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