Published September 25, 2024
| Version v1
Dataset
Open
Single-cell landscape of innate and acquired drug resistance in acute myeloid leukemia: scRNA-seq and CyTOF processed datasets
Authors/Creators
Description
This data was generated as part of the Tumor Profiler study. If you use it in your research, please cite:
Wegmann, R., Bonilla, X., Casanova, R. et al. Single-cell landscape of innate and acquired drug resistance in acute myeloid leukemia. Nat Commun 15, 9402 (2024). https://doi.org/10.1038/s41467-024-53535-4
Derived data - scRNA-seq
This is an R data set (.RDS) containing a SingleCellExperiment object with the following slots:
- Assays:
- counts: raw counts
- colData: Cell-level metadata
- barcodes: The cell barcode
- fractionMT: Fraction mitochondrial genes per cell
- n_umi: Total number of UMIs per cell
- n_gene: Total number of genes per cell
- log_umi: log10 total number of UMIs per cell
- g2m_score: Cell cycle phase score for G2M
- s_score: Cell cycle phase score for S
- cycle_phase: predicted cell cycle phase
- celltype_major_full_ct_name: Major cell type full name
- celltype_major: Major cell type short name
- celltype_final_full_ct_name: Cell subtype full name
- celltype_final: Cell subtype short name
- sample_id
- rowData: Gene-level metadata
- gene_ids
- gene_names
Derived data - CyTOF
This is an R data set (.RDS) containing a SingleCellExperiment object with the following slots:
- Assays:
- counts_raw: signal intensity based on CyTOF dual counts
- exprs_raw: arcsinh transformed raw counts (cofactor 5)
- counts: batch corrected raw counts (linear scaling based on a quantile)
- exprs: arcsin transformed counts (cofactor 5)
- scaled: 0-1 normalized exprs (clipped to the 99.95th percentile)
- colData (cell metadata)
- bc_id: barcode of the sample during staining
- run: CyTOF experiment batch, named after the first sample of the batch
- type: Sample type (blood or bone marrow)
- sample_id: TuPro sample ID
- pred_id: Predicted cell type [char]
- pred_n: Predicted cell type [integer]
- rowData (marker metadata)
- channel_name: Name and isotopic mass of the metal ion corresponding to this marker
- marker_name: Protein name
- channel_group, channel_group_integer: Biological processes the channel identifies, e.g. specific cell type, signalling, cell death
- tsne_channel: Logical - use this channel for dimensionality reduction?
- channel_order: Define the order of channels for plotting
- cluster_channel: Logical - use this channel for clustering?