Hello, I notice there are some cells that are nearly identical in both the cd4_t_cells and cd4_t_helper_memory_cells metadata files. Here is an example: ALAW-AS044-1_AAACCTGCAATGTAAG-1 ALAW-AS044-1_AAACCTGCAATGTAAG-1 orig.ident SeuratProject SeuratProject nCount_RNA 2081 2081 nFeature_RNA 950 950 nCount_HTO 1776 3745 nFeature_HTO 20 25 percent.mt 1.489668429 1.489668429 percent.ribo 35.65593465 35.65593465 log2_nCount 11.02306125 11.02306125 log2_nFeature 9.891783703 9.891783703 log2_mt 0.57499125 0.57499125 Donor_id A15 A15 Age_group A A Sex Male Male Age 26 26 Tube_id G15 G15 Cluster_names Tfh Tfh Cluster_numbers 2 0 File_name ALAW-AS044-1 ALAW-AS044-1 Batch AS044 AS044 UMAP_1 0.937649905 -3.849484207 UMAP_2 -2.161128765 0.46277586 Gender NA NA Directory_name cd4_t_cells cd4_t_helper_memory_cells The only differences are the Cluster_numbers, nCount_HTO, nFeature_HTO, UMAP_1,UMAP_2. I'm guessing these are in the Cluster 0 at the highest level (CD4+, CD8+, etc.) and then Cluster 2 within the next level down (CD4+ Naive, Helper memory, Cytotoxic, Regulatory). Should I treat these as duplicates or as unique? Appreciate your help, Peter

Created by Peter Bazeley pbazeley
Hello @pbazeley , A dataset with CD4 T helper memory cells is a subset of CD4 T cells, so you are looking at the same exact cells. Please refer to Figure S3A in the corresponding paper. Kind regards, Marina

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