4k pbmcs from a healthy donor  (10X Genomics)

Journal: Genome Biology

Article Title: DANCE: a deep learning library and benchmark platform for single-cell analysis

doi: 10.1186/s13059-024-03211-z

Figure Lengend Snippet: A summary of all supported benchmark datasets in DANCE

Article Snippet: , Clustering , 10X PBMC 4K , Human, PBMC , 4271 cells , 10x Genomics , [ ] .

Techniques:

Journal: Bioinformatics (Oxford, England)

Article Title: ASURAT: functional annotation-driven unsupervised clustering of single-cell transcriptomes.

doi: 10.1093/bioinformatics/btac541

Figure Lengend Snippet: Fig. 3. Identification of cell types in peripheral blood mononuclear cell 4k single-cell transcriptome. (a) Population ratios predicted via seven different methods. (b) Uniform manifold approximation and projection (UMAP) plots, computed using Seurat and Monocle 3, for the manual investigation of DEGs based on the adjusted P-values < 10100. (c) SSMs and scaled log-transformed read count table, which are vertically concatenated and clustered based on the SSM for cell type. Only top significant signs and DEGs are shown in rows. (d) UMAP plot of the SSM for cell type. (e) Violin plots showing sign scores of significant signs, in which separation in- dices (I) for the clusters marked with asterisks against the others show ***I > 0:9. Suffixes ‘-S’ and ‘-V’ after IDs indicate the signs are defined by strongly and variably correlated gene sets, respectively

Article Snippet: Data availability The PBMCs datasets from healthy donors are available in the 10x Genomics repository at https://support.10xgenomics.com/singlecell-gene-expression/datasets: ‘4k PBMCs from a Healthy Donor’ and ‘6k PBMCs from a Healthy Donor’.

Techniques: Transformation Assay

Journal: Bioinformatics (Oxford, England)

Article Title: ASURAT: functional annotation-driven unsupervised clustering of single-cell transcriptomes.

doi: 10.1093/bioinformatics/btac541

Figure Lengend Snippet: Fig. 4. Identification of cell states in peripheral blood mononuclear cell single-cell transcriptomes from control and sepsis donors. (a) t-distributed stochastic neighbor embedding (t-SNE) plots of the SSM for cell type, showing (top) the clustering result and (bottom) reported labels for CD45þ cells and dendritic cells (DCs) by Reyes et al. (2020). (b and c) Violin plots showing sign scores of significant signs, in which separation indices (I) for the clusters marked with asterisks against the others show ***I > 0:9, **I > 0:6 and *I > 0:4. (d) Population ratios of total monocytes (M1, M2 and M3) and subcluster M2 to all cells except for the inferred dendritic cells across each subject type. Control, uninfected and healthy control; Leuk-UTI, sub- jects with urinary tract infection (UTI) with leukocytosis but no organ dysfunction; Int-URO and URO, subjects with UTI with mild (or transient) and clear (or persist- ent) organ dysfunction, respectively; Bac-SEP, bacteremic subjects with sepsis in hospital wards; ICU-SEP and ICU-NoSEP, bacteremic subjects admitted to the in- tensive care unit with and without sepsis, respectively

Article Snippet: Data availability The PBMCs datasets from healthy donors are available in the 10x Genomics repository at https://support.10xgenomics.com/singlecell-gene-expression/datasets: ‘4k PBMCs from a Healthy Donor’ and ‘6k PBMCs from a Healthy Donor’.

Techniques: Control, Infection