidic technology. We also summarize recent efforts on developing microfluidic technology for genomic, transcriptomic, and epigenomic studies, with emphasis on single cell analysis. We envision rapid growth in these directions, driven by the needs for testing scarce primary cell samples from patients in the context of precision medicine.

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Simultaneous profiling of transcriptome and DNA methylome from a single cell

Cited by 253 publications

References 32 publications

Studying hematopoiesis using single-cell technologies

Studying hematopoiesis using single-cell technologies

Using single‐cell multiple omics approaches to resolve tumor heterogeneity

Microfluidics for genome-wide studies involving next generation sequencing

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