scholarly journals Single‐cell RNA sequencing analysis to characterize cells and gene expression landscapes in atrial septal defect

2021 ◽  
Vol 25 (20) ◽  
pp. 9660-9673
Author(s):  
Zunzhe Wang ◽  
Huating Wang ◽  
Ya Zhang ◽  
Fangpu Yu ◽  
Liwen Yu ◽  
...  
Keyword(s):  
Gene Expression ◽  
Atrial Septal Defect ◽  
Single Cell ◽  
Rna Sequencing ◽  
Septal Defect ◽  
Sequencing Analysis ◽  
Single Cell Rna Sequencing

scholarly journals The in vivo endothelial cell translatome is highly heterogeneous across vascular beds

2019 ◽  
Author(s):  
Audrey C.A. Cleuren ◽  
Martijn A. van der Ent ◽  
Hui Jiang ◽  
Kristina L. Hunker ◽  
Andrew Yee ◽  
...  
Keyword(s):  
Gene Expression ◽  
Endothelial Cells ◽  
Single Cell ◽  
Blood Vessels ◽  
Rna Sequencing ◽  
Specific Gene ◽  
Sequencing Analysis ◽  
Single Cell Rna Sequencing ◽  
Vascular Beds

AbstractEndothelial cells (ECs) are highly specialized across vascular beds. However, given their interspersed anatomic distribution, comprehensive characterization of the molecular basis for this heterogeneity in vivo has been limited. By applying endothelial-specific translating ribosome affinity purification (EC-TRAP) combined with high-throughput RNA sequencing analysis, we identified pan EC-enriched genes and tissue-specific EC transcripts, which include both established markers and genes previously unappreciated for their presence in ECs. In addition, EC-TRAP limits changes in gene expression following EC isolation and in vitro expansion, as well as rapid vascular bed-specific shifts in EC gene expression profiles as a result of the enzymatic tissue dissociation required to generate single cell suspensions for fluorescence-activated cell sorting (FACS) or single cell RNA sequencing analysis. Comparison of our EC-TRAP to published single cell RNA sequencing data further demonstrates considerably greater sensitivity of EC-TRAP for the detection of low abundant transcripts. Application of EC-TRAP to examine the in vivo host response to lipopolysaccharide (LPS) revealed the induction of gene expression programs associated with a native defense response, with marked differences across vascular beds. Furthermore, comparative analysis of whole tissue and TRAP-selected mRNAs identified LPS-induced differences that would not have been detected by whole tissue analysis alone. Together, these data provide a resource for the analysis of EC-specific gene expression programs across heterogeneous vascular beds under both physiologic and pathologic conditions.SignificanceEndothelial cells (ECs), which line all vertebrate blood vessels, are highly heterogeneous across different tissues. The present study uses a genetic approach to specifically tag mRNAs within ECs of the mouse, thereby allowing recovery and sequence analysis to evaluate the EC-specific gene expression program directly from intact organs. Our findings demonstrate marked heterogeneity in EC gene expression across different vascular beds under both normal and disease conditions, with a more accurate picture than can be achieved using other methods. The data generated in these studies advance our understanding of EC function in different blood vessels and provide a valuable resource for future studies.

scholarly journals The in vivo endothelial cell translatome is highly heterogeneous across vascular beds

2019 ◽  
Vol 116 (47) ◽  
pp. 23618-23624 ◽  
Author(s):  
Audrey C. A. Cleuren ◽  
Martijn A. van der Ent ◽  
Hui Jiang ◽  
Kristina L. Hunker ◽  
Andrew Yee ◽  
...  
Keyword(s):  
Gene Expression ◽  
Single Cell ◽  
Rna Sequencing ◽  
Expression Profiles ◽  
Affinity Purification ◽  
Specific Gene ◽  
Sequencing Analysis ◽  
Single Cell Rna Sequencing ◽  
Vascular Beds

Endothelial cells (ECs) are highly specialized across vascular beds. However, given their interspersed anatomic distribution, comprehensive characterization of the molecular basis for this heterogeneity in vivo has been limited. By applying endothelial-specific translating ribosome affinity purification (EC-TRAP) combined with high-throughput RNA sequencing analysis, we identified pan EC-enriched genes and tissue-specific EC transcripts, which include both established markers and genes previously unappreciated for their presence in ECs. In addition, EC-TRAP limits changes in gene expression after EC isolation and in vitro expansion, as well as rapid vascular bed-specific shifts in EC gene expression profiles as a result of the enzymatic tissue dissociation required to generate single-cell suspensions for fluorescence-activated cell sorting or single-cell RNA sequencing analysis. Comparison of our EC-TRAP with published single-cell RNA sequencing data further demonstrates considerably greater sensitivity of EC-TRAP for the detection of low abundant transcripts. Application of EC-TRAP to examine the in vivo host response to lipopolysaccharide (LPS) revealed the induction of gene expression programs associated with a native defense response, with marked differences across vascular beds. Furthermore, comparative analysis of whole-tissue and TRAP-selected mRNAs identified LPS-induced differences that would not have been detected by whole-tissue analysis alone. Together, these data provide a resource for the analysis of EC-specific gene expression programs across heterogeneous vascular beds under both physiologic and pathologic conditions.

scholarly journals Cryopreservation of microglia enables single-cell RNA sequencing with minimal effects on disease-related gene expression patterns

iScience ◽  
2021 ◽  
Vol 24 (4) ◽  
pp. 102357
Author(s):  
Brenda Morsey ◽  
Meng Niu ◽  
Shetty Ravi Dyavar ◽  
Courtney V. Fletcher ◽  
Benjamin G. Lamberty ◽  
...  
Keyword(s):  
Gene Expression ◽  
Single Cell ◽  
Rna Sequencing ◽  
Expression Patterns ◽  
Gene Expression Patterns ◽  
Related Gene ◽  
Single Cell Rna Sequencing ◽  
Disease Related Gene

scholarly journals Single-cell RNA sequencing of the mammalian pineal gland identifies two pinealocyte subtypes and cell type-specific daily patterns of gene expression

PLoS ONE ◽  
2018 ◽  
Vol 13 (10) ◽  
pp. e0205883 ◽  
Author(s):  
Joseph C. Mays ◽  
Michael C. Kelly ◽  
Steven L. Coon ◽  
Lynne Holtzclaw ◽  
Martin F. Rath ◽  
...  
Keyword(s):  
Gene Expression ◽  
Pineal Gland ◽  
Single Cell ◽  
Rna Sequencing ◽  
Cell Type ◽  
Single Cell Rna Sequencing ◽  
Cell Type Specific ◽  
Mammalian Pineal Gland ◽  
Daily Patterns

scholarly journals Single-cell RNA sequencing analysis of SARS-CoV-2 conventional and moonlighting receptors in human organoids

2020 ◽  
Author(s):  
Rajasekaran Mahalingam ◽  
Prakash Dharmalingam ◽  
Abirami Santhanam ◽  
Gangarao Davuluri ◽  
Harry Karmouty Quintana ◽  
...  
Keyword(s):  
Single Cell ◽  
Rna Sequencing ◽  
Sequencing Analysis ◽  
Single Cell Rna Sequencing
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