Multiomic single-cell analysis of the stem and progenitor cell compartment in chronic myeloid leukemia

This repository contains CITE-seq data generated from healthy and CML stem and progenitor cells using the BD Rhapsody Single-Cell Analysis System. 

File descriptions

RSEC-adjusted UMI count files generated using the BD Rhapsody Targeted Analysis Pipeline (v. 1.10.1):

CartridgeS1_RSEC_MolsPerCell.csv

CartridgeS2_RSEC_MolsPerCell.csv

CartridgeS3_RSEC_MolsPerCell.csv

CartridgeS4_RSEC_MolsPerCell.csv

CartridgeS5_RSEC_MolsPerCell.csv

RSEC-adjusted UMI counts for cells remaining after cell quality filtering using SeqGeq software (genes expressed vs library size):

CartridgeS1_RSEC_MolsPerCell_postQC.csv

CartridgeS2_RSEC_MolsPerCell_postQC.csv

CartridgeS3_RSEC_MolsPerCell_postQC.csv

CartridgeS4_RSEC_MolsPerCell_postQC.csv

CartridgeS5_RSEC_MolsPerCell_postQC.csv

Sample tag (sample of origin) calls for each putative cell, output by the BD Rhapsody Targeted Analysis Pipeline (v. 1.10.1). The files also contain information on BCR-ABL1 positivity for each individual cell, generated using our in-house optimized BCR-ABL1 expression detection method.

CartridgeS1_Sample_Tag_Calls_with_BCR-ABL1.csv

CartridgeS2_Sample_Tag_Calls_with_BCR-ABL1.csv

CartridgeS3_Sample_Tag_Calls_with_BCR-ABL1.csv

CartridgeS4_Sample_Tag_Calls_with_BCR-ABL1.csv

CartridgeS5_Sample_Tag_Calls_with_BCR-ABL1.csv

RDS file containing mRNA (RNA assay) and protein (Abseq assay) counts for all cells included in the analysis (from the RSEC-adjusted post QC UMI count files above). The sample of origin of each cell and information on BCR-ABL1 positivity (from the sample tag call files above) are specified in the meta data.

CITEseq_BCRABL1_postQC.rds