Human bone marrow assessment by single-cell RNA sequencing, mass cytometry, and flow cytometry

et al. 2019

Preprint

Single cell RNA sequencing (scRNA-seq) is widely used for profiling transcriptomes of individual cells. The droplet-based 10X Genomics Chromium (10X) approach and the plate-based Smart-seq2 full-length method are two frequently-used scRNA-seq platforms, yet there are only a few thorough and systematic comparisons of their advantages and limitations. Here, by directly comparing the scRNA-seq data by the two platforms from the same samples of CD45-cells, we systematically evaluated their features using a wide spectrum of analysis. Smart-seq2 detected more genes in a cell, especially low abundance transcripts as well as alternatively spliced transcripts, but captured higher proportion of mitochondrial genes. The composite of Smart-seq2 data also resembled bulk RNA-seq data better. For 10X-based data, we observed higher noise for mRNA in the low expression level. Despite the poly(A) enrichment, approximately 10-30% of all detected transcripts by both platforms were from non-coding genes, with lncRNA accounting for a higher proportion in 10X. 10X-based data displayed more severe dropout problem, especially for genes with lower expression levels. However, 10X-data can better detect rare cell types given its ability to cover a large number of cells. In addition, each platform detected different sets of differentially expressed genes between cell clusters, indicating the complementary nature of these technologies. Our comprehensive benchmark analysis offers the basis for selecting the optimal scRNA-seq strategy based on the objectives of each study.

Section: Discussionmentioning

confidence: 99%

Direct Comparative Analysis of 10X Genomics Chromium and Smart-seq2

Wang

et al. 2019

Preprint

“…GEO (https://www.ncbi.nlm.nih.gov/geo/) or Human Cell Atlas (https://www.humancellatlas.org). Totally, we curated single cell gene expression matrices of 13 human tissues, including lung [8], liver [9], ileum [10], rectum [10], blood [11], bone marrow [12], skin [13], spleen [14], esophagus [14], colon [15], eye [16], stomach [17] and kidney [18] (Table S1). For each tissue, we performed cell clustering and dimension reduction on the scaled gene expression matrix using Seurat package [19].…”

Section: Cell Type Identification In 13 Human Tissuesmentioning

confidence: 99%

Single cell RNA sequencing of 13 human tissues identify cell types and receptors of human coronaviruses

Shen

Biochemical and Biophysical Research Communications

et al. 2020

838

774

a b s t r a c tThe new coronavirus (SARS-CoV-2) outbreak from December 2019 in Wuhan, Hubei, China, has been declared a global public health emergency. Angiotensin I converting enzyme 2 (ACE2), is the host receptor by SARS-CoV-2 to infect human cells. Although ACE2 is reported to be expressed in lung, liver, stomach, ileum, kidney and colon, its expressing levels are rather low, especially in the lung. SARS-CoV-2 may use co-receptors/auxiliary proteins as ACE2 partner to facilitate the virus entry. To identify the potential candidates, we explored the single cell gene expression atlas including 119 cell types of 13 human tissues and analyzed the single cell co-expression spectrum of 51 reported RNA virus receptors and 400 other membrane proteins. Consistent with other recent reports, we confirmed that ACE2 was mainly expressed in lung AT2, liver cholangiocyte, colon colonocytes, esophagus keratinocytes, ileum ECs, rectum ECs, stomach epithelial cells, and kidney proximal tubules. Intriguingly, we found that the candidate co-receptors, manifesting the most similar expression patterns with ACE2 across 13 human tissues, are all peptidases, including ANPEP, DPP4 and ENPEP. Among them, ANPEP and DPP4 are the known receptors for human CoVs, suggesting ENPEP as another potential receptor for human CoVs. We also conducted "CellPhoneDB" analysis to understand the cell crosstalk between CoV-targets and their surrounding cells across different tissues. We found that macrophages frequently communicate with the CoVs targets through chemokine and phagocytosis signaling, highlighting the importance of tissue macrophages in immune defense and immune pathogenesis.

“…GEO (https://www.ncbi.nlm.nih.gov/geo/) or Human Cell Atlas (https://www.humancellatlas.org). Totally, we curated single cell gene expression matrices of 13 human tissues, including lung [11], liver [12], ileum [13], rectum [13], blood [14], bone marrow [15], skin [16], spleen [17], esophagus [17], colon [18], eye [19], stomach [20] and kidney [21] ( Table S1). The raw count matrix was normalized and scaled by Seurat package [22] (Materials and Methods).…”

Section: Cell Type Identification In 13 Human Tissuesmentioning

confidence: 99%

Single cell RNA sequencing of 13 human tissues identify cell types and receptors of human coronaviruses

Shen

et al. 2020

Preprint

158

166

The new coronavirus (2019-nCoV) outbreak from December 2019 in Wuhan, Hubei, China, has been declared a global public health emergency. Angiotensin I converting enzyme 2 (ACE2), is the host receptor by 2019-nCov to infect human cells. Although ACE2 is reported to be expressed in lung, liver, stomach, ileum, kidney and colon, its expressing levels are rather low, especially in the lung. 2019-nCoV may use co-receptors/auxiliary proteins as ACE2 partner to facilitate the virus entry. To identify the potential candidates, we explored the single cell gene expression atlas including 119 cell types of 13 human tissues and analyzed the single cell coexpression spectrum of 51 reported RNA virus receptors and 400 other membrane proteins.Consistent with other recent reports, we confirmed that ACE2 was mainly expressed in lung AT2, liver cholangiocyte, colon colonocytes, esophagus keratinocytes, ileum ECs, rectum ECs, stomach epithelial cells, and kidney proximal tubules. Intriguingly, we found that the candidate co-receptors, manifesting the most similar expression patterns with ACE2 across 13 human tissues, are all peptidases, including ANPEP, DPP4 and ENPEP. Among them, ANPEP and DPP4 are the known receptors for human CoVs, suggesting ENPEP as another potential receptor for human CoVs. We also conducted "CellPhoneDB" analysis to understand the cell crosstalk between CoV-targets and their surrounding cells across different tissues. We found that macrophages frequently communicate with the CoVs targets through chemokine and phagocytosis signaling, highlighting the importance of tissue macrophages in immune defense and immune pathogenesis.