Data for "Drivers of Clinical Resistance to Venetoclax and Hypomethylating agents in Acute Myeloid Leukemia and Strategies for Improving Efficacy"

Article: Drivers of Clinical Resistance to Venetoclax and Hypomethylating agents in Acute Myeloid Leukemia and Strategies for Improving Efficacy HemaSphere, DOI: 10.1002/hem3.70282 I. Annotation file File1: This file contains annotation for the entire AML cohort of 113 patients, including clinical data (e.g., VEN-HMA response, overall survival, genetics, phenotype) and RNA-seq information (blast enrichment method, batch) for the samples with available gene expression data. II. RNA-seq data for blast cell populations isolated from 74 acute myeloid leukemia patient samples. Blasts were isolated from 74 AML patient samples (BM, PB) using CD34 (StemCell Technologies, #17856), CD117 (Miltenyi Biotec, #130-091-332) or CD33 (Miltenyi Biotec, #130-045-501) immunomagnetic beads. Enrichment beads were selected based on available immunophenotyping data of blast cells. CD34 (n=54) was primarily used followed by CD117 (n=18) or CD33 (N=2) in cases where CD34 or CD117 expression was negative. RNA was extracted according to the AllPrep DNA/RNA/miRNA Universal Kit (Qiagen, #80224), sequenced on the Illumina NovaSeq system (Illumina, San Diego, CA, USA) and processed in the Illumina DRAGEN v4.2 pipeline. Raw RNA counts were normalized and transformed into log2 counts per million (CPM) values using edgeR. Lowly expressed genes were filtered out, retaining only those with CPM ≥ 1 in at least 10% of the samples. File2: Filtered log2CPM values for 13, 943 protein-coding genes for 74 AML patients. CPM ≥ 1 in at least 10% of samples was used to filter the data. Raw_RNASeq_data: Raw RNA counts for all genes (60, 579) for 74 AML patient samples (Quant.genes.sf files).