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

<p>This repository contains&nbsp;CITE-seq data generated from healthy and CML stem and progenitor cells using the BD Rhapsody Single-Cell Analysis System.&nbsp;<br> &nbsp;</p> <p><strong>File descriptions</strong></p> <p>RSEC-adjusted UMI count files generated using the BD Rhapsody Targeted Analysis Pipeline (v. 1.10.1):</p> <ul> <li>CartridgeS1_RSEC_MolsPerCell.csv</li> <li>CartridgeS2_RSEC_MolsPerCell.csv</li> <li>CartridgeS3_RSEC_MolsPerCell.csv</li> <li>CartridgeS4_RSEC_MolsPerCell.csv</li> <li>CartridgeS5_RSEC_MolsPerCell.csv</li> </ul> <p>RSEC-adjusted UMI counts for cells remaining after cell quality filtering using SeqGeq software (genes expressed vs library size):</p> <ul> <li>CartridgeS1_RSEC_MolsPerCell_postQC.csv</li> <li>CartridgeS2_RSEC_MolsPerCell_postQC.csv</li> <li>CartridgeS3_RSEC_MolsPerCell_postQC.csv</li> <li>CartridgeS4_RSEC_MolsPerCell_postQC.csv</li> <li>CartridgeS5_RSEC_MolsPerCell_postQC.csv</li> </ul> <p>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&nbsp;<em>BCR-ABL1</em>&nbsp;positivity for each individual cell, generated using our in-house optimized&nbsp;<em>BCR-ABL1&nbsp;</em>expression detection method.</p> <ul> <li>CartridgeS1_Sample_Tag_Calls_with_BCR-ABL1.csv</li> <li>CartridgeS2_Sample_Tag_Calls_with_BCR-ABL1.csv</li> <li>CartridgeS3_Sample_Tag_Calls_with_BCR-ABL1.csv</li> <li>CartridgeS4_Sample_Tag_Calls_with_BCR-ABL1.csv</li> <li>CartridgeS5_Sample_Tag_Calls_with_BCR-ABL1.csv</li> </ul> <p>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&nbsp;<em>BCR-ABL1</em> positivity (from the sample tag call files above) are specified in the meta data.</p> <ul> <li>CITEseq_BCRABL1_postQC.rds</li> </ul>