Journal: Nature

Article Title: Decoding human fetal liver haematopoiesis

doi: 10.1038/s41586-019-1652-y

Figure Lengend Snippet: a, Schematic of tissue processing and cell isolation for scRNA-seq profiling of fetal liver, skin and kidney across four developmental stages (7-8, 9-11, 12-14, and 15-17 post conception weeks (PCW)), and yolk sac from 4-7 PCW. SS2, Smart-seq2. b, UMAP visualisation of fetal liver cells from 10x using 3’ chemistry. Colours indicate cell state. HSC/MPP, haematopoietic stem cell/multipotent progenitor; ILC, innate lymphoid cell; NK, natural killer cell; Neut-myeloid, neutrophil-myeloid; DC, dendritic cell; pDC, plasmacytoid DC; Mono-mac, monocyte-macrophage; EI, erythroblastic island; Early L/TL, Early lymphoid/T lymphocyte; MEMP, megakaryocyte-erythroid-mast cell progenitor. Statistical significance of cell frequency change by stage shown in parentheses (negative binomial regression with bootstrap correction for sort gates; * p < 0.05, *** p < 0.001, and **** p < 0.0001 as per ) with up/down arrows to indicate positive/negative coefficient of change, respectively. c , Liver composition by developmental stage as the mean percentage of each population per stage corrected by CD45 + /CD45 - sort fraction. Colours indicate cell states as shown in b.

Article Snippet: We FACS-isolated CD45 + and CD45 - cells using adjoining gates for comprehensive capture ( and ) for single cell RNA-sequencing (scRNA-seq) (both 10x Genomics platform Smart-seq2) ( , , and ).

Techniques: Cell Isolation

Journal: Nature

Article Title: Decoding human fetal liver haematopoiesis

doi: 10.1038/s41586-019-1652-y

Figure Lengend Snippet: a , Fetal skin and kidney haematopoietic cells visualised by UMAP. Colours indicate cell state. Inset: colours indicate tissue type. b , UMAP visualisation of yolk sac haematopoietic cells. Colours indicate cell state. Inset: colours indicate location within yolk sac. c , UMAP visualisation of 3’ liver 10x cells post batch correction, coloured by sample. d , UMAP visualisation (top) of 3’ 10x liver sample sex mixing grouped by developmental stage, and violin plots (bottom) showing ln-normalised median expression of XIST (green) and RSP4Y1 (purple), which marks female and male samples respectively. e , UMAP visualisation of fetal liver composition by developmental stage. Colours indicate cell state. f, UMAP visualisation of fetal liver cells profiled using Smart-seq2. Colours indicate cell states as shown in e . g , Frequency (mean +/- s.e.m.) of B cells in the CD34 - cells detected in 6-19 PCW fetal livers by flow cytometry (* p < 0.05; *** p = 0.003; **** p < 0.001).

Article Snippet: We FACS-isolated CD45 + and CD45 - cells using adjoining gates for comprehensive capture ( and ) for single cell RNA-sequencing (scRNA-seq) (both 10x Genomics platform Smart-seq2) ( , , and ).

Techniques: Expressing, Flow Cytometry

Journal: Nature

Article Title: Decoding human fetal liver haematopoiesis

doi: 10.1038/s41586-019-1652-y

Figure Lengend Snippet: a, Gating strategy used to FACS-isolate cells for droplet-(10x) and plate-based scRNA-seq (Smart-seq2) for samples F2-F17. b, Gating strategy used to FACS-isolate cells for cytospins, scRNA-seq (Smart-seq2) and 100 cell RNA-seq. c, Flow cytometry gating strategy used to identify the colonies cultured in vitro from single cells as shown in , Flow cytometry gating strategy used to identify B and NK colonies cultured in vitro from 10 cells as shown in .

Article Snippet: We FACS-isolated CD45 + and CD45 - cells using adjoining gates for comprehensive capture ( and ) for single cell RNA-sequencing (scRNA-seq) (both 10x Genomics platform Smart-seq2) ( , , and ).

Techniques: RNA Sequencing, Flow Cytometry, Cell Culture, In Vitro

Journal: Nature

Article Title: Decoding human fetal liver haematopoiesis

doi: 10.1038/s41586-019-1652-y

Figure Lengend Snippet:

Article Snippet: We FACS-isolated CD45 + and CD45 - cells using adjoining gates for comprehensive capture ( and ) for single cell RNA-sequencing (scRNA-seq) (both 10x Genomics platform Smart-seq2) ( , , and ).

Techniques:

Journal: Nature Communications

Article Title: Cryptic mitochondrial DNA mutations coincide with mid-late life and are pathophysiologically informative in single cells across tissues and species

doi: 10.1038/s41467-025-57286-8

Figure Lengend Snippet: Summary of the public datasets analysed in this study

Article Snippet: The pipeline enables the analysis of scRNA-seq data (e.g., Smart-seq2, CEL-Seq2, 10x Genomics’ ChromiumTM Single Cell 3’ Solution, and 10x Genomics’ ChromiumTM Single Cell 3’ Solution (single-nuclei protocol), and ATAC-seq) but can be adapted to analyse other sequencing data and is a collection of custom-made Shell and Python code.

Techniques: