biostudies-arrayexpressMatthew UngHomo sapiensCell Ranger v6.0.0https://www.ebi.ac.uk/biostudies/studies/E-MTAB-16321CITE-seq was used to interrogate transcriptomic and surface immunophenotype heterogeneity at diagnosis and relapse. This experiment reveals cell state evolution of AML blasts at two timepoints and provides new therapeutic avenues for targeting surface antigens in AML.biostudies-arrayexpressNucleic Acid Extraction - Cells were loaded at a concentration of 18,000 for a targeted cell capture of 10,000 cells using the Chromium Next GEM Automated Single Cell 5’ Kit v2 and Chromium Next GEM Chip K Automated Single Cell Kit (10X Genomics).Sample Collection - Bone marrow mononuclear cells (BMMCs) were isolated by standard Ficoll purification methods and viably frozen from bone marrow biopsies obtained from patients with AML.Library Construction - Cells were loaded at a concentration of 18,000 for a targeted cell capture of 10,000 cells using the Chromium Next GEM Automated Single Cell 5’ Kit v2 and Chromium Next GEM Chip K Automated Single Cell Kit (10X Genomics). Single-cell emulsions were then prepared for sequencing according to the manufacturer’s protocol (10X Genomics)Sequencing - Libraries were quantified using Qubit™ dsDNA High Sensitivity Kit (Thermo Fisher Scientific) and size and quality were determined using the High Sensitivity DNA Kit on the 2100 Bioanalyzer Instrument (Agilent). Gene expression and feature barcoding libraries were diluted to 2 nM and pooled at a ratio of 4:1 (Gene expression: feature barcoding). Pooled libraries were sequenced using the P3 100 Cycles SBS Reagent Kit on the NextSeq 2000 (Illumina Inc.).OrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesSequence Alignment - Cell Ranger v6.0.0 was used to align read and generate per-cell count matrices using default parametersData Transformation - Gene expression data were log-normalized per cell. Surface antigen expression data were normalized using centered log ratio per cell. All normalization was done using the Seurat R package.MetabolomicsUnknownTranscriptomicsGenomicsProteomicsNANextSeq 200010X Genomics ChromiumRNA-seq of coding RNA from single cellsHomo sapiensMatthew UngfalseCITE-seq of 52 matched primary AML samples from diagnosis and relapseCITE-seq was used to interrogate transcriptomic and surface immunophenotype heterogeneity at diagnosis and relapse. This experiment reveals cell state evolution of AML blasts at two timepoints and provides new therapeutic avenues for targeting surface antigens in AML.2026-01-12T00:00:00Z2026-05-27T12:44:42.373Z2025-12-02T16:35:00.433ZE-MTAB-16321ERP185974EFO_0002944EFO_0004170EFO_0005684EFO_0004917EFO_0005518EFO_0003816EFO_0004184