single nucleus rna seq dataset  (Broad Clinical Labs)

Journal: Life Medicine

Article Title: Single-cell analysis reveals essential lncRNAs regulating human trophoblast lineage differentiation

doi: 10.1093/lifemedi/lnag010

Figure Lengend Snippet: Transcriptomic landscape of lncRNAs in human placental trophoblasts. (A) UMAP plot showing first-trimester and term placental single-nucleus transcriptomes (CTB, cytotrophoblast; EVT, extravillous trophoblast; STB, syncytiotrophoblast; STR, stromal cell; e, early; l, late). (B) UMAP plot showing the distribution of first-trimester and term placental samples. (C) Pie plot of the fraction of lncRNAs and mRNAs in snRNA-seq and bulk RNA-seq, respectively. The value “ n ” indicates the average number of detected transcripts per cell for both lncRNAs and mRNAs based on the experimentally measured data. (D) Box plots of transcript counts in per cell type. Statistical significance was determined by two-sided Wilcoxon rank-sum tests (**** P < 0.0001). (E) Volcano plot of cell-type-specific lncRNAs across trophoblast subtypes. The x -axis represents the difference in the percentage of cells expressing each gene between the two compared cell types (Δ percentage = pct.1 − pct.2), while the y -axis indicates the log 2 (fold change) in average gene expression. This representation integrates both expression magnitude and expression prevalence at the single-cell level. (F) Heatmap of cell-type-specific lncRNA expression atlas across trophoblast populations. (G) UMAP plots showing the expression distribution of representative lncRNAs (Color gradient represents the average expression level per cell). (H) GO biological process terms enriched in protein-coding genes (PCGs) associated with stage-specific lncRNAs.

Article Snippet: For cross-platform validation: Three independent external datasets were utilized, including two single-cell RNA-seq datasets (accession numbers: HRA003309, GSE214607 ) and one single-nucleus RNA-seq dataset (singlecell.broadinstitute.org/single_cell/study/SCP2601).

Techniques: RNA Sequencing, Expressing, Gene Expression, Single Cell

Journal: PLOS Biology

Article Title: Fibroblast-expressed LRRC15 is a receptor for SARS-CoV-2 spike and controls antiviral and antifibrotic transcriptional programs

doi: 10.1371/journal.pbio.3001967

Figure Lengend Snippet: (A) Overview of cell types expressing LRRC15 from existing single-cell RNA-sequencing datasets. (B) UMAP plot of lung single-nucleus RNA seq dataset (Melms and colleagues). (C) Feature plot and (D) dotplot shows LRRC15 is expressed in fibroblasts and neuronal cells. Expression of LRRC15 is also observed in fibroblasts of separate studies (See ). (E) Proportion of cells that are lung fibroblasts increases with COVID lungs (7.9% in control ( N = 19) and 22.9% in COVID ( N = 47); unpaired t test, p < 0.0001). (F and G) Representative micrograph of HE-stained lung tissue section obtained from (F) a human donor without COVID-19 and (G) donor diagnosed with COVID-19. Imaging performed at 200× magnification (scale bar = 50 m). All images in (Control, N = 1; COVID-19, N = 4). (H and I) Representative micrograph of immunofluorescence staining in human lung tissue section obtained from (H) donor without COVID-19 and (I) donor diagnosed with COVID-19. Images were taken at 200× magnification (scale bar = 100 m). Red = Collagen I, green = LRRC15, blue = DAPI. All images in (Control, N = 3; COVID-19, N = 4). The data underlying all panels in this figure can be found in DOI: 10.5281/zenodo.7416876 . ACE2, angiotensin-converting enzyme 2; COVID-19, Coronavirus Disease 2019; HE, hematoxylin and eosin; LRRC15, leucine-rich repeat-containing protein 15.

Article Snippet: Two single-nucleus RNA seq datasets were downloaded from the Single Cell Portal (Broad Institute, SCP1052 and SCP1219) and 1 single-cell RNA seq dataset from Gene Expression Omnibus (GSE158127).

Techniques: Expressing, RNA Sequencing, Control, Staining, Imaging, Immunofluorescence