ATAC-seq count data from primary pediatric AML samples

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ATAC-seq Data from Primary Pediatric AML Samples Data Source Primary pediatric AML patient ATAC-seq data were obtained from the St. Anna Children's Cancer Research Institute (CCRI). Bioinformatic Processing A modified version of the ATAC-seq Data Processing Pipeline (Reichl, S. et al. Ultimate ATAC-seq Data Processing & Quantification Pipeline. (2024)) was applied to the raw BAM files, accessible at: https://github.com/epigen/atacseq_pipeline. The pipeline utilized fastp (Chen, S., Zhou, Y., Chen, Y. & Gu, J. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics 34, i884–i890 (2018)) for adapter removal and Bowtie2 (Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357–359 (2012)) for read alignment to the GRCh38 (hg38) human reference genome. Duplicate marking was performed with samblaster (Faust, G. G. & Hall, I. M. SAMBLASTER: fast duplicate marking and structural variant read extraction. Bioinformatics 30, 2503–2505 (2014)). The aligned BAM files were sorted, indexed, and filtered for ENCODE blacklisted regions using samtools (Li, H. et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25, 2078–2079 (2009)). Counts over exons were obtained using featureCounts (Liao, Y., Smyth, G. K. & Shi, W. featureCounts: an efficient general-purpose program for assigning sequence reads to genomic features. Bioinformatics 30, 923–930 (2014)). Data Structure The table contains the following columns: Column Name Description NCBI_id RefSeq (NCBI Reference Sequence) accession number for a specific mRNA transcript Gene_symbol Official gene symbol ENTREZ_id Entrez Gene ID Sample00_NUP98_NSD1 Read counts per gene for this sample Sample04_NK Read counts per gene for this sample Sample08_NUP98_KDM5A Read counts per gene for this sample Sample13_NUP98_KDM5A Read counts per gene for this sample Sample17_NUP98_NSD1 Read counts per gene for this sample Sample19_CBFB_MYH11 Read counts per gene for this sample Sample21_CBFB_MYH11 Read counts per gene for this sample Sample22_NUP98_KDM5A Read counts per gene for this sample Sample23_NUP98_KDM5A Read counts per gene for this sample Sample31_KMT2A_MLLT3 Read counts per gene for this sample Sample33_CBFA2T3_GLIS2 Read counts per gene for this sample Sample38_KMT2A_MLLT3 Read counts per gene for this sample Sample39_NK Read counts per gene for this sample Sample44_NUP98_NSD1 Read counts per gene for this sample Sample45_NUP98_NSD1 Read counts per gene for this sample

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2025-04-28

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