Journal: eLife

Article Title: GLI transcriptional repression regulates tissue-specific enhancer activity in response to Hedgehog signaling

doi: 10.7554/eLife.50670

Figure Lengend Snippet:

Article Snippet: ATAC used components from the Nextera DNA Library Preparation Kit (Illumina) as described previously ( ) with the following variations.

Techniques: MicroChIP Assay, Cell Culture, Software

Journal: Nature

Article Title: Deciphering cell states and genealogies of human haematopoiesis

doi: 10.1038/s41586-024-07066-z

Figure Lengend Snippet: a , Schematic of the ReDeeM experiment for human haematopoietic cells. b , Phylogenetic tree for haematopoietic cells of donor young-1, based on shared mtDNA mutations using the neighbour-joining algorithm. The numbers of shareable mtDNA mutations for each cell are indicated, with a median of ten (cladograms are used for tree visualization in this manuscript). c , Joint multiomics clustering of young-1 (for the same cells from b ). Weighted nearest-neighbour uniform manifold approximation and projection (wnnUMAP) showing combined ATAC and RNA profile for 11,019 single cells. HSC, haematopoietic stem cell; MPP, multipotent progenitor; MKP, megakaryocyte progenitor; CMP, common myeloid progenitor; GMP, granulocyte–monocyte progenitor; MDP, monocyte–dendritic cell progenitor; MEP, megakaryocytic–erythroid progenitor; CLP, common lymphoid progenitor; LMPP, lympho–myeloid primed progenitor; ProB, B cell progenitor; EryP, erythroid precursor; Mono, monocyte; cDC, conventional dendritic cell; pDC, plasmacytoid dendritic cell; NK, natural killer cell. d , Analysis of chromatin accessibility (pseudo-bulk ATAC, left), mRNA expression (middle) and DNA-binding activity (right) of SPI1 and GATA1 transcription factors (TFs) in HSCs differentiating towards myeloid versus mega-erythroid trajectories. Deviation of transcription factor DNA-binding motif frequency was computed using ChromVar based on the JASPAR2020 human transcription factor database. e , Measurement of mtDNA mutation burdens across different cell types; n = 11,019 cells. Boxplot shows data from the 25th–75th percentile and whiskers extending to the minimum and maximum within 1.5× interquartile range (IQR). P values were derived from two-sided Wilcoxon rank-sum test. f , Integrative analysis between phylogenetic tree- and multiomics-based cell types. Examples of cell-type-restricted local clades are highlighted (clades i–viii). Enrichment P values were computed by one-sided binomial test followed by q -value correction. g , Analysis of cell-type origins based on lineage-informative mtDNA mutations (11,009 cells versus 631 variants). Colour intensity indicates the proportion of each target cell type ( x axis) within the mtDNA mutation-based k -nearest neighbourhood (KNN) of the queried cell type ( y axis).

Article Snippet: RNA and ATAC library preparation followed the standard 10X Genomics protocol, with some modifications.

Techniques: Expressing, Binding Assay, Activity Assay, Mutagenesis, Derivative Assay

Journal: Nature

Article Title: Deciphering cell states and genealogies of human haematopoiesis

doi: 10.1038/s41586-024-07066-z

Figure Lengend Snippet: a , Schematic of the experimental design. Bone marrow samples were obtained from the same individual at two different time points, 4 months apart, and were processed by ReDeeM. HSCs were enriched by fluorescent activated cell sorting (FACS) and further defined by single-cell gene expression (expr.) markers. b , Validation of HSC classification. Gene expression of multiple independent HSC markers is shown; n = 34,017 cells. Boxplot shows data from the 25th–75th percentile and whiskers extending to the minimum and maximum within 1.5 × IQR. *** P < 2.2 × 10 −16 , derived from one-sided Wilcoxon rank-sum test. c , Subpopulations of HSCs based on single-cell RNA and ATAC profiling alone, and on combined WNN space. d , Examples of differentially expressed genes across HSC subpopulations. e , Phylogenetic tree of HSCs sampled from two time points using shared mtDNA mutations (donor young-1). f , Overlap analysis between HSC clonal groups and HSC state subpopulations using hypergeometric tests. Colour intensity indicates combined enrichment FDR (Supplementary Data ). g , Comparison of HSC clone-in-state enrichment (enrich.) (as in f ) across the two time points; enrichment fold change is compared. Colour intensity indicates combined enrichment FDR.

Article Snippet: RNA and ATAC library preparation followed the standard 10X Genomics protocol, with some modifications.

Techniques: FACS, Gene Expression, Biomarker Discovery, Derivative Assay, Comparison

Journal: Nature

Article Title: Deciphering cell states and genealogies of human haematopoiesis

doi: 10.1038/s41586-024-07066-z

Figure Lengend Snippet: Panel a - g displays data for donor young-1, while h - p for donor young-2. a - e , Identify hematopoietic stem cells (HSC) based on molecular markers for young-1 a , Unsupervised clustering of hematopoietic stem and progenitor cells (CD34+ cells, and CD34 + CD45RA − CD90 + cells) based on joint ATAC and RNA modalities. b , Expression of HLF mRNA level, a molecular marker of HSCs, in each cluster. n = 14,661 cells. Boxplot displays data from the 25th to 75th percentile, and whiskers extending to the minimum and maximum within 1.5 IQR. c , Distribution of HLF expressing levels on wnnUMAP d , Define HSCs for CD34 + CD45RA − CD90 + cells with HLF hi , CRHBP hi , and CD34 hi expression levels, and in HLF high clusters from b. e , Highlighting the defined HSCs on wnnUMAP. f , HSCs distributions on UMAP from two different time points. g , Top examples of HSC subpopulation-specific gene expression profiles, based on RNA modality. h - l , same analyses as a-e for donor young-2. n = 23,114 cells. Boxplot displays data from the 25th to 75th percentile, and whiskers extending to the minimum and maximum within 1.5 IQR. m , same analysis as in main Fig. for donor young-2. n , Same analysis as g, for donor young-2. o - p , same analysis as in main Fig. for donor young-2. P-values are derived from hypergeometric test.

Article Snippet: RNA and ATAC library preparation followed the standard 10X Genomics protocol, with some modifications.

Techniques: Expressing, Marker, Gene Expression, Derivative Assay