Characterization of hematopoietic differentiation cultures by CITE-seq

Seurat object with single-cell CITE-seq object characterizing the culture conditions used in Frömel et al. (2025), Design principles of cell state specific enhancers in hematopoiesis. Primary hematopoietic stem and progenitor (LK) cells were seeded into a complex medium described in Weinreb et al., Science 2020Integrates 4 experiments performed for establishing culture conditions performed with 10x 5' RNA-seq in our laboratory, as well as original data from Weinreb et al.Relevant metadataIdents(): Cell type annotationDatasetWeinreb_day2: Weinreb et al., 2d post isolationWeinreb_day4: Weinreb et al., 4d post isolationWeinreb_day6: Weinreb et al., 6d post isolationFroemel: Initial culture characterizationCST_1_Hash1: Untreated, October 2021CST_1_Hash2: Low-medium MOI infection after 36h in culture, GFP+, October 2021CST_1_Hash3: Low-medium MOI infection after 36h in culture, GFP-, October 2021CST_2_Hash1: Untreated, December 2021CST_2_Hash3: High MOI infection after 36h in culture, GFP+, December 2021CST_3_Hash1: Untreated, February 2022CST_3_Hash2: Low-medium MOI infection after 24h in culture, GFP+, February 2022 (final conditions)CST_3_Hash3: Low-medium MOI infection after 36h in culture, GFP+For our culture (Froemel, CST_1, CST_2 and CST_3) we cultivated the cells for a total of 4 days. The experiments served to optimize the culture conditions. Initial bone marrow extraction (Froemel and CST_1) included a Ficoll-Paque gradient centrifugation which was removed later. Cell hashing in each experiment was performed to test different conditions. CST_3_Hash2 serves as final condition, which was used for the generation of all lentiMPRA data sets in primary HPCs.Relevant reductionsumapscan: uMAP obtained from scanorama integration.