single cell rna sequencing dataset scp259  (Broad Clinical Labs)

Journal: bioRxiv

Article Title: Rare variants alter mitochondrial lipid homeostasis and neuronal excitability in PD patient-derived dopaminergic neurons

doi: 10.64898/2026.04.10.717646

Figure Lengend Snippet: a) Volcano plot showed the distribution of the most significant altered proteins comparing PD-derived mesDA neurons vs HS. Proteins showing statistically significant differences in expression are located in the top right (upregulated) and top left (downregulated) quadrants. The black line represents the p-value threshold set to p < 0.01. b) Heat map representation of the most 50 differentially expressed proteins highlighting the clusters of the two groups of analysis when comparing PD-derived mesDA to HS . c) Graphical representation of DEPs detected in PD-derived mesDA, up– (in red) and down– (in blue) regulated proteins that were also deregulated in SOX6+/AGTR1+ and in DA nuclei. Data from SOX6+/AGTR1+ and DA nuclei were available from the human single-cell RNA sequencing available dataset ( https://singlecell.broadinstitute.org/single_cell/app/genes ). d) Graphical representation of the most 20 enriched pathways from IPA analysis. e-g ) Heat map representation of the most dysregulated pathways within the PD-derived mesDA when compared to the HS.

Article Snippet: However, considering the specific loss of the dopaminergic neurons of the Substantia Nigra pars compacta in PD patients, we tested the expression of the genes encoding for the 62 down-regulated proteins in the SNpc cells, by analyzing the human single-cell RNA sequencing available dataset [ ] ( https://singlecell.broadinstitute.org/single_cell/app/genes ).

Techniques: Derivative Assay, Expressing, Single Cell, RNA Sequencing

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