None of the metadata files attached to this study include the custom single cell annotations referenced in the study (https://www.jci.org/articles/view/185217). Can they please be added?
Created by Noah S User217 I was able to access their annotations via the new RDS file. Thank you for the quick resolution. Hi @User217,
The data contributor was able to provide the predicted cell type annotations. Version 3 of [`CITEseq_cell_meta.rds`](https://www.synapse.org/Synapse:syn64377383.3) now includes the column `pred_cluster`. A total of 70 unique cell types labels are listed. Please note - of 488,540 cells described in this data.frame, only 289,361 cells have a predicted cell type as these are the subset of cells that were confidently assigned to one of the major immune lineages (T cells, B cells, myeloid cells, or NK cells) based on the expression of key, broad cell-type markers.
Cells with `pred_cluster = NA` are ambiguous populations that could not be reliably classified into one of these major lineages and were therefore excluded from downstream analyses described in the corresponding publication. Thank you for the quick response and for reaching out to the data contributors. I glimpsed inside the metadata of all 16 RDS files and did not find a cell annotation column. Hi @User217,
Thank you for your interest in this data. We can reach out to the data contributors for clarification. In the meantime, please note that there are several SeuratObjects saved to Rds files included in this dataset. It is standard to store cell annotations to the column metadata data.frame saved in the SeuratObject. We recommend reviewing the SeuratObjects to see if this information is available there.
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