Extended Data Fig. 2: CITE-seq encompassing early hematopoietic states.
From: A unified multimodal single-cell framework reveals a discrete state model of hematopoiesis in mice
a-c, A cluster comparison across TotalVI processed surface protein ADT signals from; a, the hand-titrated 60-ADT antibody panel, b, the universal mix (v1.0), and (c) the final product after molecular sequence-based titration. d, Cartoon illustrating the experimental design of the titration experiment. HASH antibodies were used to multiplex titration samples from the same population. e, A bar plot illustrating the ARI score for re-classification of transcriptome defined CITE-seq labels using ADT feature values for the BioLegend Universal mix versus the final titrated mix. f, Outline illustrating the populations captured to generate the CITE-seq atlas, collected features of the CITE-seq atlas, resolving clustering using scTriangulate. g-j, The integrated transcriptome UMAP embedding, illustrating; the sort gate used to enrich for the targeted population (g), scTriangulate confidence scores (h), the RNA (i), ADT contribution values for the final cluster definitions (j) and source annotations by final stable clusters (k). l, Marker heatmap of cells from qHSC, HSC-Mac-1 and Mac-Nr1h3 (CITE-seq titrated), for RNAs (top) and ADTs (bottom). m, Flow plots of HSC-MPP gated bone marrow cells (Lin−Sca1+CD117+ gating out CD150−CD48+ for MPP3-MPP4-gate cells) reveals rare CD193+ and CD115+ populations; in agreement with predicted HSC-Macrophage populations observed with CITE-seq.
