scholarly journals Resolving early mesoderm diversification through single-cell expression profiling

Nature ◽  
2016 ◽  
Vol 535 (7611) ◽  
pp. 289-293 ◽  
Author(s):  
Antonio Scialdone ◽  
Yosuke Tanaka ◽  
Wajid Jawaid ◽  
Victoria Moignard ◽  
Nicola K. Wilson ◽  
...  
Keyword(s):  
Single Cell ◽  
Expression Profiling ◽  
Cell Expression

scholarly journals Single cell analysis of lincRNA expression during human blastocyst differentiation identifies TERT(+) multi-lineage precursor cells

2016 ◽  
Author(s):  
Jens Durruthy-Durruthy ◽  
Mark Wossidlo ◽  
Vittorio Sebastiano ◽  
Gennadi Glinsky
Keyword(s):  
Single Cell ◽  
Expression Profiling ◽  
Single Cell Analysis ◽  
Precursor Cells ◽  
Human Embryos ◽  
Cell Analysis ◽  
Embryonic Cells ◽  
Human Blastocyst ◽  
Extinction Events ◽  
Cell Expression

SummaryChromosome instability and aneuploidies occur very frequently in human embryos, impairing proper embryogenesis and leading to cell cycle arrest, loss of cell viability, and developmental failures in 50-80% of cleavage-stage embryos. This high frequency of cellular extinction events represents a significant experimental obstacle challenging analyses of individual cells isolated from human preimplantation embryos. Here, we carried out single cell expression profiling analyses of 241 individual cells recovered from 32 human embryos during the early and late stages of viable human blastocyst differentiation. Classification of embryonic cells was performed solely based on expression patterns of human pluripotency-associated transcripts (HPAT), which represent a family of transposable element-derived lincRNAs highly expressed in human embryonic stem cells (hESCs) and regulating nuclear reprogramming and pluripotency induction. We then validated our findings by analyzing 1,708 individual embryonic cells recovered from more than 100 human embryos and 259 mouse embryonic cells at different stages of preimplantation embryogenesis. Our experiments demonstrate that segregation of human blastocyst cells into distinct sub-populations based on single-cell expression profiling of just three HPATs (HPAT-21; -2; and -15) appears to inform key molecular and cellular events of naïve pluripotency induction and accurately captures a full spectrum of cellular diversity during human blastocyst differentiation. HPAT’s expression-guided spatiotemporal reconstruction of human embryonic development inferred from single-cell expression analysis of viable blastocyst differentiation enabled identification of TERT(+) sub-populations, which are significantly enriched for cells expressing key naïve pluripotency regulatory genes and genetic markers of all three major lineages created during human blastocyst differentiation. Results of our analyses suggest that during early stages of preimplantation embryogenesis putative immortal multi-lineage precursor cells (iMPCs) are created, which then differentiate into trophectoderm, primitive endoderm and pluripotent epiblast lineages. We propose that cellular extinction events in cleavage-stage embryos are triggered by premature activation of HPAT lincRNAs reflecting failed iMPC’s creation attempts.HighlightsSingle cell analysis of 1,949 human & 259 mouse embryonic cellsIdentification of 5 most abundant HPAT lincRNAs in viable human blastocystsExpression profiling of just 3 lincRNAs captures cellular diversity of human blastocystsIdentification & characterization of TERT(+) multi-lineage precursor cellsMTTH/HPAT lincRNAs regulatory axis of naïve pluripotency induction in vivo

scholarly journals Single-cell expression profiling of dopaminergic neurons combined with association analysis identifies pyridoxal kinase as Parkinson's disease gene

2009 ◽  
Vol 66 (6) ◽  
pp. 792-798 ◽  
Author(s):  
Matthias Elstner ◽  
Christopher M. Morris ◽  
Katharina Heim ◽  
Peter Lichtner ◽  
Andreas Bender ◽  
...  
Keyword(s):  
Parkinson’S Disease ◽  
Parkinson's Disease ◽  
Single Cell ◽  
Association Analysis ◽  
Expression Profiling ◽  
Dopaminergic Neurons ◽  
Disease Gene ◽  
Pyridoxal Kinase ◽  
Cell Expression

scholarly journals Dean Flow Assisted Single Cell and Bead Encapsulation for High Performance Single Cell Expression Profiling

ACS Sensors ◽  
2019 ◽  
Vol 4 (5) ◽  
pp. 1299-1305 ◽  
Author(s):  
Luoquan Li ◽  
Ping Wu ◽  
Zhaofeng Luo ◽  
Lei Wang ◽  
Weiping Ding ◽  
...  
Keyword(s):  
Single Cell ◽  
Expression Profiling ◽  
High Performance ◽  
Dean Flow ◽  
Cell Expression

scholarly journals Dean flow assisted single cell and bead encapsulation for high performance single cell expression profiling

2019 ◽  
Author(s):  
Luoquan Li ◽  
Ping Wu ◽  
Zhaofeng Luo ◽  
Lei Wang ◽  
Weiping Ding ◽  
...  
Keyword(s):  
Single Cell ◽  
Expression Profiling ◽  
High Efficiency ◽  
Cell Concentration ◽  
Critical Role ◽  
Droplet Microfluidics ◽  
Sequencing Data ◽  
High Cell Concentration ◽  
Dean Flow ◽  
Cell Expression

AbstractSingle-cell RNA sequencing examines the transcriptome of individual cells and reveals the inter-cell transcription heterogeneity, playing a critical role in both scientific research and clinical applications. Recently, droplet microfluidics-based platform for expression profiling has been shown as a powerful tool to capture of the transcriptional information on single cell level. Despite the breakthrough this platform brought about, it required the simultaneous encapsulation of single cell and single barcoded bead, the incidence of which was very low. Suboptimal capturing efficiency limited the throughput of the Drop-seq platform. In this work, we leveraged the advance in inertial microfluidics-based cell sorting and designed a microfluidic chip for high efficiency cell-bead co-encapsulation, increasing the capturing rate by more than four folds. Specifically, we adopted spiral and serpentine channels and ordered cells/beads before the encapsulation region. We characterized the effect of cell concentration on the capturing rate and achieved a cell-bead co-capturing rate up to 3%. We tested this platform by co-encapsulating barcoded beads and human-mouse cell mixtures. The sequencing data distinguished the majority of human and mice expressions, with the doublet rate being as low as 5.8%, indicating that the simultaneous capturing of two or more cells in one droplet was minimal even when using high cell concentration. This chip design showed great potential in improving the efficiency for future single cell expression profiling.

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