| Id |
Subject |
Object |
Predicate |
Lexical cue |
| T80 |
0-246 |
Sentence |
denotes |
To assess whether the findings from NHP lung cells were similarly present in humans, we analyzed a previously unpublished scRNA-seq dataset derived from surgical resections of fibrotic lung tissue collected with Seq-Well S3 (Hughes et al., 2019). |
| T81 |
247-443 |
Sentence |
denotes |
Unsupervised analysis identified multiple cell types and subtypes of immune cells (Figures 2 A–2C; STAR Methods), as defined by the genes displayed in Figure 2C (full lists available in Table S2). |
| T82 |
444-627 |
Sentence |
denotes |
Here, we found that ACE2 and TMPRSS2 were primarily expressed within type II pneumocytes and ciliated cells, in line with our analysis of the NHP-derived cells (Figures 1 and 2A, 2B). |
| T83 |
628-882 |
Sentence |
denotes |
In type II pneumocytes (identified by unique expression of surfactant proteins SFTPC, SFTPB, and SFTPA1), we found 1.4% of cells expressing ACE2 (FDR-adjusted p = 1.35E−21), 34.2% expressing TMPRSS2 (FDR-adjusted p < 1E−300), and 0.8% co-expressing both. |
| T84 |
883-1028 |
Sentence |
denotes |
In ciliated cells, we found 7% were ACE2 + (FDR-adjusted p = 5E−64), 24.6% were TMPRSS2 + (FDR-adjusted p = 3.8E−30), and 5.3% co-expressed both. |
| T85 |
1029-1177 |
Sentence |
denotes |
Figure 2 Select Lung Epithelial Cells from Control, HIV-1-Infected, and Mycobacterium-tuberculosis-Infected Human Donors Co-Express ACE2 and TMPRSS2 |
| T86 |
1178-1391 |
Sentence |
denotes |
(A) Schematic of protocol for isolation of human lung tissue from surgical excess, creation of scRNA-seq libraries by using Seq-Well S3, and computational analysis to identify cell types by using unbiased methods. |
| T87 |
1392-1520 |
Sentence |
denotes |
Shown on the right is a UMAP projection of 18,915 cells across 8 donors (n = 3 TB+HIV+; n = 3 TB+; n = 2 non-infected patients). |
| T88 |
1521-1600 |
Sentence |
denotes |
Cells represented by points, colored according to cell type (see STAR Methods). |
| T89 |
1601-1694 |
Sentence |
denotes |
(B) UMAP projection as in (A), points colored by detection of ACE2 (top) or TMPRSS2 (bottom). |
| T90 |
1695-1763 |
Sentence |
denotes |
Color coding is as follows: black, RNA positive; blue, RNA negative. |
| T91 |
1764-2055 |
Sentence |
denotes |
(C) Dot plot of 2 defining genes for each cell type (FDR-adjusted p < 0.001), and ACE2 and TMPRSS2; dot size represents fraction of cells within cell type expressing a given gene, and color intensity represents binned count-based expression amount (log(scaled UMI+1)) among expressing cells. |
| T92 |
2056-2108 |
Sentence |
denotes |
All cluster-defining genes are provided in Table S2. |
| T93 |
2109-2187 |
Sentence |
denotes |
Red arrow indicates cell types with largest proportion of ACE2+TMPRSS2+ cells. |
| T94 |
2188-2318 |
Sentence |
denotes |
(D) Volcano plot identifying significantly upregulated genes in ACE2+TMPRSS2+ pneumocytes compared with all remaining pneumocytes. |
| T95 |
2319-2403 |
Sentence |
denotes |
Red points represent genes with a FDR-adjusted p < 0.05, and log2(fold change) >1.5. |
| T96 |
2404-2477 |
Sentence |
denotes |
Text highlighting specific genes; the full list is available in Table S2. |
| T97 |
2478-2579 |
Sentence |
denotes |
(E) Expression of ACE2 across human donors by HIV and TB status (p = 0.009 by likelihood-ratio test). |
| T98 |
2580-2598 |
Sentence |
denotes |
See also Table S2. |
