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), <i>Design principles of cell state specific enhancers in hematopoiesis</i>. 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.<b>Relevant metadata</b>Idents(): 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.<b>Relevant reductions</b>umapscan: uMAP obtained from scanorama integration.